Lecture Notes for 11/16 Bio 102

If you go outside and you see organisms that seem well fit/adapted to their environment, the process of their becoming fit to the environment is natural selection. Individuals can't be fit to their environment, even though they are fit to their environment, because environments are constantly changing. There are also a variety of constraints, physical constraints (they have to obey the law of physics). For ex, there is a limit to how strong and light wings can be to be best functional. Making it lighter will be better, but if too light, it won't be strong enough. There will always be compromises. There are also historical constraints. For example, the larangele nerve appeared in fishlike creatures long ago as a direct link from the brain to gills near the heart. Over millions of generations, this nerve gradually lengthened, each small step always simpler than a major rewiring, more direct route. Natural selection leads to adaptation, but can only act on variation that is already there. Phylogeny is the evolutionary history of relationships among organisms or their genes. It is portrayed in a diagram called a phylogenetic tree. Based on similarities and differences in any traits we can measure (physical and genetic traits). We can sequence DNA and see how similar it is. Each split or node represents the point at which lineages diverged. Lineages joined together in tree have descended from common ancestry. The common ancestor of all organisms in the tree is called the ROOT. Imagine a lineage that is evolving over time, it is a population, due to the evolutionary forces talked about (selection, migration, drift, gene flow). The point at which 2 lineages diverge, to say that they are now different populations and in different geographic areas, one might be more adapted to a hotter climate than another selection may be responsible for the divergence, well the split is referred to at the NODE. The lineage evolves over time through selection, drift, mutation, and gene flow. At the split, gene flow between lineages stops so that each lineage evolves independently. This node implies there is no more gene flow between the pop., and that allows them to diverge. Implies that there is very little, sporadic, gene flow. Divergence is caused by evolutionary forces. Later as time goes on, the lineages continue to split, and a phylogenetic tree emerges. A phylogenetic tree is a way to portray the evolutionary relationships of lineages. Here is an example of a primate phylogeny, and in some cases, there is time on the x-axis. Chimps and humans are more closely related than to gorillas, etc. One point about phylogenies is that the ordering is not important, but the branching pattern. The important thing is that chimps and humans are more related than anything else on that tree. Each branch can be rotated, but it doesn't matter. People often make these with the ideas that at the top is the most derived lineage, but that is not necessary to arrange the trees in any particular way. You can arrange phylogenies in many different ways, all representing the same thing. Pay attention to where two lineages come together, that represents their common ancestor. A taxon, is any group of species that we can designate or name (e.g., vertebrates). A taxon that consists of all the descendents of a common ancestor is called a clade. Clade=common ancestor and everything after it. Tetrapods is everything from here on, amniotes, mammals, etc (examples of clades). What is Phylogeny? One of the greatest unifying concepts in biology is that all life is connected through evolutionary history. The tree of life is the complete, evolutionary history of life. Knowledge of evolutionary relationships is essential for making comparisons in biology. Tree of life (all life is connected). Darwin had this idea, showing how a tree could represent all lineages on earth, and are all somehow related. Oftentimes, people would draw, humans at the top of the tree , and bacteria at the bottom, implying that, evolution is directed, which is not the case. You could say that humans have more derived traits than bacteria, but it makes no sense to put humans at the top of the tree. So modern trees of life look more different, showing all lineages that exist, and their relationship. There is this huge tree of life that shows the rleationships of all organisms on earth, but the ones we know only make a small portion on earth. There is a huge

diversity of life, and what we know only make a small proportion of it. Now we are going to go into some more details in terms of homologous traits. Phylogenetic trees are constructed basted on shared physical or genetic features. Features shared by 2 or more species that were inherited from a common ancestor are homologous. Remember phylogenetic trees are made based on these shared traits. Homologous means its shared from a common ancestor. Traits in different species that share a common origin. Implies that both species derived from a common ancestor. All these bones colored blue and whatever are from the same common ancestor. Convergent traits; but similar traits can develop in unrelated groups of organisms: CONVERGENT evolution-independently evolved traits subjected to similar selection pressure may become superficially similar. Birds and bats both have wings, but the structures that gave rise to them are not homologous. In fact, they are independent evolutionary origins of wings. The bones in the bat and bird are homologous in some parts, but the actual wing is not homologous. They may have experience the same selective pressure, which is why the wings evolved, but it isn't due to homology. Organisms that appear superficially similar, is due to convergent evolution. Sharks and dolphins have similar bodies due to evolutionary convergence, not homology. Now we will talk about ancestral vs. derived traits. A trait that was present in the ancestor of a group is ancestral. A trait found in a descendent that differs from the ancestral trait is called derived. Derived traits that are shared among a group and are viewed as evidence f the common ancestry of the group are known as synapomorphies. Here is an example of a phylogeny,, here is the last common ancestry. The ancestral trait in this phylogeny is shown in gray, the derived trait is shown in black. A derived trait is a trait found in the descendence that differs from the ancestral trait, so in this case, you are going from gray to black, and black is the derived case, and the ancestral case was gray. Another term is synapomorphy, a trait shared between two lineages, a shared derived traits, it defines the two lineages. Some more exmaples, mice and chimpanzees, you can define a bunch of groups by fur, mamary glands, claws and nails, etc. Traits may be considered ancestral or derived, depending on the point of reference. Fur is an ancestral trait for any particular group of mammals. But in a phylogeny of all living vertabrates, fur would be a derived trait found only among mammals (a synapomorphy of the mammals). Whether we define a trait as ancestral or derived depends on the point of reference. So, jaws is a trait that is ancestral to this whole group, but we can also say relative to the outgroup, to the lamprey, or a larger group, jaws are a derived trait that defines a whole group. Fur is the ancestral group of all mammals, but is is also a derived trait relative to the rest of these lineages. A derived trait that defines mammals, so it just depends on the point of reference.

Lecture notes for 1/18/13 To review, phylogenetic trees represent the evolutionary relationships among lineages and evolutionary history of the lineages. Homologous traits are traits in different lineages that share a common origin. In contrast, traits can be similar not because of shared ancestry, but because of convergent evolution. And then I introduced the concept of ancestral vs. derived traits. The definitions are shown here, and this very simple example, is that if you have this phylogengy, there are only 2 trats shown here, the black and gray, gray is ancestal, and black is derived. The ancestral is the trait common in the group's ancestor, and the derived is only in certain groups. This will be more clear in this next figure. Now we are considered all vertebrates,so the presence of eyes and a backbone, are found in all lineages in this phylogeny, all vertebrates. We know that they were found in a common ancestor, so eyes and bakcbone are ancestral. A lambrey has ancestral eyes and a backbone, but doesnt have any of the derived traits such as jaws, some have lungs, some claws/nails,etc. The trick is that when you define ancestral vs derived, you have to take into context the point of reference, and think about one group at a time, and tis time it is all the vertebrates. You can consider ancestral traits as traits found in the common ancestor. Derived traits are the traits found in the the broken off lineages. Jaws is a derived traits, and jaws is shared derived trait among vertebrates, so it is a synapomorphy. Synapomorphy is a type of homologous trait, a shared, derived trait. Homology implied similar traits because there is a common trait. Not all homologous traits are synapomorphies, but all synapomorphies are homologous traits. Many organisms are considered living fossils, ginkos, horseshoe crab. Ginkos from a million years ago look a lot like the ones today, but even though the ginkos look very similar to the ones back then, they are not the same. All lineages are combinations of ancestral and derived traits, so if we go back here, the lampreys are characterized by eyes and a backbone, they do not have the other derived traits, but there are other traits they have accumulated over time. All lineages are a mixture of ancestral and derived traits. The same concept goes for horshoe crab today, they dont represent the exact ones of the back in the day. To explain a little further. This is a phylogeny of ants, the martialis (looks like from mars) is considered the first branch on the phylogeny of all the ants, so the suggestion is that it has a lot of ancestral ants, it is one of the living fossils, but does this look like the original ant? No, it was named because it looks weird. It may retain many traits ancestral to all ants, but it also has some derived traits relative to the original ants that existed. Living fossils are combos of ancestral and derived traits just like the rest of us. Evolution continues for all lineages: some traits and lineages may experience mainly stabilizing selection and remain constant for long periods (living fossil traits stay for many generations). Other traits and lineages may experience mainly directional selection and change rapidly. It doesn't make sense to say some lineages are more highly evolved, because evolution is always ongoing in every lineage. How are Phylogenetic trees constructed? Phylogenetic trees are typically constructed using hundreds or thousands of traits. Any trait that is genetically determined, and therefore heritable, can be used in a phylogenetic analysis. Traits such as the fossil record is useful for dating fossils, and that helps us to understand when certain branches and phylogenies occurred. Any trait that is genetically determined, and therefore heritable, can be used in a phylogenetic analysis. All kinds of traits-morphological, behavioral-are used to contrust phylogenies. Phylogenes show the evolutionary relatioships among lineages. Here is an example of HIV and other related viruses found in different primates, there is 2 types of HIV found in humans, but they are not closely related (one from chimpps, and one from monkeys). If you did not look at a phylogeny like this, you might not realize hat there are 2 types of

HIV. We can also look at more potentially closely related thins like viruses. WE can do this with flue, and see where they came from ancestrallyand geographically. How does phylogeny relate to systems of classification? The biological classification system was started by Swedish biologist Carolus Linneaus in the 1700's. Every species has two name: the genus (group of closely related species) to which it belongs, and the species name (e.g Homo sapiens). In the system, every organism has a genus and a species, and the genus is always capitalized, and the species name is not capitalized (sapeans). There is a whole system above that going from species , genus, Family, Order, Etc, but an important point is that species actually have a meaning, everything above is just arbitrary. Ideally the grouping above species level reflect evolutionary lineages, but they don't always. Unlike populations and species, higher taxonomic categories are arbitrary. How does phylogeny relate to classification? Taxa are expected to be monophyletic=a clade: one taxon contains an ancestor and all descendents of that ancestor, and no other organisms. A clade is all lineages that shared a common ancestor, and al the descendents after that. Clades are monophyletic. The definition of a monophyletic group (same as clade) is a groups that contains an ancestory and all derivative lineages. The problem in taxonomy, if you wanna name groups, is they often give names to groups are not monophyletic. So for example, this grouping containing E,F, and G, because just E and F are monophyletic, but adding G makes it not so. In one way to tell if you have a monophyletic group, a single cut on the evolutionary tree will remove a monophyletic group, so if you remove G, you get the real monophyletic group. E,F, and G is a a polyphyletic group that does not inlude the common ancestor of the group or all of its descendents. A paraphyletic group includes the common ancestor and some, but not all, of the ancestor's descendents. A monophyletic group contains the common ancestor and all of the descendents of that ancestor. A monophyletic group can be removed with a single cut. Why would you create groups that are not monophyletic. If you know the phylogeny, you are set, but in that past that people created taxonomic groups based on what they thought similarity between organisms were; made such strange groupings.Ex: Here is the phylogeny of vertebrates, and most of the things we call reptiles and birds, most people would combine lizards and crocodiles as reptiles, but this reptile grouping is not a monophyletic groups, because it includes birds too. It does not reflect evolutionary history. If you wanna call things reptiles, you need to include birds to lizards and crocodiles. To most people and the people that named the groups retiles in the past, lizards and crocodiles look similar, but birds dont to them, but they are close relatives to such species. Birds have keratinous scales on their legs. Grouping of lizards and crocodiles would be paraphyletic. Speciations: 3 concepts. Two modes of speciation (allopatric and sympatric-same-speciation). Speciation that occurs between reproductive isolating mechanisms (prezygotic, and postzygotic). What are species. The concept of species sometimes varies among different biologists. Most of the species concepts proposed by biologists are not mutually exclusive-just different ways of approaching the question what are species? There has historically been many species concept, and which makes most sense to use depends on which lineage you are studying. Many species concepts overlap. Linnaeus described species based on their appearance-the morphological species concept. Members of species look alike because they share many alleles. This makes sense, because things that look the same share genes. So grouping things by how the look is going to reflect evolutionary history, but members of the same species often don't look the same due to variation. And members of different species often do look the same. Here are male redwinged blackbirds from NY and British columbia are different species but look the same. But sometimes males and females of a species may be different, and immature individuals may not look like their parents. Cryptic species are morphologically indistinguishable but to not interbreed. Another problem is that females in birds often look very different, so if you go off of how the organism looks, this is the same species, according to the biological species concept, everyone recognizes it s a female redwinged blackbird, but it doesn't look like it. SO this is a flaw in linnaeus morphological concept. Another species concept that's really focused on evolutionary relationships is the linneage species concept; species are branches on the tree of life. Speciation: one species splits into

two or more daughter species, which thereafter evolve as distinct linneages. It fits exactly with the concept of phylogeny. Long term isolation of lineages is a consequence of reproductive isolation: when two populations can no longer exchange genes. So when linneages split, that by this definition, is a speciation event. Each branch in the phylogeny is a species according to this definition. This spliting of branches is due to the cessation of gene flow between the two lineages, in which they are reproductively isolated, and there is no longer changing any genes, so there is no longer reproduction between the two lineages. The biological species concept: in order for organisms to be in the same species, they have to be able to breed or have the potential to breed (you might have 2 geopgrafically isolated populations that never breed, but they could). They are groups of actually or potentially interbreeding populations which are reproductively isolated from other such groups. This concept does not apply to organisms that reproduce asexually (e.g. bacteria) and it is limited to a single point in evolutionary time. The lineage concept species make more sense for bacteria. So the point is that depending on what organism you study and your question, that might change the species concept you will want to use. Significant reproductive isolation between species is necessary for lineages to remain distinct through evolutionary time. The evolution of reproductive isolation is important for understanding the origin of species. Process of speciation, the splitting of lineages, to where they are considered to be different species, is all about the evolution of reproductive isolation, where gene flow between two populations stops, and when gene flow stops, according to biological species concept, we consider those two groups to be different species. How can reproductive isolation evolve? Not all evolutionary change results in new species. Speciation usually requires the evolution of reproductive isolation within a species whose members formerly exchanged genes (gene flow). So how can one lineage ever be split into two reproductively isolated species? The main mechanism that is thought most speciation events occur is allopatric speciation, allopatrick (allo=other, patrick=place) is just the physical separation of 2 populations. That is what can lead to the stopping of gene flow between the two population, and its also known as geographic speciation. Sympatric speciation, where populations are in the same place, but still somehow diverge (rare). Allopatric speciation occurs when populations are separated by a physical barrier (geographic speciation). Thought to be the dominanat mode of speciation in most groups. The main mechanism that is thought most speciation events occur is allopatric speciation, is what can lead to the stopping of gene flow between the two population, and then there is geographic speciation. Initially, a big blue blob represents a population where interbreeding and gene flow occurs, but there is a physical barrier (a mountain or a lake), and that physically prevents organisms from mating with each other. Sub populations will arise over time due to selection, mutation, and genetic drift, and then later on, this barrier may go away, and at some point, these two divergent lineages may come back into contact. What happens to them when they come into contact will tell if they will maintain being separate species/lineages or not. This area of contact between two separate lineages that have diverged is called a hybrid zone. The basic model of allopatric speciation is simple, if a continual population is split, gene flow stops, and the populations diverge, and when they can no longer potentially breed, they are called separate species. Sympatric speciation is different in which it is a partition of a gene pool withot physical isolation. This can occur when certain genotypes have a preference for distinct micro-habitats where mating takes place. It is when organisms in the same place diverge without physical islation. There are a few ways that this can happen, but it is very difficult to prove such speciation. One way is when certain genotypes prefer a different habitat. A case is where that certain geneotyes prefer to eat a specific food, they go to that food source and mate on that food source. And another genotype prefers mating on an alternate food source. Because there are habitat preferences, that goes along with mating, these two lineages, these two genotypes, can diverge and lead to sympatric speciation. An example is apple maggot flies. Ancestrally they only laid eggs on hawthorne fruits, but apples were introduced, and some genotypes started laying eggs on fruits and mated on the apple. There are a group of apple maggot flies

laying eggs on hawthorne fruits, and another on apples, and they mated on where ever they laid their eggs, so over time, these groups were not exchanging genes or mating. Although they existed in the same place, they had a habitat preference, so they diverged to the point that they cannot breed. Can changes in timing of mating lead to sympatric speciation? Yes. Within a population, where half mates in spring, and half in the fall; if that happens, divergence can happen rapidly over time even though they coexist in the same place. What happens when newly formed species come together? Reproductive isolating mechanisms include prezygotic reproductive barriers (act before fertilization to prevent mating) and postzygotic barriers (act after fertilization to prevent the development of viable offspring, or fertility. Now we will talk about the reproductive barriers, what stops the exchange of gene flow between two divergent lineages. There are different timing points that those barriers can happen. Prezygotic reproductive barriers mean before the egg and sperm (fertilization) comes together, there is a barrier. Postzygotic barriers are after fertilization, so it is all about timing. In Prezygotic reproductive barriers include habitat isolation (apple maggot flies), temporal isolationmating periods do not overlap. In sympatric populations of three closely related leopard frogs each species breeds at a different time of the year. There are many pre-and post zygotic barriers that can happen. One is habitat isolation (apple maggot flies). If 2 lineages are using different habitats and mating in different habitats, then they don't come in contact with each other and cant mate. The other one is temporal isolation, if organisms don't mate at the same time, they cannot mate. An example is the leopard frogs (3 types) that mate at different times. This temporal isolation happens often. Most ants mate in the air, and 3 closely related species go at different times of the day for mating (prezygotic reproductive barriers). Mechanical islation (found in many insects)-differences in size and shape of reproductive organs makes mating impossible (lock and key); in plants, mechanical isolation may involve pollenators. The size and shape of reproductive organs might not match. The organs don't fit together, so there is no potential of mating; the evolution of mechanical isolation can happen very rapidly. In plants, two different lineages of plants use different pollenators (hummingbirds vs. bees). Because there are different polenators, thats analogous to this mechanical isolation. Behavioral isolation-individuals reject or fail to recognize potential mating partners. Breeding calls of male frogs quickly diverge between related species. Female frogs ignore calls from other species. Individuals don't recognize each other or there is some mating behavior that don't match up. If that happens then there is no potential for mating to occur. There are often signals that have to be recognized, and they are species specific. Postzygotic reproductive barriers include low hybrid variability (zygotes or adults have low survival rates) and hybrid infertility (offspring are infertile) e.g (mules). In post zygotic barrier, after mates exchange egg and sperm. This doesn't mean the zygote has to live. The term hybrid is very vague, it is used when two different lineages are mating. How far separated lineages need to be to use the word hybrid is unclear. In fact, we talked about neanderthals and humans mating (some people considered both separate species or separate subspecies). The point is that you can use the word hybrid or gene flow depending on how closely related/far apart individuals are. Some things that are closely related, you would say gene flow, things when there is mating and potential for gene flow between divergent lineages, you would use hybrid. There is often low hybrid viability, where even the zygote doesnt live. Sometimes there is complete infertility. With the mule, the fertilized egg grows to an adult, but they are infertile. So as a review: Prezygtic barriers: habitat, behavioral, temporal, mechanical, and gamete isolation; postzygotic barriers: reduced viability, reduced fertility, and hybrid breakdown. Gametic isolation is where for some reason the sperm and the egg cannot come together either physically or chemically (mechanical is that the sex organs cant come together). What happens when newly formed species come together? If hybrid offspring survive poorly, natural selection may favor prezygotic barriers. Individuals that can avoid mating with members of another species would have a selective advantage. Strengthening of prezygotic barriers is known as

reinforcement. This is a pretty simple, important concept. Two lineages diverge, and they can mate, but what happens after they mate, after the hybridization. If hybrids have low survival, there can be selection for those lineages not to reproduce. IF offspring do very well, it doesn't matter if you mate in or outside population. And if they don;t survive well, its a sign not to mate with them. What happens when the lineages come together and start hybridizing? If the offspring dont do well/are inviable, there is reinforcement, selection to increase the reproductive isolating mechanisms (red lineage+blue lineage, and their offspring don't do well, then they wanna recognize each other as being a separate species and don't wanna mate. There can be fusion if in fact the offspring do well, then it doesnt matter who they mate with, and the diverged lineages may come together and form one lineage. There can also be stability of the hybrid zone if the hybrids do ok, but have intermediate fitness (they do ok). Or the two lineages are separate, with a small hybrid zone (small # of hybrids produced), so there can be different outcomes. Lineages can continue to diverge, or come back togeher, or stay with continual hybrids being produced. sin

Postzygotic barriers: Zygotic mortality: The egg is fertilized, but the zygote does not develop. Hybrid inviability: Hybrid embryo forms, but is not viable. Hybrid sterility: Hybrid is viable, but the resulting adult is sterile. Hybrid breakdown: First generation (F1) hybrids are viable and fertile, but further hybrid generations (F2 and backcrosses) are inviable or sterile.

11/23/2013 Lecture A bit of review now. Morphological species concept; members of species look alike because they share many alleles (cryptic species contradicts this)Lineage species concept; species as branches on the tree of life/phylogeny (works for bacteria). Biological species concept: groups of actually or potentially interbreeding populations which are reproductively isolated from other such groups. Organisms that can potentially breed together are the same species. Breed is pretty vague, it means sort of a lineage, but breed is usually referred to as a sub group of species (like dogs); same species, different lineages. So we talked about allopatric speciation (primary form of speciation). Starts with initially a population thats physically separated, and the 2 populations can diverge through evolutionary forces, and later on if the barrier is lost, a hybrid zone occurs where the populations come back together. What happens in the hybrid zone determines if they turn back to one species, or diverge into 2 species, or whether the hybrid zone is stable. We also talked about mechanisms for reproductive isolation (prezygotic vs. postzygotic). Question: Which of the following is false? E. The differences between gorillas and chimpanzees accumulated over the course of approximately 10 million years of evolution. Which two evolutionary forces contribute to the inevitable divergence of the two split populations separated by a mountain range? Selection, mutation, and genetic drift. So lets talk about genes and genome. Genomes are simply the full set of genes (protein coding regions) plus the non-coding regions of DNA (for some viruses it is RNA). In eukaryotes, most genes are on the chromosomes in the nucleus, but some are in mitochondria and chloroplasts. Let's define genes, because there are different definitions, but its usually protein coding regions that give rise to proteins. There are also organelles that contain DNA as well (mitochondria and chloroplasts). The DNA alphabet, different letters (ATGC), and whats often called the central dogma of molecular biology/genetics; DNA that gives rise to mRNA through transcription, which is translated into protein through translation. Another flow of info that can occur is through DNA replication. Information doesn't do the reverse of the dogma (protein, to mRNA to DNA). I want to make a point that the definition of dogma does not fit here (a principle/set of princicples laid down by an authority as incontrovertibly true). Nothing in science is incontrovertibly true, but there are not really authorities. Science is built on being skeptical and testing, and we can always find evidence that undo what we say before. 21 years ago, the human genome project started, a monumentous porject in sequencing. The result of that and many other sequencing projects is a string of letters (3k base pairs, 3.1% of human genome). What can this tell us? Well, remember that different strings of 3 nucleotides (codons) are transcribed and translated into amino acids, and there is redundancy in the genetic code (3 codons can give the same amino acids hen translated). SO a small portion of the DNA is involved in the direct transcription and translation to proteins, representing of 1.5% of all of our DNA involved in protein coding (21k genes, aprox), depending on the definition of a gene, where here we say it is a region of DNA that codes for a protein. A good question is, what is the purpose of the other DNA? Why is only 1.5% of DNA coding proteins. WE compare human genome to genome of closer relatives, like mammals. What are some genes conserved across these mammals, and what aren't. The ones vital for existance would of course be conserved, a core set of genes that have very basic functions. This is one approach, and you find that 5% of the human genome is conserved across mammals. You can make the assumption that because it is conserved, it has an important function. And you can take that as a lower bound for the amount of DNA that has a function. We assume that is has an important function; only 5%. What is the other 95% doing, and what is that other 5% doing if not encoding genes? Well, the 5% can regulate the expression of genes (operon, enhancer, silencer, etc). There is a variety of ways DNA can regulate the expression of protein coding regions. Don't remember the details of all the ways DNA can regulate expression. These different blocks represent protein coding regions (exons that will be transcribed). The dots show the regulating expression regions of the DNA (Promoter, enhancer). Keep in mind that

regions regulating the expression of any given gene can be close by, but they can also be far away as well.. There is a wide array of regulatory elements that affect whether a gene is expressed/transcribed or not. Since the human genome, there is a huge project called ENCODE (encyclopedia of DNA elements). The purpose of this was to look further at the purpose of the 98.5% of DNA that is noncoding, and how much of that DNA may be functional? It could do nothing, junk DNA, where you keep junk in the room, but garbage is what you throw away (it might do something). WE are still not sure what a lot of the DNA is doing, but more is doing stuff that we know. Approx 80% is transcribed with no known function. If you use the definition of function (any biochemical activity, being transcribed), then 80% is functional. 20% binds to regulatory proteins (18.5%) or encodes proteins (1.5%). The encode could help us find clues on what some of our DNA is doing. Some could just be there from past events, do something unknown, or not do nothing at all. 5% of human genome sequence is constrained across mammals (and presumed functional);5% of 3B bases= 150 M bases;Do not know yet the position of these 150 million functional bases;Lower bound for the amount that is functional. 1.5% encodes for protein (genes); Corresponds to 18-22k genes; many more than 22k different proteins. More than 3.5% is functional,but non-coding; gene regulatory elements, chromosomal functional elements, and undiscovered functional elements. WE would estimate 3.5% as the lower limit for functional proteins. Are protein coding regions evenly distributed? No, it spread all over. Variation between humans. 6 billion bases (3 from mom, 3 from dad). Compared to person sitting next to you, about 3-5 million single nucleotide differences, 10s of thousand larger structural differences. There is variation even on the biological level between individuals. Whole chunks of our genome could be different. Given all this variation, what does that do? Many do nothing, some are good in certain environments, and some are clearly bad (some of them are associated with a disease risk). You may have a dna sequence that predisposes you to something like heart disease. But there are single genes that are strongly associated with a gene. There is some common variants, or some rare genetic variants (a particular allele). Remember from one of the first lectures that mutation is the ultimate source of variation. Mistakes in DNA replication result in mutations-these are the raw material for evolutionary change. One type of mutation is nucleotide substitutions (like putting in A instead of G). What do genomes reveal about evolutionary processes? Many nucleotide substitutions have no effect on phenotype because most amino acids are specified by more than one codon (equal to set of 3 nucleotides that encodes for an amino acid). A substitution that does not change the amino acid that is specified is a synonymous or silent substitution. A substitution that does cause a change in the amino acid specified is a nonsynonymous substitution. There is redunancy, 3 different combos o letters that give rise to some amino acids. Ex: uua to uug is still leucine ( a substitution that has no affect on the amino acid). Nonsynonomous do have an effect;going from uua to uuc changes from leucine to phenylalenine, or uua to uGA is a stop signal (transcript is stopped). There is a variety of changes that can occur in nucleotide sequence that can or cant affect amino acid sequences and thus affect protein production and function. Signatures of evolution in DNA sequence; evolutionary changes are determined by comparing nucleotide or amino acid sequences among different organisms. Highly conserved regions are constrained, divergent regions are not. You can compare, lineup, different lineages, and compare directly their amino or DNA sequence to look for regions of the sequence that is highly conserved or highly variable. Regions conserved across lineages are assumed to have important function, whereas regions highly variable are less important (experiencing diversifying selection). Our genome sequence is the notebook, comparing close lineages and having close idea just by comparing DNA sequence what kinda selection has been going on, being highly conserved or divergent. For the last 3.5 million years, evolution has been taking notes ,and the genome is the notebook. You can compare the close lineages,and have some idea just by comparing the dna sequences what type of selection occurred; whether regions are highly conserved or divergent. You can compare the relative rate of sononymous

and nonsononymous mutations, differing depending on what kind of selection. Relative rates of synonymous and nonsynonomous substitutions should vary in genes undergoing different types of selection. If an amino acid replacement is neutral with respect to fitness, the two rates are expected to be similar (close to the same number); the ratio would be close to one. We expect the two rates to be aprox the same number, and the ratio of the two to be close to 1. In contrast, if the amino acid position is under positive selection for change, the rate of nonsynonomous substitutions should be much higher than sononymous. If there is contrast for change, postitive selection. People use slightly different terms for molecular evoluton (positive selection), whereas if talking about traits, it is directional selection. If there is selection for an protein to change, there is positive selection for that change, and we would expect more nonsynonomous substitutions than otherwise, because the NS changes are the ones changing the protein sturcture, so the NS:S would be higher than 1 in the ratio; more changes that would do something to accumulate. Finally, if an amino acid position is under purifying selection, the rate of synonumous substitions should be much higher than sononymous. This is analogous to balancing selection. If you compare human, to chimp, to mouse, DNA there are some regions that are the same, highly conserved, that experienced purifying selection, the idea that any change to that DNA sequence at all is bad for the organism and causes it to die. So purifying selection means there is no change, and we expect more S than NS substitutions, very few NS (fiddling with proteins is bad in this case). Just by comparing the number and proportion of NS to S changes, you have some kind of idea of what kind of selection has been going on. You can see a stretch of amino acids across plants, rice, up through mammals, and humans. Even across such a wide comparison, you find regions that are completely invariant, that experienced purifying selection (any change that is not goo for the organism). Then there are areas that are variable, wheer the constraint is not so strong across the regions. Some regions of the genome are experiencing strong purifying selection, others are experiencing other types of selection.

11/25 Lecture Notes Today we will finish talking about the evolution of genomes, and then talk about the history of life on earth. Back to the question asking about how orangutans may be expected to look more like the last common ancestry of all great apes than chimps and humans, and it doesn't make sense unless asking about specific traits. You can imagine scenarios where it would be true, but after these lineages split, the orangutan lineage has been evolving over time just like the others have, so you would expect like the ants and living fossils example that each species would include derived and ancestral traits. The orangutan has been evolving just as much as chimps and humans have, even if the splits were at different times (so the timing of branching doesn't matter in terms of similarity measures with the original ancestor). When changing one nucleotide does or doesn't make a difference. Remember that synonumous changes are changes in DNA sequence that does not affect the DNA sequence (gives you the same amino acid sequence), nonsynonymous does change the amino acid, and changes the whole sequence potentially. So, if NS# (no affect on AA) is = to #S and NS/S=1, and the number of changes to changes is the same, then the changes are neutral. For positive selection, NS/S>1, where changes are expected. And for purifying, where NS is bad, only S will accumulate, so N/S<1. Genome evolution: the locations of genes, as well as their sequences, are subject to change. The genome size can also change, where the numbers of genes can change, as well at the extent and location of noncoding DNA. We talked about how we can get things like substitutions, where the DNA sequence itself can change, but other aspects in the genome can change; the location of genes, number of genes, etc can change. And, this is not just the case for just coding regions (produce Proteins), for noncoding regions can change too. Here is a figure from the book, showing on the x-axis the number of genes (in thousands) and then the y is the phylogeny of organisms whose number of genes we know. You can see that gene number varies pretty broadly (prokaryotes have a small #), and some like rice have a lot. Similarly, puffer fish have a lot too, but there is a fairly consistent number, a lot of variation, but reasonably consistant...a big part of this figure I want to make is that there is variation, but there is less variation among say animals and plants; and this amount of variation is very small especially when we consider total genome size. Total genome size varies much more widely (a lot of DNA is noncoding). Gene number varies, but genome size varies hugely. Things that have small genomes have mostly functional coding genes, whereas the ones with larger genomes have a very small amount of protein coding regions/genes. We see some variation in gene number, but we see huge variation in genome size, and how does that occur? And how can you have similar organisms (vertebrates like fish and humans) that have such different genome sizes. Why is genome size so variable? DNA is expensive, it has a lot of stuff in it. What do genomes reveal about evolutionary processes? Species vary in the rate of gain/loss of funtionless DNA. Possible reasons are: large genomes can slow the rate of development and may be selected against. It is happening through the accumulation of DNA that is not protein coding, and presumably not doing anything. Some ideas for this is that DNA is expensive to produce (lots of Nitrogren). So organisms that have large genomes develop at a slower rate (a cost to having such a large genome): in some lineages that could have more of an affect (with streamlined genomes) that in other lineages that it doesn't matter so much. The amount of DNA is costly. Another related idea is that the amount of noncoding DNA may be related to population size. Think back to selection and drift; In small populations, genetic drift may become important and overwhelm weak selection against these sequences. Having a large genome is sort of neutral (slightly deleterious), and in a smaller population you will accumulate larger genome size because drift will overcome selection. Even though having a larger genome is slightly bad, if you don;t have a large population size, selection against accumulating those slighty deleterious larger genome, then selection may not be powerful enough to get rid of those deleterious regions. Genome size may depend on development time, but it is noted that birds and bats have smaller genomes than their relatives. *Genome size correlates with cell size, and we can measure cell size in fosilized bones (so we know dinosaur genome size). WE wanted to know if small genome

size is associated with flight; no, it is not the case. The lineage that gave rise to birds has a pretty small genome, but it didn't just happen associating with flight, for the whole lineage before also had small genomes that didn't have flight. So it is not that flight is associated with small genomes, cause all the dinosaurs giving rise to birds had small genomes. Similarly, some bats have small genomes, but other's dont. So, it has been an idea that metabolic rate an flight are associated with genome size, but we know now that flight is not. So there may be some reasons why having a large genome could be good or b, so it could be associated with population size, were small pop. size could accumulate large genomes because having a large genome is slightly deleterious, so drift can overwhelm selection against having slightly deleterious, larger genomes, but how do larger genomes accumulate. What mechanisms exist for moving genes around? How do genomes gain and maintain functions? Most multicellular orgnisms have many more genes than unicellular species. Some mechanisms must exist that increase genoe size over evolutionary time: genes can be transferred from other species, or duplicated within species. One is between lineages as gene transfer, which is where individual genes, or organelles, or fragments of genomes move from one lineage to another; some species pick up DNA fragments directly from the environment (antibiotic resistance), genes may be transferred to a new host in a viral genome, and hybridization between species results in the transfer of many genes. Some species like bacteria can just pick up genes from the environment. Other cases, vertebrates, we have lots of traces in our DNA that we supposedly got from viruses, and genes can also be transferred through the process of hybridization, so it can be between closely related, or between lineages that are widely divergent. Then there is gene duplications, that may give rise to new protein functions. This is just moving around genes, but a more efficient way is gene duplication (start with one gene, and some error in replication give you two copies of a gene instead of one, and sometimes the entire genome is duplicated). Some fish have 40k genes, whereas we have like 10k, so there are prolly 2 rounds of duplication of the whole. Copies may have one of four fates: a) both copies retain original function (more product could be made), b) both copies retain original function but expression diverges in different tissues or different times, c) one copy becomes nonfunctional from accumulation of deleterious substitutions and becomes a pseudogene, and d) one copy accumulates substitutions that allow it to perform a new function. Both copies could be function and do the same thing, creating more product. Second possibility is that both can retain original function but can be expressed at different times or in different tissues, and another where one copy just loses function, and finally the last option that one copy accumulates substitutions that allow it to perform a new function. So duplications can give rise to new functions by expressing the same proteins in a different time or place, or expressing a different protein. Duplication is thought to be a major way for the evolution of new functions. Sometimes the whole genome is duplicated, providing many opportunities for new functions to arise (ex: jawed vertibrates have 4 diploid sets of many major genes). Two genome duplication events may have occurred in the ancestors of these species. It has allowed specialization of individual genes. We have in all organisms, certain genes that have many copies of the same gene, or gene families, or even the whole genome duplicated. What does gene transfer mean? It is analogous to gene flow, but gene flow is restricted to within a species. Gene transfer is between divergent lineages. In the case of bacteria, it could be as simple of sucking up a chunk of DNA from another lineage in the case of something like neanderthals and humans as a gene transfer due to hybridization. It is sort of fuzzy line between what you call gene flow and hybridization. The sequencing explosions; sequencing is become more and more affordable, even in the time of computing. The point is that, if you wanted your genome sequenced, you could do it easily. Not just humans are being sequenced, there are groups that try to sequence insects, all of the vertebrates, etc. There is lots of genome data already available. What will this mean for us? With all this genome data, we are able to associate variation with disease prevalence. Most variance asociated with a disease are not in protein coding regions; they fall out of it, so probably some regulatory region. Livin in the post-genomic age; everyone will be confronted by genome-related issues and should be

educated; doctors need to explain to patients if they are biased to get a disease, researchers need to figure out how to use new data, society need to decide how to deal with new info. The limitation is how to analyze the new data. Should our genome be our public info, or should it be shared with the public? Etc. Imagine that as a population is accumulating more genome size, say a population is accumulating slightly larger genome, and getting a larger genome, and getting a larger genome is slightly deleterious, because DNA is costly. Think back to selection and drift; when something is slightly deleterious, those differences will accumulate in a small population because selection cannot act very efficiently. Drift becomes more important, and that is why a larger genome can accumulate. WE expect an association between small population size and a large genome. The history of life on earth. 1) Life on earth is almost as old as the earth (3.8 vs. 4.5 billion years ago), but the plants and animals we're familiar with are relatively young. Life has completely transformed the Earth. Life was largely wiped out by earth several times. As soon as life could evolve, it did evolve, but for most of the history of life on earth, life that was there, things like prokaryotes, bacteria, etc, you wouldn't see anything you would recognize as life. Another point is how the environment has changed a lot over time, but part of it is also due to life itself on earth. There used to not be any oxygen on earth; life changed that. The final point is that there have been huge mass extinction events several different times where nearly all life were wiped out. The earth is very old, if you go to the grand canyon, the rocks at the bottom are pretty old, but the earth is a lot older than that. So what happens? How do we know the age of the earth? Well, there is tons of evidence (different lines of evidence), the most importatn being dating using radioactive isotopes of atoms. Radioactive isotopes of atoms can be used to determine the age of rocks. Isotopes decay in a predictable pattern. Half-life is the time interval over which one half of the remaining isotope decays. Over time, the remaining radioactive isotope degrades into another isotope. WE can use carbon 14 to date things that are at certain years old, and other isotopes to figure out how old which is what. By knowing the decay rate of these isotopes,and by comparing the quantity of the two, we can figure out how old a substance is. There is other radioisotopes that allow u to date much further. WE started out with no oxygen, and then I want to point out these huge mass extinction events, for example, at 480 mya, 75% of all species on earth went extinct. Researchers can tell this by fossil evidence. There is a period in time where you see a bunch of fossils, but all of a sudden there isn't. The largest mass extinction was at 96%. A lot of these extinction events were associated with meteorites hitting the earth. The one you all know about is the end of the age of dinosaurs (76% of all species disappeared). So, a point I want to make is that with these extinction events, they have been incredible. Life has evolved over the past billion years, and there have been points where almost all life was wiped, and it took millions of years for diversity to build up after those mass extinction events. Earth (4.56 bya), life first evolved (3.8 bya), eukaryotic organisms had evolved (prokaryotes first) by about 1.5 bya-plants, animals, fungi. A key point here is the origin of photosynthesis, which involves converting CO2 to oxygen, which is where we think O2 came from, which is photosynthesis. A geologically rapid diversification of life took place called the cambrian explosion. Most of the major groups of animals living today appeared in the cambrian. A bit over 500 million years ago; before this we do not see a lot of fossils of the phyla of animals that characterizes the groups of life we see today. Changes over time besides the evolution of life including the position of the continents changing over time, the position and size of land masses influencing ocean circulation patterns, sea level, and global climate, and mass extinctions of marine animals that occurred when sea level dropped, exposing the continental shelves. There has been continental drift, which had huge effects on ocean circulation, climate, etc, which effects mass extinctions associated with ocean drops (points where the ocean has gone way down, causing mass extinction in the sea). In terms of oxygen levels, the early atmosphere contained little or no free oxygen (O2). O2 began to increase when certain bacteria evolved the ability to use H2O as a source of H+ ions in photosynthesis (O2 was a waste product and as poisonous to anaerobic prokaryotes). There was no O2 before life began, and some bacteria found a way to use water

to get hydronium for photosynthesis, but original organisms were anaerobic, so O2 poisonous to them. Some organisms evolved the ability to metabolize oxygen, where aerobic metabolism provided more energy per calorie, aerobes replaced anaerobes in most environments, and it enabled evolution of larger and more complex cells (eukaryotes, with chloroplast and mitochondria with higher levels of oxygen; allows multicellularity. Its enabled subsequent types of life. First there is photosynthetic bacteria, then aerobic bacteria, then first eukaryotes, then first multicellular organisms, then chrodates, invasion of and, giant flying insects, and first flowering plants. A huge peak where O2 levels where double the O2 existed, and insect size was limited by how much o2 was in the air (more o2=bigger insects, ew). O2 concentrations incerased during the Carboniferous and Permian periods because of the evolution of large vascular plants; extensive burial of plant debris in swamps formed coal deposites and the buried organic material was not subject to oxidation, allowing the buildup of O2. All the plants we use for fossil fuels didn't decompose from that time, and because they did not decompose, there were a buildup of oxygen. The fossil fuels we use utilized the stored carbon from that time. Earth's climate has changed over time. Earth was sometimes considerably hotter than today; sometimes colder, with extensive glaciation. Major climatic shifts that have occurred over periods as short as 5k to 10k years are primarily the changes in earth's orbit. Then to these extinction events, there are really good evidence, that they were caused by extraterrestrial collisions (meteorites slamming into earth). A large crater has been located beneath the northern coast of the Yucatan Peninsula, Mexico, from 65 mya. A massive plum of debris from the impact heated the atmosphere, ignited fires, and blocked the sunlight. Settling debris formed the iridium rich layer. It is rare on earth, but it is found in extraterrestrial things. Conclusions then is that we know the earth's age from radiometric dating, we can use phylogeny in combo with the fossil record to reconstruct the timing of major events in evolution, and changes to the physical environment on Earth have clearly influenced the great diversity in living organisms we see today, and life has influenced the physical environment. The organisms that are there have also affected the history of the earth as well.

11/28 Lecture: Subject of our lecture today are, the major division of life. The domains of life. I want to emphasize how in the past 20-30 years, our conception of the major divisions of life on earth has really been revolutionized. We are gonna talk about the shape of the tree of life; the 3 domains of life and their common characteristics, the prokaryotes and what they are. Then we'll talk about differences among the domains, and the origin of the eukaryotes, and the protists (bizarre collection of things that are not monophyletics or cladistic). We'll talk about endosymbiosis, and major patterns of eukaryote phylogeny (what does kingdom mean anymore in classification). This is an early, full scale tree of life by heckle, a follower of darwin. Here are some features of this tree, to get us thinking about the tree of life. We know there is a conception that everything is descended from everything else upto a common ancestor. Heckle's tree divides everything into 3 things, plants protists, and animals. The protists were alll the itty bitty things that could be seen only under a microscope. This tree is only of historical, not scientific meaning. In middle school, we were taught the 5 kingdom system, monera, protista, plantae, fungi, and animalia. The 5 kingdom system is obsolete, in fact we dunno how many kingdoms there are. What a kingdom is is still arguable. Then is the 3 domain system, that corresponds to our current conception of the largest classification of the major types, the domains, the largest possible division of living things. The guy who did the work that launched us into thinking about domains is Carl Woes, who just died last year. He was trained as a physicist, but he began to work on microorganisms and took an approach nobody else did. Besides putting them under a microscope, looking at how they look, staining them, adding antibiotics, what they grow on, what they eat to classify them;He said no, let's do it using sequences, and use ribosomal rna's, the things that encode the ribosomal rna's in the genome. The reason why this is effective is because they are universal among all free living things (everything has to make proteins that are free living and thus need ribosomes), they are so important to the functioning of the living cell that the likelihood that the gene that encodes that would be laterally transferred to some distantly related cell and be successful, and remain in that distantly related genome is practically zero because it wont agree with the existing machinery that are there, and the rna's that are encoded in the genome by the DNA evolve very slowly, they don't change over time easily, they are conserved. Over vast stretches of evolutionary time, the sequences that code the ribosomal rnas won't change so much that its impossible to allign/ compare them. If you take rapidly evolving sequences and allow enough time to go by, they will become so different that you won't recognize them as having come from a common ancestory. This is not true for ribosomal RNA's, so it was a great choice. Woes was ridiculed for doing it, like a lot of scientists with great forsight, it was considered that he was wasting his time. Instead, he made a fundamental discovery about life. Life on earth would continue ok if all eukarytoe organisms were wiped out. Life would continue, would be the microbes. If you wipe out all the microbes, that would be it for life on earth. You are dependent on microbes in your gut, plants have associations with mircobes. All of the biogeochemical processes depend on microbes, so they are hugely importance. The real unseen diversity and biomass lies with microbes. The actual pattern is not certain. We know that these three groups are sufficiently distinct to be the largest catgories of life on earth (Bacteria, Archaea, Eukarya). These are the highest categories (domains), and woes found them based on these RNA comparisons. So the 3 domains are bacteria, archaea, and eukaryotes. Bacteria and archaea are collectively referred to as prokarya, but the term prokaryotes does not fit if we looked at how they were branched, as it is not a monophyletic classification, because it doesn't include all of the descendents of that common ancestor, because that would include everything (all life on earth), and we have no outgroup for the tree, something that is everything that's currently in existence on earth evolved from to make a comparison. The 3 groups have certain shared derived cahracteristics derived from LUCA, but we don't have that LUCA, so determining the branching pattern of tree is difficult. Members of all domains have (from LUCA): conducting glycolysis, replicates DNA semi-

conservatively, have DNA that encodes peptides, produce proteins using essentially the same gnetic code, has plasma membranes and ribosomes. They all split up glucose, dna that encodes proteins, produces proteins using essentially the same code, and have plasma membranes and ribosomes, and replicate DNA semi-conservatively. Everything Is descended from some common ancestor, but does that mean that common ancestor was the only possible common ancestor of life on earth. No, There could have been multiple origins of life, and LUCA could have been the only one that lucked out and is the ancestor of everybody. Here is a little overview of what we sort of think about how the domains are related, and then the phenomenon of endosymbiosis. The branching pattern here sort of reflects the branching pattern from the earlier one in the figure with the ribosomal RNA tree. That is, to say, that they have the last universal common ancestor, and very ancient prokaryotes going back 3.5 billion years. And then we have bacteria, and we believe that eukarya and archea are more closely related to one another than either are to bacteria, but its not a certainty. Importantly, the origin of the eukaryotes involved what are called endosymbiotic events in which bacteria, 2 different kinds, were engulfed by a eukaryote ancestor, did not get digested and died, but instead persisted and set up a symbiotic relationship with that eukaryote. You yourselves are part bacteria, with these things called mitochondria in your cells, and as we will discuss later, descended, from bacteria. You are also part bacteria in another way that might gross you out later. Here are some remarkable facts about prokaryotes. A gram of rich soil, roughly a teaspoon, it contains almost 10 billion prokaryotic cells of various kinds, and in fact we don't know all of the kinds of prokaryotic cells (they have not been characterized) of different species. A very small fraction of prokaryote species are culturable. How would we know this? What is a prokaryote species anyway? BY sequencing. We can take a gram of soil, extract the DNA from it, amplify in sequence DNA corresponding to ribosomal RNA, and look at how many types, distinct sort of types ,of RNA there are. When we do such things, and we can use different types of sequence as well, we find that compared to the number of bacteria that we can culture, there are far far more apparent species of bacteria and archea out there in nature that we can't culture because they are too fussy, they won't grow in the lab as they need special conditions and etc. So there are potentially millions of bacterial and archeal species in nature, and we can only mess around in the lab with a small number. I just used species for prokaryotes, and we learned the biological species concept and why we think species of organisms like ourselves are species, but the prokaryotes divide by binary fission. They don't have sex like we do and have offspring that are descended from two parents. So in some sense, prokaryote species don't fit the interbreeding biological species concept as prokaryotes by nature do not interbreed. They do pass along genes by lateral gene transfer, and that stick some of their populations together, but the key point being made here is that the biological species concept in some sense doesn't even apply very well to prokaryotes. Now that's kind of weird, given what you've already learned because it may be that there are more prokaryote species than all of the rest of the species on earth by far. And yet the species concept we taught you does not apply to that. Welcome to biology, lots of exceptions. You have on and in your body, more prokaryote cells than human cells. In fact its been estimated in and on you body that you have more prokaryote cells than all the people who have ever lived. So your gut is teeming with prokaryotes, your mouth, for as often as you brush or floss, and your skin, ears, nose. Many form symbiotic relations, for instance, you couldn't digest your food very well without beneficial prokaryotes in your gut. Some of them of course as you know, don't. We tend to know and pay more attention to the ones that don't help us than the ones that do. The lining of your gut functions with the help of a vast number of prokaryotes (many of which have yet to be characterized), and here is some research news I want us to take a look at, cholic in human infants. Cholic is the phenomon in which an infant just cries and cries and arches his back and screams, and its hard on parents. If you could find the cause of cholic and treat it, it might be a good thing. I saw an article that was an alert to it. A dutch group compared 12 infants who weren't cholicy to 12 that were. And they characterized their intestinal

microbiota using sequence methodology. So they got the DNA from them and sequenced them using a micro-array method. And they found the following interesting thing, they found that infants who had cholic seemed to have more of these groups called proteobacteria in them. Infants that didn't have cholic had lactobacilli and some other things that are here, mostly lactobacilli and bacterial things like these. So, they found differenecs in the bacterial communities between the cholichy vs. noncholicy infants. This might be really worthwhile to know. I want to ask you a question though, are you convinced that the different bacterial communities explain cholic? No. Think a bit about what you would want to know or do to convince yourself that it's a correlation between the manifestation of cholic and the manifestation of certain bacterial groups in the lining of the gut. You would want to figure out something about causation if you could. Prokaryotic cells differ from eurkaryotic cells in that they lack a cytoskeleton, they divide by binary fission (but there are processes that allow exchange of genetic info between some prokaryotes: transformation, conjugation, and transduction), their DNA is a single, (Often) circular molecule not in a membrane-enclosed nucleus, and they have no membrane-enclosed organelles by contrast to eukaryotes. There are a lot of ways in which bacteria and eukaryotes group together and ways that archea groups together; most bacterial and eukaryotic cell membranes have lipids with fatty acids connected to glyceral by ester linkages whereas Archaea cell membranes have lipids with fatty acids linked to glycerol by ether linkages. Here is a table lookin at differences among them, archea, eukarya, and bacteria. The figure as they give it to us is incorrect, as archea have ether, not ester linked. There are ways that archea and eukarya are linked together. For example, they have introns (not listed in the figure), but there are some ways that they are grouped together, and same for bacteria being grouped with archea. Ribosomal RNA though, unequivically, separates the three. Most prokaryotes have a thick cell wall, different in structure from plant, algal, and fungal cell walls. Bacterial cell walls contain peptidoglycan, a polymer of amino sugars. Bacterial cell walls contain peptidoglycan, a polymer of amino acid sugars. Antibiotics such as penicillin interfere with the synthesis of the cell walls peptidoglycan, but don't affect eukaryote cells. Archaea do not have peptidoglycan, although some have a similar molecule called peudopeptidoglycan. Now I mentioned in the early days of microbiology before Woes, a lot of the charactization of bacteria was done in various sorts of ways such as staining cells, and etc. Now we are looking at gram staining result for bacteria. One of the ways of dividing them up is gram positives and negatives. It is not useful in classification, but it is useful in medicine. Gram positive bacteria have a uniformly dense cell wall consisting primarily of peptidoglycan and they don't have an outer membrane. They have the peptidoglyan layer on the outside, and the membrane under it. Gram-negative bacteria have a very thin peptidoglycan layer and an outer bilipid membrane. So they will stain differently with the gram stain. The gram stain is a purple stain that sticks to the outer cell wall of these gram positives, and tey will come out as purple. If you stain the gram negative and wash it off, the safron encounter stays, the gram stain leaves, and you get pink. Gram negatives include lots of interesting organisms we study (E Coli). Prokaryotes utilize a diversity of metabolic pathways. We have to go through some of the metabolic pathways that the prokaryotes use; the true measure of the diversity of life on earth means a downward shift towards the microbial realm. Prokaryotes have a tremendous diversity of ways of getting by, of getting energy, compared to eukaryotes. And, not only that, much of the metabolism the eukaryotes do is derived from prokaryotes to start with. Eukaryotes use far fewer metabolic mechanisms. Much of their energy in metabolism is done in mitochondria and chloroplasts that are descended from bacteria. The long evolutionary history of prokaryotes has resulted in a variety of metabolic lifestyles. Here is a list of things you gotta remember, various ways of classifying prokaryotes. A lot of them are anaerobes, who don't use oxygen as an electron acceptor in respiration. Obligate anaerobes cannot live in the presence of oxygen-it will kill them. Aerotolerant anaerobes do not use oxygen for cellular respiration, but are not damaged by oxygen if it is present (they tolerate oxygen). Facultative anaerobes can shift their metabolism between aerobic and anerobic modes, such as fermentation. Obligate aerobes

cannot survive in the presence of oxygen. More terms, a grand classification of how organisms obtain their energy and carbon. We have photoautotrophs (found in all three domains), that use light for energy and carbon dioxide as a carbon source. They include plants. Then there are photoheterotrophs (some bacteria) that use light as an energy source and organic compounds as a carbon source. They use light as an energy source, but get carbon from compounds made by other organisms (purple nonsulfur bacteria). Then there are chemolithotrophs (chemoautotrophs)(some bacteria, many archaea lie the ones at the bottoms of hotsprings) that oxidize inorganic substances for energy and utilize CO2 as a carbon source. They get energy by oxidizing inorganic compounds, and use the energy to fix CO2. Deep sea hydrothermal vent ecosystems are based on chemolithotrophs that oxidize H2S (hydrosulfide) and other compoiunds released from volcanic vents. And finally chemoheterotrophs (found in all 3 domains) that use organic compounds for both energy and carbon source. They obtain both energy and carbon from most complex organic compounds (from what we eat, because we cannot use light as an energy source (most bacteria, achaea, all fungi, many protits, and you!). So the proteobacteria figure pretty importantly cause inside our cells are something that was descended from a proteobacteria, are mitochondria. The incredible diversity of bacteria and archea by showing you this figure of all of the different modes of nutrition in just the proteobacteria. We know that there was a photoautotrophic ancestor of proteobacteria. And, if we look at the pattern of descent of modes of nutrition, we find 3 different kinds evolving independently in that phylogeny repeated in the proteobacteria. There are lots of shifts-These shifts are probabily caused by taking up a new way of light (no light in the gut). And this happens over and over in the history of archea and bacteria. Now, back to the overview slide. We have bac here the origin of life, and these 3 major branches, and we will discuss how things like our cells arose, how did eukarya rise? Here is a more detailed overview of the three domains of life. We have the origin, bacteria, and eukarya, and archea. We know now that mitochondria (the power plants in our cells that produce ATP) arose as a consequence of some sort of ancestral eukaryote engulfing a proteobacterium. How is likely is that, that is truly wacky, but in the present day, there are many examples of endosymbiotic bacteria that aren't mitochondria, there are bacteria like rekatcias and other kinds that live inside of the cells of the host organism, so it is not all that improbable. The mitochondria having gotten in there experienced good times, their genome slimmed down, and they evolved to become a endosymbiote. Sometime later, a cyanobacteria experienced the same situation, engulfed by ancestral eukaryote and gave rise in ways that are somewhat complicated as we'll see, to chloroplast, the light harvesting structures inside of photosynthetic organisms. Now we talk about the uncertainties of eukaryotic cells. Uncertainties remain about the origins of eukaryotic cells. Eukaryotic cells arose as the envionment was changing dramatically from anaerobic to aerobic. Lateral gene transfer complicates the study of relationships and accounts for the number of bacterial genes found in eukaryotes. A recent study suggestion is that eukarya arose from the fusion of a Gram-negative bacterium/proteobacterium and an archaean. The timing of that even is somewhat complicated. Phylogeny of eukaryotic lineages is a subject of research and debate. The oxygen revolution from an anaerobic to aerobic environment due to cyanobacteria giving off oxygen as a biproduct. Lateral gene transfer is the transfer of genes between organisms in a manner other than traditional reproduction. It can make figuring out phylogenies rather difficult because the same gene can sort of move across branches in the tree and we know that in our own genomes and in the genomes of other eukaryotes there are examples of genes that were originally in bacteria. And some of these are descended from things like mitochondria and chloroplasts. We know of good examples of endosymbiotes that lose their genes to the host, and the genes get moved over to the host, and the endosymbiotes' genome strips down. To get to eukaryote cells, a bunch of things had to happen. Several steps preceded the origin of eukaryotic cells: Origin of a flexible cell surface. Origin of a cytoskeleton, origin of a nuclear envelope,

appearance of digestive vacuoles. Acquisition of some organelles by endosymbiosis. We don't really know how some of these steps occurred, so I will only show you is to some extent speculative. We that there the cell surface of prokaryotes is inflexible. The cell surface of eukaryotes, the ones that don't have cell walls, is flexible. Eukaryotes have a cytoskeleton, that had to originate. Thy have a nuclear envelop, digestive vacuoles, and organelles. The advantages of a flexible cell surface include that with the loss of the prokaryotic cell wall, cells can grow larger. As cell size increases, surface area-to-volume ratio decreases, but with a flexible surface, infolding can occur, creating more surface area. A flexible cell surface also allwed endocytosis to develop. This is important for engulfing other cells and the development of mitochondria and chloroplasts. The cells can get bigger, as cell size increases, if you have a flexible cell surface, you can have infolding in the surface, and that will increase the SA-to-Vol ratio (a problem encountered repeatedly in the lecture), solving the SA to Vol problem for organisms. It allows you to gobble things up, you can loop around it and take it in through endocytosis. Advantages of a cytoskeleton is that it provides cell support. It allows cells to change shape and move materials around the cell, including daughter chromosomes. In some cells, microtubules gave rise to the flagella. You have heard about mitosis and meiosis, the cytoskeleton is involved in producing structures that allow the disposition of daughter chromosomes within cells. And gives rise to flagella as well in some. The DNA of a prokaryote is attached to the plasma membrane. One of the ways in which we think the nuclear envelop of eukaryotes might have evolved is from the plasma membrane. The nuclear envelope of eukaryotes may have evolved from the plasma membrane. Infolding of the membrane could have been the first step in development of the nucleus/toward the origin of the nucleus. Now let's discuss the origin of mitochondria. When the earth was young, cyanobacteria were photosynthesizing and producing poisonous O2 gas (to the early prokaryotes). At some point, an ancestral archean phagocytic eukaryotes ate but did not digest and kept intact a proteobacteria that could handle oxygen. This proteobacteria evolved into mitochondria (theory of endosymbiotic theory). Mitochondria have genomes that can be compared to that of proteobacteria (they are very similar). The first function of mitochondria might have been to detoxify O2 by reducing it to water. Later this reduction became associated with ATP production. Figure shows ancestral eukaryote and infolding of a flexible cell surface after its lost the cell wall, creating a nucleus, Then the step of engulfing a proteobacteria to create mitochondria, and later, the step of engulfing a cyanobacteria to create a chloroplast. The origin of chloroplasts is quite complicated. Evolution of chloroplasts probably occurred in a series of endosymbiotic events. Evidence comes from looking at geneome/nucleic acid sequencing and electron microscopy (looking at the cell and membrane structure) . Three different kinds of chloroplasts, which depend on number of endosymbiosis events: Primary endosymbiosis: eukaryotic cell, or ancestor of one,engulfs a cyanobacterium (blue-green algae), secondary endosymbiosis: euglenid (freshwater flagellate) ancestor engulfs a chlorophyte (green algae), retaining the chloroplasts and gave rise to choloroplasts in the other photosynthetic eukaryotes. The cynaobacterium was engulfed by something, which was engulfed by another thing, and gave rise to the chloroplast present in plants and tertiary endosymbiosis (not talked about this semester). The primary endosymbiosis: they are the chloroplasts of green algae (chlorophytes and charophytes) and the red algae. The cyanobacterium was gram-negative (it had an inner and outer membrane, with peptidoglyacan between). A small number of peptidoglycan from the bacterial cell wall is found today in glaucophytes. Red algal chloroplasts retian some pigments that were present in the original cyanobacterium. Here is a picture of the primary endosymbiosis. And notice that whats shown in the picture is the outer membrane persists, and the inner membrane persists, and here is now the chloroplast with two membranes. Secondary endosymbiosis (more comlplicated): these are the chloroplasts found in vascular land plants and most other photosynthetic eukaryotes. Chloroplasts have a third membrane. Their euglenid

ancestor of land plants engulfed a chlorophyte and retained its chloroplasts, and in the process surrounded it and retained the membrane. Present-day euglenid chloroplasts have the same pigments as green algae and land plants. This is a chloroplast containing a eukaryotic cell that is being engulfed by another guy, and now comes in and gets a third membrane after being engulfed (this is a clue to secondary endosymbiosis). The word protist does not describe a formal taxonomic group, but is a term of convenience. Protists is not a monophyletic classification. The protists are an extremely diverse group. Some groups of protits are closely related to animals and fungi-others are related to land plants; other are not closely related to any of these groups. Most are single-celled and microscopic, but some are large. Paramecia, stuff like that. They are a weird group (protist), lumps up a group of things that don't fit monophyletically. Giant kelp is a protist. How/why they are not monophyletic. If we just look at this, here are some familiar organisms called plantae, protists (half of eukaryote tree). Some of this tree used to be called separate kingdoms, the rest of it is still called protist (doesn't contain all the descendents of the common ancestor, so its just called protists). How many kingdoms are there. Systematist now generally recognize 60 major eukaryote lineages based on rRNA data. Some advocate designating all of these lineages as Kingdoms, but there is not agreement on this. Here is the summary: The past 20-30 years have seen a remarkable revision of our understnading of the tree of life: rRNA sequences have shown that microbial diversity is far greater than the visible diversity of multicellular organisms. We now think of life as consisting of 3 domains: the relationship among these Domains is somewhat uncertain, but Archaea may be more closely related to Eukarya than to Bacteria. Prokaryote metabolic and nutritional diverisity, numbers, and biomass dwarf those of the eukaryotes. The origin of eukaryotes from prokaytoes clearly involved endosymbiosis. Protists are a non-monophyletic grouping of eukaryotic taxa. How many kingdoms of life are ther? Who knows? Among eukaryotes alone, there are many more things we might call Kingdoms based on rRNA sequences than were previously suspected.

11/30 Lecture Anchor some points we went over. So one of the points I tried to get across in this lecture is that the way we classify the major grouping of organisms has changed tremendously in the last 20-30 years. Largely under the influence of obtaining molecular data from rRNA. One of the real things done is replacing the 5 kingdom system with the 3 domain system and an unknown number of kingdoms, is creating a downward shift of the appreciation for diversity of life. The true diversity of life lies at the microbial level, far more diverse than the visible diversity of multicelluar organisms. We now think of life as consisting of the three Domains: the relationship among these Domains is somewhat uncertain, but Archaea may be more closely related to Eukarya than to bacteria. The terms prokaryote is a nonmonophyletic group, their metabolic and nutritional diversity, numbers, and biomass, dwarf those of the eukaryotes. The origin of eukaryote from prokaryotes clearly involved endosymbiosis events. They give the lie to the notion that all of evolution can be understood as the consequence of simple changes in the composition of a population from within that population, because what happens there is that something completely different joined the lineage from another branch of that tree, so life is complicated. The protists are a non-monophyletic grouping of eukaryotic taxa. Who knows how many

protist kingdoms there are. The general question of how many kingdoms of life there are, I think is interesting because the answer is not known. There are perhaps about 60 major eukaryote lineages. Where are we going today? The metazoa (creatures like ourselves, animals). There is a lot else in that tree besides us. A lot of biology that we learn focuses on the animals, the metazoa. We see metazoa, but that is not the whole tree. What is an animal? They are multicellular, heterotrophic (must acquire their own organic compounds by eating other organisms) eukaryotes. They lack cell walls (which also fungi have). Their cells are linked with collagen and have intercellular junctions. They have specialized tissues for movement and impulse conduction (muscles, nerves). They have specialized development, and finally hox genes (body plan genes that come in sets, the number of hox gene sets an animal lineage has correlates in ways with how complex the development of that animal lineage is. The animals are monophyletic. There are about 35 phyla of animals. The ancestor is thought to be a colonial flagellated protist related to present day choanoflagellates. A choanoflagellate colony. I had a question after the previous lecture, are there these things called choanoflagellates today, and all the animals that exist descend probably from them? I said no, everything that lives today, lives today, it is not the ancestor of anything today, unless there is a another generation tomorrow. When we look at present day chanoflagellates, they look like what we think the ancestor of animals looked like well over 500 million years ago. It wont do to say that archaea and bacteria are primitive, they have been evolving for over 3.5 billion years, with incredibly sophisticated metabolic capacities. Everything that has evolved , going back to the LUCA, has had the same amount of time; if we say that something looks like an ancestor of the animals, we are saying that when we look at the present day form, we think that is perhaps what the ancestor well over 500milion years ago looked like. One hypothesis for the origin of the animals is from a flagellated protist. Notice there is a flagellated protist and that it is a ball of cells, and of course what you probably already know about animals is that most animals in their development go through an early ebryogeny, a ball of cells stage. And then the ball of cells does some interesting things like invaginates, and you come up with 2 tissue types, and perhaps a 3rd tissue layer and so forth. The notion here is that perhaps different cells became specialized for different roles in this colonial flagellated protist. Note that there are reproductive cells that are sort of flagged there, this is all a hypothesis. And that there was a division of labor in this primitive multicellular organism. And from there you got the gradual evolution of increased division of labor, evermore elaborate modes of development, and so forth. You know about natural selection, and you know that one way of thinking of it is that every organism in a population is in competition with every other organism. But think of this colonial organism, consisting of a bunch of individual cells that have agreed to hang out with each other. And now you get the division of those cells into two classes, somatic cells and reproductive cells. Now is where it gets complicated, because its as if to say you live in a town, hanging with all your neighbored, but there is a division of labor,where some of you get to have kids, and some of you don't. The ones that don't wouldn't like that idea, and in evolutionary terms, that is not considered a good thing either, because it is all about passing your genes on. So the early evolution of multicellularity of whatever kind presents an interesting problem for evolutionary thinkers; how does the conflict of interest get resolved. How is it that some cells get to be the ones that get to pass their genes on to the next generation, and others don't? Big tree from the textbook, a pretty well accepted phylogeny of the animal lineages, and we are going to go through some of this today. The stupidest thing to do is just try to memorize the whole thing without thinking about it. The right approach is to try to get a feel for why the various splits in the tree are made; why do we classify certain groups of animals with others? We talked about the definition of animals, so lets look here at the root of the animal tree, where the common ancestor would be. There are a few things we could consider to be shared primitive characters of all animals, and a couple are listed here; unique cell junctions, collagen and proteoglycans in an extracellular matrix-these are unique features of the animals, but they don't distinguish any animal group from another because they

are shared primitive characteristics among all animals. So we look at the first split among the animals, which is between the sponges (porifera/perazoans) and the group of placazoans, ctenophoras, cnidarians, which arediploblastic (2 tissue types/layers: ecto and endoderm), which is the ancestral character then for the next split with respect to tissues, where we go to these groups right here, the bilaterians, that are triploblastic (they have 3 tissue layers: ecto//endo/mesoderm). There are other things that happen (the nodes); between the perizoans and the eumetazoans, we see the origin of 2 embryonic layers (diploblasty). And then between these weird little group we're not gonna talk about (the placozoans) and the rest, we have the origin of distinct organ systems (another shared derived character) of the rest. We can also make a classification based on symmetry. We have here for the tedophores and the cnidarians radial symmetry; for the rest we go towards bilateral symmetry. And there are also differences in development : protostomes (mouth first) and deuterostomes (mouth second). So what I am trying to tell you is the way to understand the tree and the lecture is to understand it as a series of branching points in the evolution of animals, a series of origins of shared derived characters that bound a group of animals away from its ancestral group. Let's take a look at a summary of living members of the major animal groups and don't memorize the numbers of collumn two, but get a good feel of the relative numbers (which has more species; arthropods or placozoans; arthropods). We're gonna spend all our time today as far as looking at specific groups up here, sponges, tinophores, cnidarians, placozoans (read this), and then go on about the protostomes and the duetoerostomes. We are deuterostomes (bottom of table), where there are groups of echinoderrms, hemichordates, urochordates, cephalochordates, and us, the vertebrates (things with backbones). Now, one of the things to tell you about this tree and the animals we are looking at is that in the middle of this month we'll get the california bucket (a bunch of seawater with a lot of live creatures in it). The interest there is that if you are lucky, you will have a large fraction of the animal phylum represented in that bucket of green organism. Outline of major groupings of animals: we have the parazoa (sponges), and eumetazoa. Among the Eumetazoa there are the diploblastic with radial symmetry=cnidaria, ctenophores), then the triploblastic, bilateral eumetazoa. Among the latter includes protostomes, determinate development, and usually spiral cleavage). This splits into lophotrochozoans- splits into (lophophorates-bryozoa, brachiopodia) and, trochozoans (annelida, mollusca)-and ecdysozoans (nematoda, arthropoda). Then compared to the prostostomes are the triploblastic, bilateral deuterostomes, which have indeterminate development and radial cleavage (including echinodermata and hemi,uro, and cephalochordates. Major dichotomies (splits in the tree). Be able to draw out the major splits of the tree on a piece of paper. So you have the parazoa vs. eumetazoa, then the diploblastic vs. triploblastic tissues, the prostostomes vs. deuterostomes, and the acoelomate, pseudocoelomate, and coelomate organization (not mentioned yet-major characteristics of whether a species has a body cavity or not; and if it does, what kind of body cavity it has). So let's talk about diploblastic vs. triploblastic. These layers are distinct layers of cells that form in early devlopment. The diploblastic animals have radial symmetry and also have 2 cell (tissue) layers: ectoderm and endoderm. Triploblastic animals have bilateral symmetry (right, left), cephalization (eggs have a head end, and tail end), and 3 cell layers: ectoderm, mesoderm (the layer between the ecto and endo; labeled red for muscle tissue), and endoderm. Radial symmetry-think of a sea animone. If you put it base down, and take a razor blade, you can cut it on any plane, and the 2 halves will be the same (any plane along the main body axis of this sea anemone (a cnidarian) divides the animal into similar halves). Bilateral symmetry we have a frog, belly side (ventral side) down, take a sharp knife, cut right down in between the eyes and the tailbone, and the right and left halves were the same. We couldn't have the same halves cutting the top away from the bottom, but only vertically down, not horizontally across. The top part is the dorsal, the bottom part (belly down) is the ventral, and in fancy words the front is the anterior (head), and the back is the posterior (tail-end). A single plane through the anterior/posterior midline divides the animal into mirror-

image halves (bilateral symmetry). One of the things I haven't told you about ( I am gradually making it more complicated) is that there are also interesting differences in the way the first fertilized cell of the zygote starts to cleave and develop. Cleavage and early development; the first divisions of a zygote. The two major patterns distinguish animal groups. Spiral cleavage is found usually in protostomes in which it is determinate; the cell fate is fixed at the first division. The deuterostomes have something called radial cleavage; it is indeterminate: the cell fate is not fixed at first; twinning is possible. An interesting difference between the two is that spiral cleavage is what's called determinate: once the cleavage has occurred, the fates of the different cells are settled, and you cannot get twins. Whereas with radial cleavage, if you separate the embryo early enough, the separate groups of cells can still go on to form a complete and fully functioning animal. Just a little aside: the patterns of cleavage can also be influenced by configuration of the yolk (realize that a chicken egg, when newly fertilized is a single cell which contains that yolk. Once the parental, mom and pop chromosomes start dividing up into cells on top of that yolk, it would be a big job to divide the yolk all the way through every time and in fact in the development of the organism, the yolk is kind of apportioned differently for good reasons. So what happens there is that the cleavage is incomplete; it sort of dices up the stuff on the top of the yolk, but doesn't cut through the yolk. So in reptiles and birds, cleavage is incomplete). Early development. So, there was a famous biologist that once said that the three most important events in life are birth, gastrulation, and death. What we are looking at here is just a little cartoon of gastrulation. So here we have the zygote, the fertilized egg. It starts to cleave into 8 cells, and then it forms a ball called the blastula. The blastula has a little cavity in it, the blastocoel. And then, gastrulation occurs. So what gastrulation is is the invagination, the folding in of the outside of the ball to form an inside layer. So then we have this outside layer, the ectoderm, and this inside layer, the endoderm, and a hole here, the blastopore (in between theendoterm and the ectoderm). Remember I mentioned protostomes, and deuterostomes? Protostomes are mouth first, so in protostome development, this hole goes on to be the mouth (the blastocoel). In deuterostome development, the blastocoel extends all the way to the other end and pokes another hole in the blastula (now the gastrula), and that second hole is the mouth (and the first hole is the anus) of that organism. Body cavities. The thing about body cavities-the different types of body cavities. So, acoelomate animals (coelom is the word for body cavities, so acoelom means possessing no body cavity) lack a fluid-filled body cavity. The space between the gut and the body wall (for acoelomates) is filled with a collection of cells called mesenchyme, and movement is done by cilia. The pseudocoelomate animals' (they have a psuedo/fake coelom, they do not have a true body cavity; a real body cavity is wound all the way around with mesoderm tissue layer) cavity is a fluid-filled space in which the internal organs are suspended, but its not lined with mesoderm (thus it is called a pseudocoel). The muscles are only on the outside wall of the animal (not on the inside as well). Then we have the coelomate animals (us), which have a true coelom that develops from the mesoderm, and their coelom is lined with a layer of mesodermal muscle tissue called peritoneum (peritoneum covers the organs). Inside your body cavity you have all this connective and muscle tissue that is involved with your organs. Here is an acoelomate (a flatworm). And, in making an illustration, we imagine we take a sharp blade and cut the flatworm in cross-section (back to belly). So its gut, where all the food goes, is endoderm, it has the mesenchyme outside of the gut, and outside of that it has a muscle layer (the mesoderm), and outside of that it has ectoderm. What it does not have is the hole in the mesoderm that makes the coelom; in fact, it has no coelom at all (no fluid filled body cavity). Here is a pseudocoelomate (a roundworm). Its gut is endoderm, and it has a cavity now, that is not filled with this mesenchyme, it has this cavity now where the organs are suspended, and that cavity is made in the mesoderm, but it is not made by a hole in the mesoderm in the sense that we didn't split this mesoderm here to make the cavity. Instead, we go ecto, meso, endo. The order form the center is

the gut (endoderm), followed by the mesenchyme cells, then the muscle layer (mesoderm), and then the ectoderm. This is more complicated. We have here a true coelomate (an earthworm). Its an earthworm (we are coelomates), and here what we have is ecto, and then we have meso, and then we have a hole in the meso (the cavity, the coelom), and in that cavity suspended by mesoderm are the organs, including the gut (which is endo). In the center is the gut (endoderm), followed by the cavity, then the peritoneum (mesoderm) covering the internal organs, then the muscle mesoderm, and then the ectoderm. Now, one thing to think about is you start with a single cell with mom and pop chromosomes in it, the fertzilized egg that is, and that thing starts to divide, and somehow, a sequence of choreographed instructions take place, that produces you, or a frog, or a roundworm, with far more complicated structures than we looked at here, but nonetheless, we need to think about what exactly goes on to produces all of those tissues and different layerings. We have already started to see the beginning of it, the makings of a hollow ball, the gastrulation, and so forth. Well, what does the body cavity do (functions of the body cavity). It cushions internal organs (if they are suspended, if there are fluid or mesenchyme in there), can provide a hydrostatic skeleton (a skeleton related to fluid pressure-textbook this-ex: a snail coming out of its shell. What is happening is that one part of the snail is squeezing the fluid in the other part, and its like squeezing a balloon cause then the other part grows) , it allows external layer of muscles to move independently of organs and gut, and provides space to store reproductive cells (eggs) and wastes. Protostomes vs. Deuterostomes (study this slide). Protostome cleavage is spiral and determinate (meaning after cleavage, cell fate is settled). Notice that the cleavage planes here don't align; contrast that to the radial cleavage of the deutterostomes, where the cleavage planes do allign (where now it is possible to have twins). You don't have to know the following words: schizocoelous, and enterocoelus. What you ought to learn though is that the way the mesoderm arises in the two types are different. The key thing I want you to know is this mouth first, mouth second distinction. So here we have the protostomes, and here is the blastopore, the invagination that happens at gatrulation; that is mouth first, and the anus is at the other end. Deuterostomes, the mouth comes second. We have this invagination at this end, and then it goes up to there and makes a new hole, and that new hole is the mouth. So mouth second in the deuterostomes. So just a little foreshadow here, I said that phylogenies are based on molecular and morphological/developmental data conflict a little, and we are gonna have to learn this at some point. There is agreement on the deepest clades/ branches in the animal trees. There is definitely agreement on the dueterostomes, they all hang together. Ribosomal RNA (rRNA), tells us that there are two distinct protosome clades: lophotrochozoa and ecdysozoa. It also realizes the realignment of acoelomates and pseudocoelomates. The key thing to say about this is that all of this body cavity, symmetry, coelom, was all done well before rRNA studies or genomic comparisons were done. It was done by classical embryologists working in labs, cutting things into bits, looking at them, and so forth. And it is what we could do, its what could be seen in the patterns seemed evident and it is the case that as we look at organisms with molecular data, sometimes the molecular data really surprises us. We used to think for example that all animal phyla originated 500 million years ago or a little bit before then, and then molecular data showed us that the dating of the animal phyla probably goes back much closer to a billion years ago. A little bit about sponges (porifera). This is a little section of the tree here (the sponges, the placozoans, and the eumetazoans). Porifera, sponges, were considered plants until 1765 (late 18th century. Their habitat is mostly marine and sessile (they don't move). Their body plan consists of pores and central cavity; their cellular organization is that they have no true tissues or organs. They have these different types of cells (epidermis, mesohyl, spicules). They are filter feeders, they have to take things then into their cells to digest them (intracellular digest them). There are two things animals need to do in order to survive: osmoregulation and excretion. How you do balance the salts in your cells with the salts in the

environment, and how do you get rid of waste? For sponges, they do it the same way single cells do by vacuoles. Obviously when we get to higher organisms, things get more complicated. Sponges are hermaphrodites and they reproduce through asexual budding. Here is a little picture, we won't go into too much detail here. Sponges have osculum, pores, atrium, and spicules; they are made up of choanocyte and amoebocyte cells. I would like you to notice that we have a choanocyte here, remember we were talking about choanoflagellates as free living colonial organisms, maybe looking like what was the ancestor to all life, and so it stands to reason that some of the most primative life that lives now, we would find those types of cells that is consistant with the choanocyte. Sponges feed by water flow, they have cilia that beat the water through pores and through the main internal cavity, and then there is this fancy word at the bottom here- also they move the water by Bernoulli effect. Basically, if this is your sponge here, and there is a current coming across the top of the sponge, that current coming across the top of the sponge produces a suction effect, a negative pressure on top of the sponge which draws water up through it. Much the same way that on a windy day, your chimney in your house (if you have a fireplace) might have a really good draw. Ctenophores; these are also called comb jellies, these creatures we're talking about here are diploblastic (2 cell layers). Their nature; they are all marine and feed on small planktonic organisms. They are radially symmetrical. They have two cell layers are separated by a thick, gelatinous mesoglea (jelly part of jellyfish; full of cells, proteins, and water-goo). The ctenes (major synapomorphy of the ctenophores) are comb-like rows of fused cilia; they move through water by beating the cilia in beautiful patterns (to move and feed). They have bioluminescence. The feeding tentacles are the feeding apparatus, which is covered with cells that discharge adhesive material when they contact prey. Simple life cycles with external fertilization and with the zygotes developing directly into small ctenophores. In enclosed bays populations can explode and damage local ecosystems. Cnidarians, these include jellyfish, sea anemones, and corals. They are in there with Ctenophores (they are a diverged lineage at the same time with cnidarians). Their are radially symmetrical (jellyfish)and their habitat is mostly marine, with some freshwater. Their body plan consists of radial symmetry; tentacles in 4 or 6 multiples; 2 tissues layers with some connective tissue (mesoglea); specialized cells (nerve cells, muscle fibers, etc). They feed as carnivores; they have extracellular proteolytic enzymes. They have nospecialized organs for osmoregulations, excretion, or respiration/circulation. Their reproduction involves polyps and medusa and are hermaphoditic. Cnidarians are predators and use toxins in their nematocysts to subdue prey. They have specialized feeding apparatuses in which they have cnidocytes, specialized cells with a specialized organelle called a nematocyst. They are predators, and they harpoon their prey and poison it. Cnidarians have an asexual stage that is sessile (the polypsthe sea anemone: the dominant stage for sea anemones), and their medusa, or sexual stage (jellyfish), is free swimming. Their gastrovascular cavity for digestion, circulation, gas exchange, and a hydrostatic skeleton. There are 3 major classes of Cnidaria. Anthozoans (sea anemones, sea pens, and corals) are those in which their polyp stage dominates the life cycle. The sea anemones are all solitary and the sea pens and corals are colonial. The corals and anemones have photosynthetic endosymbionts in their tissue that provide some of their nutrition. The scyphozoans (jellyfish; all marine) are those in which their medusa stage dominates their life cycle. And the hydrozoans (hydra, portuguese man of war, or fire corals); in some species polyps dominate in some species while others have only medusae, and most are colonial; the polyps are connected and share a single gastrovascular cavity; some polyps are specialized for feeding while others produce medusae. Finally, we come to corals. Corals. The polyps of most species of corals secrete a matrix of organic molecules on which they deposit calcium carbonate, which forms a skeleton. Living polyps form a layer on top of the growing mass of skeletal remains. It forms coral reefs and islands. Corals grow in nutrient poor tropical waters. They have photosynthetic dinoflagellates that live endosymbiotically in their cells. They receive nutrition from the dinoflagellates. The dinoflagellates receive nitrogen and a place to live in turn.

(Ocean) Warming can lead to the loss of endosymbionts (coral bleaching). Ocean acidification, a consequence of warming with the accumulation of carbonic acid, contribute to dissolving coral skeletons. The reef-forming corals are restricted to clear surface waters where light level are high enough to support photosynthesis. Todays lecture only went int sponges and diploblastic animals.

2/1/2013 I had a question that suggested that I need to make sure that we have something clear: I have thrown around monophyletic, paraphyletic, and polyphyletic around. I am not going into detail of those things, but I want to make clear is that monophyletic is the good thing, what we are striving for. When we say that the animals are a monophyletic grouping, that is the goal, what we want. Darwin said in the origin of species our classifications will become as much as we are able to make them reflective of geneology. So descent from an ancestor. So, when I speak of something like the protists, the protists are a nonmonophyletic grouping between poly and paraphyletic. When I say they are nonmonophyletic, what I mean is that is a bad thing. That means we haven't been able to sort out the pattern of common ancestry that would group things together as a clade., as a group of things that descended from a common ancestor. And as you can see as we go through the animals, well, that is understandable, because there are lots of ways in which we can fool ourselves. We are going to see today that this character that we spent some time discussing in the previous lecture, mainly the presence of a body cavity or not, whether it's a true coelom or a pseudocoelom, after tormenting you with the previous lecture, today it turns out that character isn't very useful. Once we started to look at things using molecular methods, we realized quite often that character is lost, secondarily. There is a clear example I can give of that for you. Snakes are tetropods (for feet)-snakes have no feet. Their ancestor had four feet and lost them, so we classify the snakes with the tetrapods, even though now they have no feet. SO they lost a defining character of the clade, but they are still with the clade because they descended from that common ancestor that had that That is what secondary loss is. So, in the previous lecture we talked broadly about what an animal is. We talked about the hred derived characters of animals, the evolutionary origin of animals. We talked about body plans, aspects of development and major living animal groups. And then we sort of noticed in passing that molecular data are revising some of the classifications of animals. Now, I would bet that a number of you find this frustrating, where the textbook says some people think they are, and some dont', and this goes on and on. If you are gonna be in the sciences, get used to it. This is what happens, people find new ways of analyzing data sets, and they say maybe we should change our mind. Part of being a working scientist, is to hold that uncertainty in your mind and encompass it, knowing what the other parties keep in mind and present to you, but realize also that it is not the once and for all truth. And then we looked at perazoans and diploblastic animals Here is our big tree. So this is the tree we looked at last time. We got as far as the Ctenophores and the Cnidarians last time. We saw gooseberry, we saw coral, jelly fish, things like that. WE are now going down into the prostostomes. We will save for two lectures from now the dueterostomes,which include ourselves. We are going to spend 2 lecturs on the protostomes, and part of the reason for that is that the Ecdysozoans include arthropoda group, which includes crustaceans and the insects, spiders, and these things are extraordinarily diverse. So we need to give a whole lecture to the arthropods or the ecdysozoans aside from the pnematodes, which I will also present in this lecture. Now let's look at some of the shared derived characters to remind ourselves of how we get through this tree and the logic behind building this tree. So here is the common ancestor of animals, and it has a couple of shared derived characters listed here: unique cell junctions, collagen, and proteoglycans in extracellular matrix compounds. And we go here to the sponges, and we didn't talk about it, but spicules and choanocytes are their shared derived characters for the sponges, and going away from the sponges (perazoa), we get to the animals with 2 embryonic cell layers, the diploblastic animals. Now we are going to go away from the diploblastic animals to the three embryonic cell layer animals, that are bilaterally symmetrical. Along the way to those groups we have certainly the evolution of distinct organ systems, we won't talk a lot about those today, but you'll start to see them appear when we look at these organisms. We are not gonna talk much about them because we have a whole central part of the course devoted to physiology and organ system and in that intro part of the course we'll go into the comparative aspect of organ systems in different animals. And so we are going to spend out time here

in the protostomes today. This is another way of looking at what we just looked at. We have the parazoa (sponges), then the eumetazoa. Eumetazoa splits into diploblasts (radial symmetry like Cnidaria and Ctenophores) and triploblasts (which have bilateral symmetry. The triploblasts split into protostomes and deuterostomes. The protostomes have determinate development and usually spiral cleavage. The deuterostomes have indeterminate development and racial cleavage. The protostomes consist of lophotrochaoans and ecdysozoans. The lophotrochozoans are made up of lophophorates (bryozoa, brachiopodia) and trochozoans (Annelida, Mollusca)/ The ecdysozoans consist of nematodes and arthroppods. The deuterostomes split into echinodermata and hemi, uro, and cephalochordates. Diploblastic vs. Triploblastic animals. So there are distinct layers of cells that form in early development. The diploblastic animals have radial symmetry and also have two cell tissue layers, ectoderm and endoderm. The triploblastic animals have 3 cell tissue layers (ectoderm, , mesoderm, and endoderm), bilateral symmetry, and cephalization (they have a head end and a tail end). Major dichotomies include parazoa vs. eumetazoans (which we are looking at now and from last lecture), diploblastic vs. triploblastic, protostomes vs. deuterostomes, and acoelomate/pseudocoelomate/coelomate organization (coelomic status is not always a reliablesomething you can build a phylogeny on that follows cladistic principles and groups things monophyletically-phylogenetic character: it is sometimes lost/modified secondarily [like the snake losing its legs]. We know this because of molecular phylogenies because as the morphology changes, the sequences in the genes are not going to change that rapidly during evolution. So we can us various genomic sequences like from rRNA to trump morphological characters, but there are other ways to find if something that is characteristically lost). Today we are looking at eumetazoan, triploblastic protostomes. We saw this before: protostomes vs. deuterostomes. The protostomes have mouth first; deuterostomes have mouth second. Protostomes typically have spiral cleavage, and deuterostomes have radial, and then we have determinate in protostomes vs indeterminate in deuterostomes. What is a protostomes. The common ancestory had a coelom, but some lineages have modifications. For example, some Flatworms are acoelomate and Some lineages have a pseudocoelom (rotifers have a pseudocoelom). In arthropods, the body cavity became a hemocoel and is part of the open circulatory system (what passes for blood in an arthropodkinda sloshes off in there) . In mollusks, the open circulatory system is similar to the hemocoel, but it retains the vestiges of an enclosed coelom (enclosed by mesoderm). There are 2 major clades of protostomes: lophotrochozoans and ecdysozoans. We will look at both of them. The lophotrochazoans have a couple of structures we will learn about: the lophophore and trochophore larvae. The ecdysozoans are the molters, they shed their exoskeleton periodically in order to get bigger. Now, whats interesting is that prior to molecular phylogenetic methods, the classifications of these things right here (lophotrohazoans and ecdysozoans) were much diferent, mixed up in very different ways and classified in different ways. A lot of it was based on whether there was a coelom or not, and that can be misleading, and there were other ways in which people we misled by that. Now, just taking a step back, there is also the term that you all learned in high school bio, and everybody knows that, and that is invertebrates, animals without backbones. And so I have listed here, inverebrate groups, and numbers of species roughly speaking. There is one that stands out really big, and thats the arthropods. And 1.5 million species is most likely a gross underestimate. The arthropods are incredibly speciose, incredibly diverse. Now, I said something in the last lecture, the stupid way to study this will be etc, and thus this list here would be to memorize it. But what I would love to think of you trying to do is to connect these groups up in a tree-like structure that has the right branch patterns. That would be a smart way to study them: porifera, cnidaria, ctenophoria, platyhelminthes, rotifera, lophophorate phyla, mollusa, annelida, nematoda, arthropoda, echinodermata, and chordate subphyla. The lophotrochozoans are split into 2 groups: one with a lophophore, and ones with trochophore

larvae. The ones with a structure called a lophophore have a circular, U-shaped ridge around the mouth with 2 rows of hollow, ciliated tentacles. Basically if I had those around my mouth I would gather food with it. It functions in food collection and gas exchange, and has evolved several times OR it is ancestral and has been lost by some groups. It is nonetheless, one of the characters by which we classify lochotrochazoans. The lophophorate phyla includes bryozoans, brachiopods, and phoronids. The other group are the ones with trochophore larvae. They move by beating a band of cilia, which helps with food capture. It is probably ancestral, that is to say you can build things into a monophyletic group based on the trochophore larvae structure, but its lost in some groups as well (remember the snakes, this can happen!). It covers a lot of phyla; we have mollusks, annelids, ribbon worms, and bryozoans (bryozoans are in both groups!) Here is a table from your textbook (32.1) and it lists some major protostome groups and their characteristics. I want to go over that coelom column to point out some of the subtlety of it. I have some of the groups we will talk bout today. And, I'm not gonna talk about the other groups, and so really you could know about them and should read about them, but we'll focus in lecture on these groups (flatworms, rotifers, bryozoans, brachiopods, annelids and mollusks [all the listed are lophotrochozoans], and nematodes [ecdysozoans]). Let's go over this coelom column here and the digestive tract column. Okay, so, here are your groups (you should read about arrow worms). Notice the arrow worms are outside of these two clades (L-troch and Ecdys) they are of uncertain classification. But let's look at the L-troch's with respect to coelom or not. Well, its all over the place. Rotifers have a pseudocoelom, flatworms have no coelom, mollusks have a reduced coelom, and bryozoans, brachiopods, and annelidshave a coelom. The ecdysozoans, the molters, have a psuedocoelem with the exception to the arthropods, which have a hemocoel. There is a variety of evolved digestive tracts and circulatory systems as well. One of the sort of general things to point out about this in an evolutionary sense (back to our example of snakes) is that characters can be lost and will be lost if the loss benefits the organism. Classic example of this is loss of sight in cave organisms. They posses these marvelously evolved eyes, and yet once a lineage s trapped for a sufficient amount of time underground where there is no light, the eyes are lost. So, evolution, once something has evolved, it need not be maintained in a lineage. Evolution doesn't occur in backwards, forwards kinda ways. Forwards is whatever increases fitness, of individuals. And if that means loss of eyes, that's forwards. If it means loss of coelom, thats going forwards. The digestive tract is complete in most of the mentioned species except flat worms (dead end sac), and the circulatory system is nonexistent in flatworms/rotifers/bryozoansnematores, but open in brachiopods/mollusks (cept in cephalopods), and closed or open in annelids. Here is one of our groups that we are going to look at (platyhelminthes-flatworms). They are parasitic or free-living flatworms. Their body plan consists of dorsoventrally flattened bodies, 3 tissue layers (triploblastic), well-developed nerves, and organs of reproduction and excretion. They lack coeloms and an anus (their digestive system is a blind sac-it doesnt have an end). They don't have circulatory, respiratory, or skeletal systems. They have specialized organs of attachment or adhesive glands (a lot of these are parasitic). Nearly all of them are hermaphroditic (they have male and female function). And traditional groups (some may not be monophyletic) include the flatworm (turbellaria) which are freeliving, the trematadotes which are parasitic, and tapeworms which are parasitic. Here is a little picture of a couple of representations of a flatworm. One is a real flatworm (left-a free living flatworm). The other is a diagram, and I am not going to ask you to remember all of this stuff here, but get the general impression of the list if gave you of characteristics of flatworms. They have an anterior and posterior end, as you can see. Anatomy of a tapeworm. The scolex: not really a head but an organ of attachment. They are human parasites that can get very long. It's a type of flatworm. It has these segments that contain reproductive organs, and some nerves, and an interesting term pops up. A special organ type that is a type of solution to a problem that will occupy us quite a bit. So protonephridia is thought of as a primitive pre-kidney

like function in the organism. We won't talk about the details of it now, we'll come onto it later. I want you to be horrified by the front end of the tapeworm; its not really a head, it's an organ of attachment, and it really is a horrible thing to look at. It's got all these hooks, and the suckers there. The things that evolution make are not always beautiful, but are always effective, and thats what this is. The proglottids are segments with reproductive organs, some nerves, and protonephrida. The rotifers. These are tiny little freshwater animals. Look at the size scale here, 1/10 of a mm. This thing is maybe 30-40 mm in some length, and there are some that are really tiny, to the point that they cannot be seen. So details about them. They are tiny (50-500 nm-wrong-should be smaller) but have specialized internal organs-some of them are as small as protists. About 1800 of them in species, most of them being in freshwater. They have a complete gut. The body cavity is a psuedocoelom that functions as a hydrostatic skeleton, but most propel themselves by cilia. The corona is a ciliated organ on the head. Beating the cilia sweep foo particles into the mouth and into the mastax gizmo, an organ that grinds the food. Some can protrude the mastax through the mouth and capture prey with it. Bdelloid rotifers have been asexual for 60 million years (they consist of only females); how do they do it? What we know from evolutionary theory; if a population doesn't have recombination going on between individuals, if it isn't mixing its gene between individuals, some kind of sex, then its going to go extinct for various reasons, (deleterious mutations have a tendency to accumulate if there is no recombination in a population). How do the rotifers get away with 60 million years of no sex? It turns out that the latest stuff that is out suggest that rotifers have sex with the world, in the sense that they have a life cycle where in when times are bad they form a dry-cyst like structure. And they wait around for water to appear on the surfaces of vegetation and other surfaces where they are. And when that water appears, they rehydrate, and apparently they are very good then at taking up environmental DNA and incorporating it into their genomes. And so this comes from molecular studies that have come up in the last 3-5 years. They are not only not asexual, they are about the most sexual organisms around in that they don't discriminate at all as to what kind of DNA they'll bring in. If you take a glass of water, set it on your roof, and leave it for 4-5 days, and look in it (sterile water), it will be teeming with rotifers when you set it out there. They are in the air, and they go about from place to place by wind dispersion of the dry life stage. Here are some pictures of rotifers, and they're kinda beautiful creatures. The main idea I want you to get from here is just to get into your head that as small as this creature is, it has internal organs, it has a body composed of multiple cells, it has a pseudocoelom, and so forth. It's an animal. A little teeny animal. Lophophorates-we are not gonna spend much time on this, and the lophophorates are not a true monophyletic group. They are a group that used to be taught as a classification, a monophyletic classification, and we now know that they are not. There are things that have this lophophore, this structure of cilia for beating things into the mouth. They include such things as ectoprocts, phoronids (lophophore and mouth are at one end of elongated trunk), and brachiopods (they have a hinged shell; 2 parts of it being dorsal and ventral). The brachiopods are shelly organisms. They look like sea shells, but most sea shells are mollusks. In brachiopods, the top and bottom parts of the shell are the dorsal and ventral aspects of the organism. In mollusks, the top and bottom are the left and right aspects of the organism. So there is a difference. Bryozoans. They have both the trochaphore larvae and the lophaphore. Their colonies grow via asexual reproduction of the founding member. Colonies may contain as many as 2 million individuals called zooids. Individual zooids are 1-2mm in size and are connected by strands of tissue. New colonies are produced sexually-sperm is released into the water and carried to the individual; eggs are fertilized and brooded internally; larvae are then released to find new attachment sites and start new colonies. Individuals can rotate the lophophore to increase contact with prey. In some species, individuals may be specialized for feeding, reproduction, defense, or support. Here is a picture of a colonie in the sea shore and fresh water, that create reef-life structures even. The mollusks (50k species). Their body plan contains highly diverse group but usually 3 distinct body

regions (head, muscular foot, and visceral mass which contains well-developed organs). The mantle (a shared derived characteristic) covers the visceral mass and in cases where mollusks have a shell, they secrete the shell and encloses the gills. They have a complex digestive system with radula (snail). They have paired ventral nerve chord, which loops around the gut ( a squid's esophagus goes right through its brain), and modified trochohore larvae. They also have a reduced coelom; usually an open circulatory system. Major classes of mollusca include polyplacophora (chitons), gastropoda (snails, slugs), bivalvia (clams, mussels, scallops, oysters), cephalopoda (squids, octopi, nautiluses). Chiton is a polyplacophora, gastropods include snails, slugs, nudibranchs, a bivalve includes a scallop (2 halves), and the cephalopods (head-foot). The chambered nautilus has an external shell shell, even though its grouped with octopi and squid, it is a cephalopod. Features of the cephalopods include that they have tentacle, camera eyes, and more. Analogous characters are similar not by virtue of common descent, but instead by convergent evolution. Homologous characters are those characters similar in organisms by virtue of common descent from an ancestor. Look at these eyes in this picture here of the vertebrate eye and the eye of an octopus; remarkable similarity. Both have a pupil, both have a lense that is suspended and can be moved backwards and forwards to sharpen focus. It moves backwards and forwards by slightly different mechanism we won't go into right now. There is one striking difference between them, which should show you that they evolved from different ancestral conditions. Famously, the vertebrate eye, the optic nerve goes through the retinae, and the receptors (the innovation of the receptor cells) is basically behind the branches of the optic nerve. So light must shine through to get to the receptor cells in the vertebrate eye. Not only that, but because the retinae goes through the vertebrate eye, the vertebrate eye has a blindspot. So vertebrate eyes are great, but in that respect, the cephalopod eyes are better because they dont have the optic nerve going through the retinae. Instead, the optic nerve plugs into the back end of the receptor so that the receptors are hit first by light rather than nerves being hit first by light. And, that difference between the two of them is underlain by a sort of a profound developmental difference in the way which the eyes emerge in the developing organism. The eyes of vertebrates emerge as the inversion of the developing brain. How much more we have here: the body plan of the mollusk: we already talked about this stuff a bit, but this is a hypothesized mollusk ancestor. This mantle, this guy has a shell, not all of the mollusks do. Here is the bit about the mollusk nervous system. See this ring-like structure here? And this purple thing is the mollusks gut, so all of its food passes through its brain on the way through the digestive system. The interesting thing is that we already know the mollusks are diverse, and you take that ground plan, the original ancestral mollusk, and evolution has changed it in various ways to produce this remarkable diversity of forms, which we will talk about later, and then we'll talk about the pnemotodes and arthropods

2/4 Lecture Know the nature of the shared derived characters. In cases where we're grouping things together, where organisms don't fit together because of a modification is solved by molecular data. A recent tree of arthropods that pretty much say that insects are crustaceans. What happens with these sorts of things is the morphological characters are not always reliable, they will tend to disappear or never happened to evolve or something like that, and so then you can go at the gene sequences, make a new evolutionary tree with those, and often those will resolve things. Finishing up the previous lecture, we got at about this far, the hypothesized body plan of a mollusk ancestor: how much of that stuff do we have to remember? Here are the three things I want you to remember: the 3 characteristics of a mollusk: a mantle, a foot (muscular), and the visceral mass. Now, here I am showing you a typical generalized mollusk body plan, and all I want to do is to show you that that plan, and in particular, the anterior-posterior ventral-dorsal relationship of that plan changes when we get to the four different groups of mollusks that we looked at. Here is our typical, generalized mollusk off the shelf. There is dorsal, there's ventral, posterior, and anterior, mouth, anus and so forth. If we look at the chiton, A-P sort of fit with this kind of scheme here, but look at a bivalve (this is a scallop), anterior-posterior, but this is a ventral view, we're looking at this thing from it's stomache, as it were, so the dorsal side is where the hinge is, and the shells are left and right. Anterior and posterior in a snail. Anterior and posterior in a cephalopod correspond to above the eyes and below the eyes. So all of that is to say that whats happened in the mollusks is that this basic body plan has undergone evolution of quite spectacular diversification. We saw the extent to which the mollusks have diversified when we looked at the video last time of the octopus and the cuddle-fish and so forth. Alright, this now gets us onto segmentation (metameric segmentation). Now we starting to talk about organisms that are segmented. It's also known as metamerism, and it basically involves segments that formed from pouches (formed as pairs of pouches) that are lined with mesodermal tissue (they form during development). It's found in annelids, which is where we're gonna go next, and arthropods, where we'll spend a good amount of time in this lecture, and in chordates, that is to say, in organisms like ourselves. We are segmented, and in case you don't believe that, here is a segmented human being for you. Lateral muscle blocks are segmentations in humans, vertebrae are evidence of segmentation, ribs, but even jaws and highloid bone and so on are part of different segments from an ancestral organism in the human. And probably when we talk about development, we'll come onto this a bit more. Serial homology is part of the picture with segmentation. What metameric segmentation allows an organism to do is to specialize segments independently of one another, more or less. This is going to be a grand theme that we're gonna encounter in the evolution of body plans and development from now on. That is to say repeat, then vary, produce many different segments, but vary the segments, and as you might imagine, what we now know about and are learning about the molecular genetic mechanisms that control the variation of the segments to produce different types of organisms. Just for a second in the annelids, which we will look quickly at, each primitive segment contains a pair of: metanephridaakin to kidneys-addressing how to deal with wastes (compare to protonephrida [primitive kidney function] in tapeworm), hearts, appendages (parapodia), coelomic ducts for release of gametes (reproduction), and ventral ganglia (part of the nervous system). Let's take a quick look at the annelids. They live in all habitats as free living. They have a trochophore larvae (polychaetes).They have a hydrostatic skeleton (fluid pressure) with thin cuticle, which allows them to respire via skin (they need to live in moist environments (earthworm)). They have CNS (central nervous system); brain and paired ventral nerve chord. They use metanephridia for excretion, coelomic ducts for reproduction, and closed tubular circulatory system. Molecular resolving phylogeny things: the traditional view put the annelids with arthropods because of segmentation (morphological theory). Alternative view: annelids with mollusks because of how some of them (polychaetes) have trochophore larvae. Molecular based phylogenies support annelids with mollusks. Here the trochophore larvae is a reliable character.

Polychaetes: not a single clade; mostly marine, many burrow in soft sediments. They have one or more pairs of tentacles for prey capture of filter feeding (tentacles). Parapodia on each segment: (they have extensions of the body wall, it functions in gas exchange, and is sometimes for movement). Worms with feathery gills. Pogonophorans-polychaetes that have lost their digestive tract. They secrete tubes fof chitin in which they live. They have endosymbiotic bacteria in a specialized organ called the trophosome. The endosymbiotic bacteria fix carbon using energy from the oxidation of Hydrogen Sulfide. They are found in the deep oceans living near hypothermal vents. The largets are up to 2 meters long. They live near deep sea hydrothermal vents (chemolithotrophs?). They feed primarily as a consequence of this specialized organ they have (trophosome) which is full of endosymbiotic bacteria. The bacteria help fix carbon by using energy from the oxidation of hydrogen sulfide. Here is an interesting example of endosymbiosis. Clitellates (ologochaetes and leeches). Oligochaetes have no parapodia, eyes, or tentacles, and few setae. They are hermaphroditic; each individual gives and recieves sperm during copulation. They dont't have parapodia on the side, they don't have eyes or tentacles, setae are the little bristles often that are along the side of these things, in every segment. Leeches (also clitellates) lack parapodia and tentacles. They coelom is not divided into compartments. Segments aat either end are modified to form suckers-temporary anchors that aid in movement. They are freshwater and terrestrial. All live on blood. They make an incision in the host. They also secrete an anticoagulent into the wound. Hirudo medicinalis is used to treat wounds and prevent scarring. They are used in reattaching a finger, by having them keep bloodflow going in the region of suture to prevent coagulation and keep blood flow going. The ecdysozoans. They are the other split in protostomes aside from lophotrochazoans.THe distinction between the two is fine because its confirmed by molecular phylogeny. The molecular phylogenies are working on the same logic you learned from linksvayer, to find shared derived characters that link groups of organisms to bound those away from shared primative characteristic that bound larger groups.They are the molters. They have a cuticle (the exoskeleton) that is secreted by the epidermis. To grow, the exoskeleton mus be shed or molted, and replaced with a larger one. Molting evolved at least 500 mya (fossil evidence). All ecdysozoans have a single common ancestor; this is supported by phylogenetic analysis based on genomic sequences, including a shared set of Hox genes. Then are nematodes, which were thought to have been grouped somewhere else, there was abig argument a while ago, and the winners were the ones that said the nematodes are the ecdysozoans, (Round worms). They have a very thin cuticle that they shed 4 times in their life. They have unsegmented, thic, multilayred cuticle, gas and nutrient exchange occurs through the cuticle and the gut, which is only one cell thick. The pharynx, a muscular organ at the anterior end, moves materials through the gut, and they move by contracting longitudinal muscles. They are hugely diverse (25k species). Many are miscroscopic but the largest is 9m long; a parasite in placentas of female sperm whales. Caenorhabitis elegans is used as model organism in genetics and developmental biology research (genome was sequenced early-has completely determinate development as a protostome). Diverse feeding habits: scavengers in soil, freshwater, marine sediments and vinegar. They are many predators, feeding on protists and other animals. Many are parasites. Parasites of humans cause trichinosis, filariasis, and elephantiasis. We have now finished the previous lecture. Let's summarize. WE took a look at the animal clade of protostomes and deuterostomes. We defined the two clades. We have pointed out how molecular data have revised some animal groups, and looked at selected protostomes (cephalopods and mollusks, anellids and origin of segmentation, and just looked at ecdysozoans). Now to go on talking about ecdysozoans and arthroppods. Arthropod means jointed foot in greek. Almost all arthropods have jointed feet or legs. They are the creepy-crawlies. Survey of the diversity of life: there has been a tremendous diversity of life from 3.8 billion years of evolution caused by

mutation, gene flow, genetic drift, and selection and maybe endosymbiosis. There are many different ways/strategies to make a living among living things. We look at convergent solutions; many ways to do the same thing. But many may often use similar sets of genes. We already looked at the convergent evolution of the cephalopod eye and the vertebrate eye. And we'll see more and more of these convergent solutions. Often these convergent solutions have arisen from underlying genetic mechanisms that themselves are homologous. So the characteristics that evolve based on these mechanisms evolved separately, they are analogous, but some of the genetic basis for it comes down from a common ancestor and is homologous, an interesting distinction. So here I just show you some structures with convergent functions and are morphologically very different-the eyes of various creatures here, and in some cases the underlying genetic basis for these diverged eyes, eyes of insects, eyes of vertebrates, even though the eyes are analogous, the underlying developmental genetic basis has some homologous genes involved. And here is a picture of the legs of a horse vs legs of an insect. Here is our tree again, the big animal tree that we looked at before. Remember that in this textbook, these red dots are various shared derived characters that you can pay attention to. We are at ecdysozoans right now. Ecdysozoans have a cuticle, secarete by the epidermis (outermost cell layer). For the animals to grow, the exoskeleton must be shed or molted, and replaced with a larger one. Molting evolved 500 mya, apparently only once. All excdysozoans have a single common ancestor. Now we will look at arthropods. Arthropod; in other ecdysozoans, mainly arthropods, the cuticle is an exoskeleton, thickened by proteins and chitin, a waterproof polysaccaride (same shit in fungal cell wall). It prevents dessication. The exoskeleton restircts movement and gas-exchange; new mechanisms for these things evolvedmainly muscle appendages and gills. Appendages manipulated by muscles evolved in the late Precambrian, leading to the arthropod (jointed foot) clade. Appendages are used for locomotion, food capture, gas exchange, copulation, and sensory perception. Muscles are attached to the inside of the exoskeleton. Each segment has muscles that operate that segment and the appendages attached to it. The hard exoskeleton allowed for walking on dry land, and prevented drying. Aquatic arthropods were excellent candidates to invade land. With this waterproof skeleton, and their ability to move undre muscle power, they were well equipped to invade land, which they did, in a big way. Some things about arthropods. They are invertebrates with exoskeleton, segmented body, jointed appendage (arthropod from Greek jointed feet). They have a rigid cuticle, replaced periodicaly by molting. They have repeated segments with pair of appendages, very versatile body plan living swiss army knives (those appendages can be modified to adjust to many different things). Over 1 million species, about 80% all animal (90% of all animal species). Only animals aside from anmiotes (mammals, reptiles) that are very successful in dry environments because of the waterproof exoskeleton. Arthropods break into 4 groups: Crustaceans, hexapods (insects and their relatives), myriapods, and chelicerates. Arthropods include trilobites (extinct). Chelicerata (arachnids[spiders, scorpions, mites] and horshshoe crabs), myriapods (centipedes, millipedes, etc). Crustacians (barnacles, shrimp, losters, crab, etc)-these muthafuckas are not a monophyletic grouping) and hexapods [they are a subgroup within the crustaceans](insects, springtails, etc). Some arthropods are large (japanese spider crab: up to 3.8m or 12ft, and 41 pounds-this is a chilicerate). Arthropod features: the key features that contributed to the success of arthropods are segmentation (each segments mas muscles that operate a segment and its appendages. Allows complex movement patterns and specialization of appendages) and the rigid exoskeleton (which provides support for walking on land, preventing drying, and providing some protection against predators. They evolved from ancestors with simple, unjointed appendages. Some arthropod relatives with unjointed appendages survive today. Argument over whetehr Onychophorans (velvet worms thatlive in leaf litter in the humid tropics) were arthropods or not. WE have concluded that they are arthropods, they don't have jointed feet, but we concluded that they are arthropods due to molecular phylogeny. Their thin,

flexible cuticle; use fluid-filled body cavity s a hydrostatic skeleton for movement. Arthropod diversity: trilobites flourished in the Cambrian and Ordovician seas, but went extinct at the end of the Permian. They left an abundant fossil record. Jointed legs first appeared in some trilobites. Some appendages were modified for different functions. Myriapods(centipedes and millipedes) have a head and long flexible trunk with many pairs of legs. Centipedes have one pair of legs per segment, millipedes have 2 pairs (2 segments are fused). Centipedes prey on insects and other small animals, millpedes scavenge and eat plants. Some centipedes can get quite large. There are centipedes in the tropics that are really long and venemous. Chilicerates (2-part body: head has 2 pairs of appendages modified into mouthparts). Many have 4 pairs of walking legs. Pycnogonids (sea spiders) are small marine species. Horseshoe crabs (4 living species) have changed very little over their evolutionary history. Arachnids: spiders, scorpions, harvestmen, mites, and ticks. Abundant in terrestrial environments (mites and ticks: 50k described species; many are parasites of plants and animals). Crustaceans (dominant marine arthropods today; also terrestrial and freshwater). Shrimps, lobsters, crayfish, crabs=decapods. Sowbugs are isopods. Copepods are abundant in the plankton. Amphipods and ostracods are found in freshwater and marine waters. Barnacles are sessile as adults. They resemble bivalve mollusks, but use appendages to move food into the mouth. Appendages on different regions are specialized for different functions. Some appendages are branched with each branch serving a different function (I want to know major shared derived characters) I want you to see how this all fits into the pattern of diversity. Insects=hexapods. They are abundant and diverse in terrestrial and freshwater habitats; only a few live in salt water. Body has 3 regions head, thorax, abdomen. One pair of antennae on the head 3 pirds of legs on thorax, and no appendages on the abdomen. They are common in fresh-water, but very few live in saltwater (possibly due to competition with the crustaceans who mastered the marine world). Insects use nearly al plant species and many animal species as food. Herbivores can consume massive amounts of plant material. Many are predators, others are detrivores (dungbeetle) that are important in recycling materials in ecosystems. Some are internal and external parasites of plants and animals. Insect development: immature stages of pterygote (with wings) insects do not resemble adults. Metamorphasis: substantial changes that occur between changes; incomplete metamorphasis (little guys look more like their adult form): changes are gradual, or complete metamorphasis (caterpillar to butterfly): changes are dramatic. Insect diversity: pterigotes insects were the first animals to fly. Flight opened up to many new possibilities for feeding and probably contributed to the success of this group. Adults of most species have 2 pairs of wings. True flies have 1 pair plus a pair of stabilizers. In beetles the forewings have become heavy, hardened, wing covers. In neopterans are all other pterygote insects that can fold their wings (some have incomplete metamorphisis like grasshoppers, roaches, mantids, stick insects, termites, etc). Holometabulous insect have complete metamorphisis (beetles, lacewings, caddisflies, butterflies, moths, sawflies, true flies, bees, wasps, ants). Bees, wasps, and ants display unique and highly specialized social behaviors. Molecular data indicate that insects began to diversify about 450 MYA: about the time the first land plants appeared. Ancestral hexapods invaded a terrestrial environmenthat lacked any similar organisms like them. This, plus wings, contributed to their success. Insects are extremely abundant. In terms of biomass and important diversity, the insects are all out of proportion to their size as individuals because there are a lot of them. Social insects (nesting bees, ants, termites, etc) are huge in terms of biomass. Relative proportions of the total biomass of animal groups represented in Brazillian rain forest near Manaus. Insects are the successful animals on dry land.

2/6 Outline is up there. Today we are doing a dash through the deuterostomes. At the end of the lecture, I will give you some hints and advice for the exam. The deuterostomes are characterised by radial cleavage, the mouth developing opposite the blastopore (the anus develops from the blastopore first) and the coelom develops from the mesodermal pockets from the cavity of the gastrula. The first two are though to be ancestral states for all bilaterian animals. DNA sequences supports the monophyly of the deuterostomes. What resolves anythung as a deuterostome or protostome is molecular phylogeny. Living deuterostomes comprose the 3 clades: echinodersm, hemichordates, and chordates. Echinoderms (starfish, sea urchins), are deuterostomes that have bilateral larvae but the adults have 5 arms coming out of a single disk (pentamerous radiate)-they are 5-fold symmetry, no defined head/excratory system. Their endoskeleton of calcified plates that originates from the outside (dermal tissue). This water-vascular system: network of water-filled canals, various features, useful for gas exchange, locomotion, and feeding. They have these tube feet to grasp prey (they can open bivalve). ****Hemichordates: 3 parts: collar, probiscus, trunk Chordates: made up of cephalochordates, chordates, and vertebrates (us). As you know (in the tree). The synapomorphy of the echinoderms are radial symmetry as adults, calcified internal plates, ad loss of pharangeal slits. The synapomorphy of the chrdates involve the notochords, dorsal hollow nerve chords, and post-anal tail. So, these all have shared derived characters in one part of their lives, but no in their adult lives. Evolutuonary relationships are most evident in the early developmental stages. Chordates and their synapomorphy: notochord, dorsal hollow nerve chord, pharangeal slits (basket-like, evolved for feeding in the pharynx (filter for feeding)-when you look at the development of vertebrates, in the early embryo, the pharyngeal slits are present, and they govern to some extent,structually, patterns of development in the early vertebrate embryo-they disappear as pharyngeal slits in the adult), muscular, postanal tail. When you get to the later devlopmental stages, they may look a lot different from the canonical chordate. The notochord: it is a flexible rod that runs the length of the animal. It is located between the dorsal nerve chord and the digestive tract (n=dorsal/digestive-> n=dd=support). Inside are the large fluid filled cells. Outside has the stiff fibrous tissue. It provides support (not a nerve chord), in most vertebrates, this is present only in the embryo. The dorsal, hollow nerve chord develops from a fold of ectodermal tissue. It's contrast to most invertebrate phyla, which have a solid ventral nerve chord. Pharyngeal slits: they are slits located just posterior to the mouth in the pharynx. The slits run from the pharynx to the outside of the animal. Water can flow into the mouth and out the slits. Original function is for suspension feeding. They are modified to serve as gills, jaw support, organs, etc. The muscular, postanal tail extends beyond the anus. The Muscles are grouped into segments called somites. The somies develop from blocks of mesodermal tissue. Thus chordates have thrue (metameric) segmentation. Notochord provides support for muscles. Now we go back, coming back to the slides (living deuterostomes comprise 3 clades). Now we want to look at the sea squirts (urochordates) and lancelets (cephalochordates). Cephalochordates are small, their notochord id retains throughout its life. It extracts prey from water using the pharyngeal basket. They are remeniscent of a small fish, they are on the line toward things like fish, these blocks of muscle look like blocks of fish muscle. They are weak swimmers. One set of hox genes. Urochordates, they are known as tunicates-tough tunic like structures around them (sessile species) and salps (planktonic species). Their chordate traits are often found only in the larva. They have only one set of hox genes. Theories that hox genes get duplicated as we get into vertebrate. Now we come back to the big picture of the animals, and we note the deuterostomes have 3 clades. We are coming to vertebrates, our group. The shared derived characters involve the vertebral column, the anterior skull, large brain, and ventral heart. A jointed, dorsal vertebral column replaces the notochords

during early development. It is the key shared derived character. Other characteristics involve an anterior skull with a large brain, neural crest cells (notochords-specialization), multiple sets of hox genes, rigid internal skeleton supported by vertebral column, internal organs are suspended in a coelom, well-developed circulatory system with a ventral heart. Here we come to this strange group, a figure of the vertebrate clade, and it includes this group called the hagfish (lumped with lamprey). Notice that the hagfish are lumped descriptively with lampreys and they are both jawless fish (agnatha). These guys (hagfish) don't have vertebrae, so there is argument of whether the hagfish should or shouldn't be grouped in the vertebrae clade. Hagfishes may be the sister group of all other vertebrates, in which the skeleton and skull are cartilage. The notorchord is present in adults, not vertebrae (opposite of urochordates). They have a weak circulatory system with 3 small hearts, no stomache, and no jaws. But gene sequencing suggests that hagfishes may be more closely related to lampreys; if so then hagfishes must have secondarily lost many vertebrate features. This is an example where morphological characters can be secondarily modified and lost. Lampreys have no ossified bone; all cartilage. The notochord is present in adult and a second tube with dorsal projections that partially enclose the nerve cord (primitive vertebral column). They are typically parasites. Now into the vertebrates themselves, the gnathosomes (they have jaws). Let's talk about the evolution of jaws. Jawless fishes were common in the Devonian period, but only hagfishes and lampreys survive today. Gnathostomes (jaw mouths) evolved from skeletal arches that supported the gills. Jaws improved feeding efficiency and prey capture. Here is a schematic of how this happened. We have here jawless fishes, where the skull is cartilagenous, with gill arches and gill slits. And so the early jawed fishes (placoderms) began to develop from these gilled arches jaw-like structures that hooked up to muscles and have the capacity to open and close forcable, and catch things, suck things in by producing suction and so forth. The modern jawed fishes (cartilaginous-sharks and bony fishes) have an even further developed capacity for this. These structures are actually bone, and have teeth. Let's look at chondrichthyans (rays, skates, sharks, chimaeras). They are finned fishes with skeletons of cartilage. They are called cartilage fishes but their skeleton has mineralized granules, bony teeth, cartilaginous skin is derived; ancestors had bony skeletons. No swim bladder (will sink if not swimming, in sharks, there are pectoral and pelvic fins that provide lift). The bony skeleton has been secondarily lost. The ray finned fish have a swim bladder and allows them to adjust their bouyancy, which is later related to lungs in land animals. If a shark wants to suspend in motion must be swimming in water. The pectoral and pelvic fins and indeed the tail itself, which has heterocircled tail, is longer than the bottom, and it helps to provide lift for the animal as it swims through the water. Here were are with the ray-finned fishes, the yellow perch. Notice the shared derived character s the bony skeleton, the swim bladder/which gives rise to the lung, and farther down. The ray finned fishes radiated during the tertiary into a diversity of lifestyles. Trails include 4 pairs of gills, operculum (opening on the side for the gills), bones ossified with calcium phosphate, scales (like the rest of the vertebrates), and a swim bladder (allows fish to maintain position at specific depths). Now we're going into the transition from water to land. We've come up into the tertiary, and now we are at the points that vertebrates come to the land. How did they do it? So, in one group of bony fish called the sarcopteridians, which are the other forms (the tetradpods), what joined were bony fins, fins that had bones in them. These are also called lobed fins (shared derived characters. Those jointed fins served as a handy precondition for the evolution of a terrestrial lifestyles with the evolution of lakes. How did vertebrates colonize the land? Well, there was the evolution of lunglike sacs that set the stage for the evolution of land animals. The swim bladder evolved from the lung-like sac. Changes in the structure of fins allowed some fish to support themselves in shallow water, and later move onto land. The swim bladder started out as a lung-like sac in the early fish, then evolved into the swim-bladder, and then evolved into lungs. Once again, an interesting back and forth going on in the history of the

structure. And then there are the fins changes that let the fish occupy shallow waters and evolve to function on land. Now we get to tetrapods. It is believed that sarcopterygians evolved into tetrapods (4 legged vertebrates). The tetrapod legs evolved from jointed fins. There are two clades here mentioned: the amphibians and the amniotes. The amphibians are confined to moist habitats; they lose water easily through the skin; eggs without a shell will dry out if exposed to air. The amniotes are those that have the embro protected from drying by a shelled eg or maternal tissue impermeable to water. Humans are amniotes too, the egg is fertilized and developed internally, and you're gonna see though that the egg has an extra layer set of emrbionic membrane. Amphibians, are in a lot of trouble ecologically-they seem to die off at alarming rates. The golden toad is now extinct. The caecilians are wormlike limbless, tropical burrowing animals (secondarily lost its legs), the anurans are frogs and toads, and then there are salamanders. Amniote clade: has several features contributed to success on dry land: amniote egg: adults have a tough skin with scales and other modifications to prevent drying. The excretory organs allow production of concentrated urine, allowing extretion of nitrogenous wastes without losing excess of water. The amniote egg: the shelled egg is an adaptation to life on land: has yolk providing embryo's food and allows offspring to hatch at advanced stage. 4 extraemrbyonic membranes to protect embryo from drying, to assist gas exchange, and allow excretion of nitrogen. Most reptiles have leathery and flexible shell. Birds have calcareous shells. Most mammals lack shell but retain membranes. The four egg layers with its functions are amnion (protects embryo), the allantois (gas exchange), the yolk sac, and the chorion (gas exchange). During carboniferous period, amniotes split into 2 major groups: reptiles and mammals. The classical way of classifying birds was to classify them as a group equivalent to the reptiles. Now what we know are that birds are reptiles (molecular sequence), and are evolutonarily derived from dinosaurs (therapods). They survived the disaster at the end of the cretacious 65mya. Reptiles have keratin scales, and have gas excahnge via lungs (cloacal in turtules), ectothermic (their body temp. matches the environmental temp). Archosaurs (crocadilians, dinosaurs), lepidosaurs (tuatara and squamates-snakes and lizards), and turtles (their phylogenetic position is debated). The birds: they have distinct reptilian traits: amniote egg and scales on the legs. They are adapted for flight: honeycomed bones, reduced organs (1 ovary), no teeth (gizzard=muscular grinding organ), 4 chambered heart, small lungs but additional air sacs. Endothermic, feathers evolved from scales. Birds emerged from therapod dinosaurs. They are predatory bipedal (2 legged) dinosaurs that had hollow bones, a furcula (wishbone), 3 fingered feet and hands, a pelvis that pointed backwards. Cretacious fossils indicate some predatory dinosaurs had scales modified into feathers. Archeopteryz is the oldest know fossil bird. Clawed fingers on its forelimbs probably assisted it in clambering over tree branches. Archeopteryz: late jurassic (150 mya). Bird and reptile traits. Bird: feathers, wings. Reptile: forelimb claws, teeth, tail. It is not the ancestor of modern birds, just a branch representative of what was going on back then, and it is a convincing intermedian. The rise of the mammals. Small mammals coexisted with dinosaurs for millions of years. They increased in size and number after the extinction of non-avian dinosaurs 65mya. 3 extant groups: prototherians, marsupials, eutherians. Mammals. Possessed hair composed of keratin. Endothermic. Eddicient gas exchange; 4 chambered heart, diaphragm. Mammary glands. Teeth are differentiated. Unique jaw joint (evolved from the reptiles; parts of it turned into tiny little bones inside the ear of the mammals): 3 auditory ossicles. Secondary palate: can breathe and swallow at same time. Prototherians (duck-billed platypus and the echidna), lack a placenta and lay eggs. They have reptilelike egg, hair, mamary glands but no nipples. Monotreme means (one opening); they have a cloaca, not a rectum.

Therians include marsupials and eutherians. Marsupials include opposums, kangaroos, koalas, etc.They have a marsupium; young are born into it, they mature in there for some time before they come out. The eutherians (us)-true-therians. They have placentas and are more developed at birth than marsupials. Herbivores have influenced evolution of plant spines, tough leaves, toxic compounds, and difficult-toeat growth. Herbivored in turn evolved adaptations to the teeth and digestive systems: an example of co-evolution. Large size evolved in many herbivore lineages, which favored evolution of large carnivores able to prey on them

*Note: the last lecture for the first midterm is not included in these notes due to a time constraint. The date of that is 2/6 2/11 Lecture: We finished out detailed discussions of the evolution and diversity although both themes will persist through the rest of the course, even in this section of the course, we will make connections to evolution and diversity as we go along. So here is our outline for today, course business, and then we will start on animal development. We will start rather general today, with some principles and some overall patterns. We will go into development and physiology, but the themes in the course of evolution and diversity will carry on through the semester. There was an error in one of my slides. I said pharyngeal slits were a synapomorphy of chordates, but according to the book it isn't. It is another one of those case that were in the ancestor, and was lost in the echinoderms, but maintain in the chordates (but not in some adult chordates). So I posted a corrected slide, and here it is. It is titled Chordates and Their Synapomorphies. Chordates have 3 clades: urochordates, cephalochordates, and vertebrates. The evolutionary relationships are most evident in the early developmental stages. The chordate synapomorphies include the notochord, the dorsal hollow nerve chord, and the muscular postanal tail. Pharyngeal slits were present in the common ancestor of all deuterostomes, but is not a synapomorphy of chordates. Here we go on development, an I want to start just with some general thoughts, and I'd like you to grasp the wonderful nature of the problem of development. We have multicellular organisms: you, yourself are made of millions of cells, and some organisms considerably less, but the problem nonetheless is the same. We start off with a single cell, or fertilized egg/zygote, and somehow, that thing, through processes of division, cell movement, things that go on at the molecular level, somehow that thing develops into a highly patterned (in 3D space) organism in which the cells that make up the different cell types, tissue types, organs, and so forth, are all generally stably differentiated, meaning they are not going back to what they were before (they are staying with what they are now). Right away we can make a biomedical connection, which is that once in a while in multicellular organisms, cells that are stably differentiated go rogue, and don't stay stably differentiated, they start growing selfishly. We call that cancer. So, the sort of wonderful behavior of cells, their sort of agreement to participate in a parliament as it were, where everybody is working for a common good, is something that evolved from the very first animals, to the present day. As we get deeper and deeper into development, we're gonna talk a little bit about some of the evolutionary connections, but it's an extraordinarily deep and rich subject, and we will only glance off of what I pick to be kind of the major aspects of it. So this is the problem of development: how does a single cell give rise to the order and function of an entire organism, with many different tissue types, organs, etc. all stably differentiated? How does it give rise to all this order and function? Embryonic development involves: cell division, cell determination, cell differentiation (cells become specialized in structure and function), and morphogenesis (different kinds of cells are organized into tissues and organs) (How to remember: My Dear Dead Dog). The physical processes giving an organism shape constitute morphogenesis, the creation of form. The processes of cell division and determination, differentiation, and morphogenesis overlap during development. Early events of morphogenesis lay out the basic body plan very early in embryonic development. Later morphogenetic events establish relative locations within smaller regions of the embryo, such as the digits on a vertebrate thumb. Obviously to get from one cell to many cells, you have to divide. The more important thing here is the determination part. There is something that happens even before cells differentiate, that sets it up such that they are going to differentiate, and we call that thing that happens before differentiation DETERMINATION. It must involve something/things that go on at the molecular level. So after determination we have cell differentiation, where cells become specialized in their structure and function, and then at a larger level, we have morphogenesis, that is to say, cells become organized into tissues and organs and etc. Morphology is a fancy term for form. The processes of all four do not

occur in separate compartments; they are occuring, more or less, continously, once the embryo forms and the organism starts to develop, more or less continously, and they kind of overlap with one another as they go along. We are going to focus on the early events of morphogenesis that lay out the most basic of body plants very early in embryonic development. And then later on we will see that morphogenetic events establish relative locations within smaller regions of the embryo, setting up things such as the digits on a vertebrate thumb. So here is just a picture of animal development for you to just get into your head what happens. We have a zygote, a fertilized egg. Typically this is what it requires in animals, a fertilized egg, but not always. There are some animal species that can reproduce parthogenetically where female just produce eggs that develop (be aware of this). And that thing begins to undergo cell divisions, which we will call cleavage, the classical embryological term for it, but they are just early cell divisions. Eventually we get to, in many different creatures, essentially a mass of cells, quite typically a ball of cells with a cavity in the middle. So we have a ball of cells (developed from 8 cells) with a cavity in the middle. In some organisms, this thing is called a blastula, like a sort of tennis ball in the sense that it has an outside but no inside. And then wonderful things happen to the blastula; it begins to undergo changes, this multicellular thing now, it undergoes changes and in particular, turns itself partly inside out as we'll see, and that is the step called gastrulation, that establishes the first instance of the three tissue layers (cell layers or germ layers) in the organism: the ectoderm, endoderm, and mesoderm that we learned about in diversity earlier. And then a whole bunch of other stuff happens, and in the end you get an adult organism, in this particular picture, an echinoderm. Just as a little evolutionary aside here, recall our sort of our slides we saw when we were talking about diversity, it was about a hypothetical early animal, and it was a protist that was a ball of cells. It was a ciliated protist that was a ball of cells. And the observation that early developmental stages often involve a ball of cells (hollow), and some colonial protists are hollow balls of cells. So it set people to thinking,well, maybe this is an inkling about how multicellularity evolved. So the thing is that we have a single cell starting, a single fertilized egg, a zygote, and this thing is going to start dividing and the cells are going to become determined and differentiate into different kinds of cells, and so on. So as I said, events at the molecular level, we ought to think, are what underlies this. The study of development didn't start out at the molecular level, that is the scientific study of it way back then in the early part of the 20th century we didn't have molecular biology, and it was all done by looking at things under the microscope and messing around with moving cells around, little bits of tissue, and so forth. But as molecular biology matured in the second half of the 20th century, one of the things that was realized right away was that what must be going on as an embryo develops, is that during differentiation and morphogenesis, embryonic cells, when they start behaving differently from other another, the things that drive these differences are probably going to be due to DIFFERENCES IN GENE EXPRESSION. So, we think of the genome of an organism as the blueprint for the organism, but really, that blueprint is useless unless at specific times and places, only certain sets of the instructions in it are carried out. If every cell in your body carried out every set of instructions in your genome, you wouldn't be here. It's the selective deployment of those sets of instructions that gives you your different tissue types and so forth, and those are caused by the regulated establishment of differences in gene expression in different types of cells. These differences arise during development and arise as regulatory mechanisms that turn specific genes on and off. We're not gonna take a close look at that stuff today, but we'll zero in on it more in the second lecture, but we'll allude to it a couple times to keep it in our heads. But we're gonna talk about it a bit more in general right now and for the next 2-3 slides. So the thing here is that different cell-types make different proteins. And those different proteins are made typically as a result of transcriptional regulation, that is to say, the mRNA's that correspond to those proteins are transcribed in certain cells and not in others, or transcribed more frequently in some than others, and then those mRNA's

themselves are translated into proteins. So the outcome of this determination, this setup where the genome is being differentially expressed in different types of cells is then cell differentiation, where cells now take on a different phenotype itself. This is caused by the expression of those genes that encode tissue-specific proteins. So differentiation, just to go over it, begins with the appearance of mRNA, and is finally observed as changes in cellular structure. In most cases, the pattern of gene expression is controlled at the level of transcription. At the end of this differentiation process, an embryonic cell is typically irreversibly committed to its final fate. It now is only going to be a certain kind of thing, and it cant go back and be some other thing. This is not always true, you've probably already heard about embryonic stem cells, which aren't committed. We'll talk a bit more about it later, but for our purposes today, we're gonna think in terms of the stable committed differentiation of of cell lineages in a developing organism. So here is an example: lens cells, which make up the lens in your eye, and only lens cells, devote 80% of their protein synthesis to making just one type of protein, called crystallins. And crystallins form transparent fibers that allign so as to make a transparent lense that transmits and focuses light on the retinae in your eye. So those cells are stabily differentiated to do that job. Here is another example, and we'll look at it in just a little detail as we go along. The vertebrate skeletal muscle cells have high concentrations of proteins specific to muscle tissues (eg, a muscle-specific version of the contractile protein myosin, the structural protein actin (needs to be expressed at high levels), and membrane receptor proteins that detect signals from nerve cells that tell it to contract). The muscle cells themselves develop from embryonic precursors, and those precursors that have the potential to develop into a number of alternative cell types, including cartilage cells, fat cells, or multinucleate muscle cells. As the muscle cells differentiate, they become myoblasts and begin to synthesize muscle-specific proteins and fuse to form mature, elongated, multinucleate (with many nuclei inside them) skeletal muscle cells. Let's take a look at how that happens. So the determination stage is this commitment to a particular cell type during development, and we think of it at least for today's purposes, as irreversible. Here's our example: signals from other cells result in activation of a master regulatory gene (myoD=myoblast determination gene). It makes the cell synthesize a MyoD protein (a transcription factor). The cell (myoblast) is now determined (it is irreversibly committed to becoming a skeletal muscle cell). In our picture here, here is an embryonic precursor cell, and as a result of signals arriving at that cell, MyoD is changed from being in its offstate to its on state. It now expressed the MyoD mRNA, and then the MyoD protein is synthesized. The myoD protein is something called a transcription factor, that is, it binds to DNA and either stimulates or inhibits the transcription of other genes, and I show just a set of other genes here that are turned off in the precursor cell, and they are vaguely called the muscle-specific genes. When MyoD is turned on, those are turned on, and that sets the state for differentiation into a muscle cell. Now it need not always be the case that turning something on is what leads to differentiation, what it really has to happen is that the state has to turn from on to off or from off to on. There has to be a switch thrown, a molecular switch in order for differentiation to occur. Here is a classical experimental demonstration of irreversible determination from the early days of emrbyology. Today you will see a lot of frog emrbyos, and sea urchin embryos, and we'll talk about bird embryos and chicken embryos. And this is kind of historical fact, these are the things that were worked with early on in the history of developmental biology in the classical phase of developmental biology when there wasn't much molecular developmental biology. And so, we're gonna learn some of that classical stuff today. These days though the organisms that are worked on more are things like drosophila, sea elegans, things that are more tractable at the molecular level. And the feel of this kind of coming together where the old morphological models are becoming more molecular. And vice-versa. Alright, so let's look at this experiment from the classic, early days of emrbyology. So, this is an amphibian, a frog embryo, and what's done here-this is the frog embryo at the four cells stage, so we have 2 divisions-4 cells here-and here's a frog egg cell, and what we do with this frog egg cell is you

can either hit it with UV to break up the nucleus and destroy it, or use a micropippette and punctuate the membrane and suck out the nucleus, and remove it from the cell. The point is that what we're trying to do is set up a ennucleated experimental condition where there is no nucleus in there to direct the development, and then we're gonna ask, well, if we take a donor nucleus, suck it out with a pipette, and put it into this egg cell from an early embryo, what happens? If we instead, take a donor nucleus from a fully differentiated cell in the intestine of a tadpole and stick that into our ennucleated egg cell, what happens? And so going down from the bottom, here we can see the result. If we take a nucleus from an early emrbyonic cell and gave it to an ennucleated egg cell, then development typically proceeds alright. There is something about the nucleus there that makes it ok, it starts out with the right set of instructions, and goes on to develop appropriately. On the other hand, typically, You can see down here that less than 2% of the time, if we took our nucleus instead from an intestinal cell, and we put that into the ennuclated egg, it doesn't work very often and get development into a tadpole. Later we will talk about experiments like Dolly, where if actually worked with mammals, but this is an early line of evidence that was very convincing to embryologists that there is something that happens to the genes in the nucleus in a developing organism that changes them such that they no longer will direct appropriate development, even if they are put in the appropriate cytoplasmic environment. In the early days, in the early 19th century, late 18th century, when microscopes first started becoming available, and people began to look at sperm and eggs, the inventor of the miscroscope, LevanHook, was the first to see sperm. It was apparently his own sperm, but there were different ideas about how development would happen. One of the ideas were that there would just be something about the nature of that sperm or that egg that didn't even know that the sperm and egg had to come together in many cases, something about that, that would cause an unfolding of form. This idea that the sperm and the egg were not formed, the were in some sense some set of instructions for creating form. Another idea though, was maybe, every sperm had a little man in it, and that little man just got bigger and bigger and bigger during pregnancy. Now the problem with that, if you think about it, is that little man had to have sperms with little men in them, and on the way down, and that quickly becomes absurd and makes no sense. But the other thing we might think though in the modern sense, once we got past all that nonsense, we might have thought, ok, we know that there are a set of genes in every cell, we know there is a set of genes in every cell, but there are still 2 rather contrasting ways that development could occur under the influence of those genes. You could say, well, what happens to the genes in the cells is that they are kind of edited, ones that are not needed in differentiated cells are snipped out and removed, and so differentiated cells have a different set of genes, actually a different genome from undifferentiated cells. And we now know, that's not true either. There are exceptions, we'll talk about the immune system later, but typically, what goes on is that the full set of instructions is retained in almost all the cell and tissue types, its just that only certain instructions are being executed in certain types of cells. That gets us now to fertilization, cleavage, and gastrulation. I've written in the beginning here, this is how you all began. A sperm, many sperm, vying to get in, met an egg. Here this big thing is the egg, and typically eggs are a lot bigger than sperm, and we're gonna learn that there are various reasons for that. This cartoon epitomizes the problem of the sperm, there are many many many sperm, typically one egg, and all the sperm wanna get in, but only one can. What we wanna look at next here is how it is in sort of cell physiological terms, that only one sperm makes it into the egg and fertilizes the egg, fuzing its genome with the egg genome and so forth. There's a good reason for only one to get in; if more than one gets in, then it's a disaster. You have unbalanced genomes, things don't segregate properly at subsequent mitosis, chromosomes don't line up properly, and so forth. So we're gonna go through the classic setup here of the sea urchin egg, and the events that lead to fertilization of the sea urchin egg. Here is a sort of cutaway illustration of the sea-urchin egg, and let's go from the outside in. So around the eggs of sea urchins, and other echinoderms, we have what's called a jellycoat, and we're gonna have to see the sperms get through that jelly coat. And then inside that jellycoat, is something called the vitelline envelope, the sperm have to go through that as well, and

then finally we come to egg membrane right here, and the sperm membrane has to fuse with the egg membrane, and there's a kind of lock-and-key aspect once the sperm has gotten that far-the sperm has to have the right key, as you'll see-, and once that happens then some other things happen with these things called cortical granules and so forth, and they all sort of combine to produce this effect of blocking polyspermate, but allowing the right sperm in, and only one. So this is a figure from chapter 43 of your book, Let's go through the adventures of one sperm that make it through to fertilization. Here is our sperm. Sperm have mitochondria near their tails (sperm are little more than DNA delivery vehicles-the egg is where all the action is). The fact that there are some animals that can develop without fertilization should tell you that. Males are not necessarily needed. There are mitochondria here in the sperm. Between the actin and mitochondria of the sperm is the sperm nucleus. There is a resovoir of actin, and a something called acrosome up at the front of the sperm. This acrosome is very important because when the sperm hits the jelly layer, something called the acrosomal reaction takes place. The acrosome spills out digestive enzymes, which have the effect of melting their way through the jelly coat. Another part of the acrosomal reaction is that polymerizaton of actin (in the sperm head) is stimulated, and so this thing right here, the acrosomal process grows this red, jabby thing cone-projection on the diagram that grows out of the head of the sperm. On the tip of it are these molecules called BINDIN. Bindins are the key that the sperm needs. The lock is the bindin receptors on the vitelin envelope. These are highly species-specific as it turns out, and they tend to evolve rapidly even. So these bindin molecules then find the receptors on the vitellin envelope, not the eggmembrane, onto the vitellin envelope. When they find those receptors, another reaction occurs where you get fusion of the sperm, they drive right through the vitellin layer there, and fusion of the sperm membrane and the egg membrane occurs, where they become continuous with one another. And what happens is that the sperm nucleus gets dumped into the egg, the acrosomal process gets dumped into the egg (the jabby thing) and gets recycled, the mitochondria (which are not shown here) also get dumped into the egg, and they get degraded. So mitochondria are typically inherited down the female line; the sperm don't typically contribute mitochondria to the genetic line. Once in a great while they will. Also the sperm centriole goes in, and it goes on to become the centrosome of the fertilized egg and to set up the spindle apparatus for the first division. So let me go over this again, So we have the 2 blocks to polyspermae, we have here where we got the acrosomal reaction, which dissolved through the jelly layer, we hit this vitelline envelope, and once we hit the vitelline envelope, we get polymerization of actin. Binding is at the tip of the acrosoal process, and the bindin receptors are on the vitelline envelope. This is the lock-and key. Once that is made, then the acrosomal process, drives onto the egg's plasma membrane. Once contact with the plasma membrane is made, the first interesting thing that happens is an influx of sodium into the egg. What that does is to change the electrical potential of the membrane in a way that makes it very unlikely that another sperm is gonna be able to bind and get in. And that first step is called the fast-block. To polyspermae. The acrosomal process is the name of the thing projecting out of the actin, so its not a series, its a thing. That fast-block is a change in the plasma membrane polarity as a result of this influx of sodium. We've gotten as far as the fusion of the membrane. Once the membranes have fused, calcium is released from the endoplasmic reticulum of the egg cell, and that causes the dumping of the contents of cortical granules into this space here between the egg membrane and the outside of the vitellin envelope. Once those cortical granule contents get in there, they have enzymes that separate the vitelline envelope from the egg-membrane and cause them to come apart, and another set of enzymes that cause the material between them to absorb water. So this whole thing now swells, and the outside of it hardens, under the influence of other proteins, and it becomes a fertilization envelope, and that last step is called the slow block to polyspermae. So put together the fast-block and the slow-block, the sudden membrane-potential's shift, due to contact of the sperm membrane with the egg membrane, and then this swelling of the vitelline layer is moving away from the egg-membrane, the swelling with water and the hardening, the establishment of the fertilization envelope , that's the slow-block. So put that together almost all the time, they succeed in

keeping polyspermae from occuring. Once we've had fertilization, what's gonna happen is that the cells are going to divide. Let's look at some patterns of cleavage here. I dropped a hint that cleavage wasn't complete in birds when we were talking about diversity before, and so now we're gonna see 3 different patterns of cleavage early in development in this thing. So, this is the typical thing that we think about when we think about cleavage, because so much work has been done on it. This is the cleavage of an amphibian egg, and cleavage goes right the way through. So there we have 4 cells, and then we get some horizontal cleavage here, so cleavage goes right the way through the egg. Notice a little bit though that the planes of the second cleavage are displaced up toward the top end of the embryo, and the bottom cells are bigger. One side of the fertilized egg is the yolky side in the amphibian development; it has more yolk, and cleavage moves more slowly through that, and as a consequence, after a few rounds of cleavage, one end of the egg has larger cells than the other. The other end of the egg has smaller cells. The end of the egg with the smaller cells are traditionally called the animal pole, and the end of the egg with the larger cells is called the vegetal pole. Another way of thinking of it is that the larger end is the yolk end, where the larger cells are. Now here's cleavage in birds, eggs, and reptiles. These eggs have a lot of yolk, and remember that it would be hard to cleave right the way through all of that yolk, and in fact, it doesn't happne that way. So you get these interesting sort of partial cleavages that go on, you get cleavage furrows, and you get things that sort of look like thanks-giving rolls or whatever on top of the egg. Even tually they cleave all the way through-there are cleavages that go underneath them as well. And you get something called a blastodisc, that sides on top of the yolk, a little white-spot gray on top of the yolk. Just to make it even more complicated, in drosophila development, you get superficial cleavage, which is in other insects too, where the nuclei divide, and these are stained nuclei, and mitosis occurs without no cell division. And then the nuclei migrate out to the inner edge of the plasma membrane of the egg and then they get cellularized into cells, creating a blastoderm. A single cell with many nuclei is called the syncycium. Here is a look at cleavage in mammals, which is even more different. And we will talk about this very much when we get to reproduction later, but mammalian cleavage gets to be asynchronous, its a little misleading here how its shown (8-16-32). Cleavage is not synchronous in mammalian embryos, so you don't get these 8-16-32-64-128 etc kinda things going on. And also, really interesting things about the cleavage planes are there. But yes, its a mass of cells, with gap in the middle, a hollow mass of cells. The early rounds of cell division (cleavage) give rise to a mass of cells containing a hollow cavity. This mass of cells is called different things in different animals (amphibian/sea urchin=blastula, reptiles/birds=blastodisc with the partial cleavage and emergence of flat group of cells on top of the large yolk, mammals=blastocyst, less regular shaped (mass of cells with a cavityl the cavity is called the blastocoel)). In gastrulation, this early mass of cells undergoes changes (part of it goes inside of the rest of it; the ouside of that mass of cells is gonna go into that cavity in the middle) that ultimately lead to the devlopment of an embro with major body axes established and the 3 major tissue layers (also called germ layers) of the animal: ecto/endo/meso-derm. Here is a look at a frog blastula, with lots more detail on it. Notice the animal-pole, and the vegetal pole. These are typically in yellow (vegetal) to indicate bigger cells for the yolk origin that will become the source of the endoderm (forms the lining of the gut, liver, and lungs). Notice we have the blastocoel (cavity). Up at the top here these cells up the animal-pole are notated in blue and will give rise to the ectoderm (epidermal layer of skin and nervous system). There is this thing called the gray crescent, the site where major cell movement will begin. It persists into the blastocoel stage; is where the action begins with gastrulation. And then these red cells here (between inner vegental polle and blastocoel) denote mesoderm, which gives rise to muscle, bone, kidneys, blood, gonads, and connective tissue. How would one know that these cells had all these fates in the future? It is a process of something called fate-mapping, where needles were taken and little dies that wouldn't kill the cell were injected in groups of cells, and then under the microscope you watch the cells move, give rise to other cells, and

trace the dyes through the developing embryo. Here we are with gastrulation. The most important stages in life is not birth, but gastrulation. Here is what a sea-urchin blastula looks like-it fits our scheme here. It is a hollow ball of cells with larger cells on the bottom, animal hemisphere on the tope (vegetal hemisphere on the bottom), and what happens is like someone poked a finger into the bottom of it, like one of those wine-bottles where the bottom goes up. So these cells start to change shape and move inward. They form this thing called the archenteron (the primitive gut-the beginnings of this animal's gut). Notice we have some cells that break free and are denoted in red (everything else is blue), those are the primary mesenchyme that give rise to mesoderm in this organism. This archenteron pushes, and pushes though, Mesenchym cells at the tip of the archenteron extend processes called phylopodia, which contact the top of the blastocoel and provide a kind of traction effect to pull the archenteron even further up, and eventually we get something that looks like this. So now, we have the blastopore. Remember protostome, deuterostome? This is the blastopore, these things are deuterostomes, so this is going to be the anus, and the mouth is going to be formed up where the archenteron meets the ectoderm. Now lets look at gastrulation in an amphibian in the frog embryo. We looked at the frog blastula before. Basically certain kinds of cells called bottle cells form at the dorsal lip (the top) of the gray crescent. They form a blastopore, and the blastopore forms an opening over which cells pour in, around like that, and into the blastocoel, and as they go, they form the archenteron of the embryo. To the outside of the endoderm cells that are involuting, in the end here, all the endoderm is on the inside. Here it's on the outside. But to the outside of those inside the embryo, between the endoderm and the ectoderm, you get the origin of the mesoderm. Ultimately. You get the archenteron, a kind of blastopore, and a yolk-plug, that is, leftover endodermal cells on the ouside, that form almost a perfect circle. The idea here is that essentially by this process, the hollow ball of cells turns partly inside; some of the outside goes inside, and an inside pocket is made. Your gut, when you swallow it, it doesn't actually go inside of you. You are a doughnut, a tube. The gut was formed by taking the outside, and pushing it through, and forming your mouth up at the other end. Contribution of the germ layers (form as a result of gastrulation), forming to include the ectoderm (lining of the digestive tract=gut, respiratory tract, pancreas, liver), ectoderm (nervous system inc. eyes, ears; epidermal layer of organism=skin/scales/feather/hair/nails/claws/teeth/mouth tissues), and mesoderm (largely muscle:heart, blood vessels, muscles, bones).

2/13 Lecture: We have to talk more about the egg today. I will go over the sea urchin fertilization process again. We will go into early development using amphibians as a model and look at the origin of this thing that we went over that we call the gray crescent. Well go from the gray crescent to experiments on gastrulation and the fates of cells right down to the level of transcription factors and early development in amphibians. Well go into talking about the next major step in development of vertebrates, which is the formation of the neural tube or neurulation. Gastrulation gives rise to the 3 tissue layers. THe sperm are largely just vehicles for transmission of paternal DNA into the egg. The egg is where the action is, setting things up for organization of the developing embryo. What is it about the egg that would trigger early differentiation/determination to subsequent differentiation of cells in the developing embryo. In the egg you have mRNAs, proteins, and some other substances, and organelles, incorporated into the egg before fertilization occurs. The egg is in some sense provisioned and set up before fertilization with things that it will need and make use of early in development, and the distritbution of these things are uneven. Right away we should not think of the egg as some undifferentiated bag of cytoplasm; it is a structured thing. There are some

substances with higher concentration in some regions than others and etc. Right away that sets up for us the potential for an explanation as to why an organism will develop axis, why things develop dorsal and ventral and so forth. Some of the action lies with the egg. How did the egg get provisioned in that way? We are touching on the basic details of the molecular basis of development, and it will just get more complicated. Looking at this egg, we have a cartoon here, and it identifies an animal and vegetal pole (the vegetal pole tends to be bigger and divides more slowly than the animal pole). It is a picture of unequal distribution of cytoplasmic component such as mRNA. THis egg here is fertilized, and it will go ahead and divide, and when it divides, you can see the nucleus propogating up here. When it divides, you get an unequal distribution of that cytpolasmic component in descendenet cells. So right away in early cleavage you have cells different from others. THis sets up he phenomenon we will look at. Just to talk about it a bit more here we have a more elabrate cartoon, There are many cytoplasmic components affecting distribution, and many are unknown even now. Here you have molecules of another cytoplasmic determinant, 2 differnt one,s the thing gets fertilized, it starts to divide, and you get an uneven distribution of these two cytoplasmic components here. There is another process that goes on that we wont talk directly about it, something that induces formation of the emrbyo and induces gastrulation, which is the process of induction. Induction is another thing that goes on, just thingking broadly. We have a single fertilized egg of uneven distribution of cytoplasmic factors. It starts to divide, and now you have an uneven distribution among the cells that result from cleavage, setting up determination of those cells and ultimately differentation. As a consequence of differentiation, those cells then in the developing 3d embryo might secrete certain substances (proteins, etc), signaling molecules that can induce neighobring cells to differentiate. This process is called induction. This is one of two ways in which molecular inteactions can start to develop an embryo. Lets summarize the last lecture. We talked about processes of development in overview, and I want you to think about the problem of development. There is a single fertilized cell; how does it give rise to the enormous 3d and stable structure of a developed adult organism. It is also a process of development that evolved from single celled ancestors that gradually over time, as multicelularity was a benefit, natural selection put in place the pathways we look at now. Natural selection is very good at producing things that work well, but when you go down to the molecular level, you see that natural selection doesnt always set up pathways that are as simple as they might be. There are lots of switches and moleculars involved,and we don t understand them that well yet. We have cleavage and detemrination, then differentation, and then mophogenesis. The 3 events that we looked at previously were fertilization, cleavage, and gastrulation at the morphological level. Lets look more at fertilization in the sea urchin since last time it wasnt explained so well. So, there is nothing new here. We have here, the top surface of an egg, and here is a sperm that is gonna get lucky. When it makes contact, this triggers, exocytosis rom the head of the sperm (the acrosome), and hydrolytic enzymes come out. These then dissolve their way to the vitellin layer, and this actin based structure called the acrosomal process(its a structure, not a series of events) extends, so the reaction of the hydrolytic enzymes dissolving the jelly component, actin filaments grow, form the process, it protudes, penetrates the jellycoat, it binds because of the bindins on its surface finding their cognate receptors-it binds its receptors in the egg-cell membrane, and those receptors go through the vitelline layer, and it has now bound those receptors. The next step then, after being bound to those receptors, is fusion of the sperm and egg membrane. The fused membranes then become depolarized, and this rapid depolarization is called the fast block to polyspermy. The next step is the entry of the sperm nucleus, the sperm centriole and the inside contents go in, the mitochondria degrade, the centriole goes and becomes the centrosome of that egg, the nucleus eventually joins up with the egg nucleus. When the membranes trigger, there is another reaction that occurs. This triggurs release of calcium from the endoplasmic reticuluminto the cytosol of the egg, and the cortical granules near the vitelline layer fuse with the cell membrane, and discharge proteolytic enzymes, and these degrade proteins that bind the

vitelline layer to the egg membrane. Then this thing called the perivitelline space (the space around the egg) swells up by soaking up water in pert, and this hardens the vitelline layer, the receptors(spermbinding) are clipped off;this is referred to as the slow block to polyspermy. There are 2 blocks to keep sperm from getting in. And then this calcium release we talked about also activates a rise in metabolism in the egg, and protein syntehsis. In 20 min the sperm and egg nuclei fuse in the sea urchin egg. Herei s a picture of the slow block to polyspermy showing the waves of calcium ions (look at the slide for a diagram of the timing of the events for egg/sperm fusion). I showed a picture of a frog/amphibian blastula. It multiplied into many cells, had a blastocoel, and recall to mind that there were different parts of the blastula labelled for the different types of tissue it would give rise to (the endoderm, ectoderm, and mesoderm). The gray crescent region was denoted. We will go through how the gray crescent is established and what it means for subsequent development. Here we have an amphibian egg, and it is about to be fertilized. There is the sperm and sperm entry point. You already know that. The egg has a higher concetration of yolk in one pole (the vegetal pole) than the animal pole. The sperm is gonna come in at a certain point, the cortical scytoplam of the egg,