Joseph Nguyen

Homework #6 : Chapter 25,26 (141010)

Concept Map: 10 Points
Objectives

Phylogenies are based on Common Ancestries
1. Distinguish between phylogeny and systematics.
-evolutionary history
-biological diversity
Phylogenies are the evolutionary history of a species or group of related species.
Systematics is the study of biological diversity in an environmental context.
2. Describe the process of sedimentation and the formation of fossils. Explain which
portions of organisms are most likely to fossilize.
-insulate remains
-exoskeleton
-sediments bury exoskeleton
When the plant or animal dies and falls into the water, the water insulates the
remains. Mostly the exoskeleton becomes fossilized because bacteria in the water
would consume the softer body parts. During sedimentation, sediments bury the
exoskeleton over time and fossilizes the animal or plant remains.
3. Explain why it is crucial to distinguish between homology and analogy before
selecting characters to use in the reconstruction of phylogeny.
-similarity in characteristics
-shared ancestry
-similarities
-convergent evolution
Homology is the similarity in characteristics from a shared ancestry. Analogies are
the similarities between two species that is tied to convergent evolution.
4. Explain why bird and bat wings are homologous as vertebrate forelimbs but
analogous as wings.
-same origin
-not same structurally
-same function
Homologous means that it evolved from the same origin; however the forelimbs of
bats and birds are not the same structurally.
5. Define molecular systematics. Explain some of the problems that systematics may
face in carrying out molecular comparisons of nucleic acids.
-evolutionary relationships
-sequences
-bases
-lengths
Molecular systematics uses molecular data to determine evolutionary
relationships. Some problems arise when some distinctly related species have many
different bases and lengths.
Phylogenetic Systematics: Connecting Classification
with Evolutionary History
6. Explain the following characteristics of the Linnaean system of classification:
a. binomial nomenclature
-genus
In binomial nomenclature, the genus is always capitalized and the specific epithet
are never capitilizaed as well.
b. hierarchical classification
-comprehensive groups
Species are placed into more comprehensive groups.
7. List the major taxonomic categories from most to least inclusive.
-closely related
-family
-orders
-classes
-phyla
-kingdoms
-domains
Species are grouped to the same genus based on how closely related they appear to
be. It goes from families to orders to classes to phyla to kingdoms and to into
domains.
8. Define a clade. Distinguish between a monophyletic clade and paraphyletic and
polyphyletic groupings of species.
-ancestral species
-decedents
-common ancestors
-different species
A clade is a grouping of species that include the ancestral species and its
descendants. A monophyletic clade includes all common ancestors and its
decedents. A paraphyletic grouping includes groups deriving from two or more
species.
9. Distinguish between shared primitive characters and shared derived characters.
-shared by clade
-evolutional
-particular clade
Primitive characters are a character shared by members of a particular clade. A
shared derived character is an evolutional novelty that is unique to a particular
clade.
10.Explain how shared derived characters can be used to construct a phylogenetic
diagram.
-arose in history
All of the features of an organism arose at some point in life, so it is possible to
determine which clade in which each derived character appeared.
11.Explain how outgroup comparison can be used to distinguish between shared
primitive characters and shared derived characters.
-related to monophyletic group
An outgroup comparison shows that a species or group is related to a
monophyletic group.
12.Define an ingroup.
-evolutionary relationship
An ingroup is a species or group of species whose evolutionary relationship is
what we want to determine.
13.Distinguish between a phylogram and an ultrameric tree.
-character changes
-root-to-tip
-lineages
A phylogram tree branches the character changes,while a ultrametric tree has
root-to-tip path lengths for all lineages.
14.Discuss how systematists use the principles of maximum parsimony and maximum
likelihood in reconstructing phylogenies.
-simplest explanation
-consistent facts
-DNA change over time
According to the principles of maximum parsimony, we should investigate the
simplest explanations that are consistent with the facts. The principle of maximum
likelihood states certain rules about how DNA changes over time.
15.Explain why any phylogenetic diagram represents a hypothesis about evolutionary
relationships among organisms.
-no way to measure
Any phylogenetic diagram is viewed as a diagram because there are no ways to
measure of the hypothesis is accurate or not.
16.Distinguish between orthologous and paralogous genes. Explain how gene
duplication has led to families of paralogous genes.
-homologous genes
-gene duplication
Orthologous genes are homologous genes that are found in different species
because of speciation. Paralogous genes result from gene duplication. There are
more than one copy found in the same genome.
17.Explain how molecular clocks are used to determine the approximate time of key
evolutionary events. Explain how molecular clocks are calibrated in actual time.
-absolute time of evolutionary change
-graphing genetic differences
A molecular clock measures the absolute time of evolutionary change, based on
observations. Molecular sticks or a gene can be calibrated by graphing the
numbers of genetic differences.
18.Describe some of the limitations of molecular clocks.
-DNA changes
-past fossil evidence
Some of the limitations include DNA changes and the when the molecular clock
extends over the fossil evidence.
19.Explain the neutral theory of evolutionary change.
-fitness
-natural selection
The neutral theory of evolutionary change is that evolutionary change in genes and
proteins has no effect on fitness and therefore is not effected by natural selection.
20.Explain how scientists determined the approximate time when HIV-1 M first
infected humans.
-comparing sequences
Scientists determined the approximated time when HIV-1 M first infected humans
by comparing sequences of HIV viruses from samples taken during various times
during the epidemic.
21.Describe the evidence that suggests there is a universal tree of life.
-ribosomal RNA
-Three major categories
The tree of life is based on ribosomal RNA sequences. All life on earth can be
placed in one of the three major categories, which leads scientists to believe that
all life started from a common ancestor.

Concept Map Words:

analogy
binomial
clade
cladistics
cladogram
class
domain
family
fossil record
genus
homoplasy
ingroup
kingdom
maximum likelihood
maximum parsimony
molecular clock
molecular systematics
monophyletic
neutral theory
order
orthologous genes
outgroup
paralogous genes
paraphyletic
phylogenetic tree
phylogeny
phylogram
phylum
polyphyletic
shared derived character
shared primitive
character
specific epithet
systematics
taxon
taxonomy
ultrametric tree

Memorize the Word Roots
analog- 5 proportion (analogy: similarity due to convergence)
bi- 5 two; -nom 5 name (binomial: a two-part latinized name of a species)
clado- 5 branch (cladogram: a dichotomous phylogenetic tree that branches repeatedly)
homo- 5 like, resembling (homology: similarity in characteristics resulting from a shared
ancestry)
mono- 5 one (monophyletic: pertaining to a taxon derived from a single ancestral species
that gave rise to no species in any other taxa)
parsi- 5 few (principle of parsimony: the premise that a theory about nature should be the
simplest explanation that is consistent with the facts)
phylo- 5 tribe; -geny 5 origin (phylogeny: the evolutionary history of a taxon

Chapter 26
Concept Map: 10 Points

The Tree of Life: An I ntroduction to Biological Diversity

Objectives
22. The Origin of Life
1. Describe the four stages of the hypothesis for the origin of life on Earth by chemical
evolution.
-nonliving synthesis
-protobionts
-origins
-macromolecules
The four stages include the abiotic synthesis of organic molecules, the joining of
those organic molecules into macromolecules, packaging them into protobionts, and
the origin of self-replicating molecules that make inheritance possible.
2. Describe the contributions that A. I. Oparin, J.B.S. Haldane, and Stanley Miller made
toward developing a model for the abiotic synthesis of organic molecules. Describe
the conditions and locations where most of these chemical reactions probably
occurred on Earth.
-organic molecules
-conditions
Oparin and Haldane discovered conditions on early earth led to the formation of
small organic materials. Miller simulated conditions on early earth.
3. Describe the evidence that suggests that RNA was the first genetic material. Explain
the significance of the discovery of ribozymes.
-information transfer
-copied abiotically
-variety of catalytic functions
-pre-date enzymes
RNA is central to information transfer and can be copied abiotically. Ribozymes
have a variety of catalytic functions, they are pre-date enzymes.
4. Describe how natural selection may have worked in an early RNA world.
-stability & replicability
-complementary catalytic functions
-covalent linkage
-amino acids
RNAs with stability and replicability are favored, complementary catalytic functions
allow for groups of RNA, and covalent linkages with catalytic function.
5. Describe how natural selection may have favored the proliferation of stable
protobionts with self-replicating, catalytic RNA.
-self-replicating
-catalytic
-inherited characteristics
A protobiont with self-replicating, catalytic RNA would be different. If a protobiont
could grow and pass on its RNA to its daughters its limited inherited characteristics
could be affected by natural selection.
23. Introduction to the History of Life
6. Explain how the histories of Earth and life are inseparable.
-geological events
-chemical changes
The history of Earth and life are inseparable because geological events affect
biological evolution. Likewise organisms cause major chemical changes on Earth.
7. Explain how index fossils can be used to determine the relative age of
fossil-bearing rock strata. Explain how radiometric dating can be used to determine
the absolute age of rock strata. Explain how magnetism can be used to date rock
strata.
8. Describe the major events in Earths history from its origin until 2 billion years ago.
In particular, note when Earth first formed, when life first evolved, and what forms
of life existed in each eon.
-4.6 bya
-3.5 bya prokaryote
-2.1 bya eukaryots
The Earth was formed about 4.6 billion years ago, 3.5 billion years ago prokaryotes
appeared, and 2.1 billion years ago, eukaryotes evolved.
9. Describe the mass extinctions of the Permian and Cretaceous periods. Discuss a
hypothesis that accounts for each of these mass extinctions.
-marine animals
-major volcanoes
-cretaceous-comet
The extinction of the Permian period killed nearly all marine animals and that was
due to major volcanoes. The cretaceous period reached it end because of a comet.
24. The Major Lineages of Life
10. Describe how chemiosmotic ATP production may have arisen.
11. Describe the timing and significance of the evolution of oxygenic photosynthesis.
12. Explain the endosymbiotic theory for the evolution of the eukaryotic cell. Describe
the evidence that supports this theory.
-endosymbiont
-inner membranes
-organelles replicate
-single circular DNA
Some of the evidence that supports the endosymbiosis theory includes when a cell
lives in a another cell, when organelles share traits with prokaryotes, when inner
membranes have homologous enzymes.
13. Explain how genetic annealing may have led to modern eukaryotic genomes.
14. Describe the timing of key events in the evolution of the first eukaryotes and later
multicellular eukaryotes.
-4.6 bya
-3.5 bya prokaryote
-2.1 eukaryotes
The Earth was formed about 4.6 billion years ago, 3.5 billion years ago prokaryotes
appeared, and 2.1 billion years ago, eukaryotes evolved.
15. Explain how the snowball-Earth hypothesis explains why multicellular eukaryotes
were so limited in size, diversity, and distribution until the late Proterozoic.
-earth was frozen over
The snowball-Earth hypothesis refers to the idea that some point in Earths history,
the entire earth, including oceans were frozen over.
16. Describe the key evolutionary adaptations that arose as life colonized land.
-reproduce on land
-avoid dehydration
Some key evolutionary adaptations that took place were the ability to reproduce on
land and to avoid dehydration.
17. Explain how continental drift explains Australias unique flora and fauna.
18. Explain why R. H. Whittakers five-kingdom system has been replaced by a new
system with three domains.
-Nutritional characteristics
-evolutionary similarities
Whitakers system has been replaced because it grouped by nutritional
characteristics and the three domains system groups by evolutionary similarties.



Concept Map Words:

colony
genetic annealing
geologic record
half-life
magnetic reversal
Pangaea
protobiont
radiometric dating
ribozyme
serial endosymbiosis
snowball Earth
hypothesis
stromatolite
three-domain system

Memorize the Word Roots
proto- 5 first (protobionts: aggregates of abiotically produced molecules)
stromato- 5 something spread out; -lite 5 a stone (stromatolite: rocks made of banded domes of
sediment in which are found the most ancient forms of life