Ch.20 lecture presentation1

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Phylogenies and the History of Life

Chapter 20

Figure 20.1

• The life of a bee is very different from the life of a flower, but the two organisms are related. Both are members the domain Eukarya and have cells containing many similar organelles, genes, and proteins. (credit: modification of work by John Beetham)

Systematics• “Unity in diversity”

• Biologists group organisms based on shared characteristics and newer molecular sequence data

• Systematics– The field of biology that involves reconstruction

and study of evolutionary relationships• Phylogeny

– A hypothesis about patterns of relationship among species (“evolutionary tree”)

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• Darwin envisioned that all species were descended from a single common ancestor

(how does this relate to cell theory?)

• He depicted this history of life as a branching tree

Figure 20.12

• The (a) concept of the “tree of life” goes back to an 1837 sketch by Charles Darwin. Like an (b) oak tree, the “tree of life” has a single trunk and many branches. (credit b: modification of work by “Amada44”/Wikimedia Commons)

Figure 20.2

• Both of these phylogenetic trees shows the relationship of the three domains of life—Bacteria, Archaea, and Eukarya—but the (a) rooted tree attempts to identify when various species diverged from a common ancestor while the (b) unrooted tree does not. (credit a: modification of work by Eric Gaba)

7These cladograms all communicate the same

relationship hypothesis

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Variations of a Cladogram

Gibbon Human Chimp Gorilla Orangutan Gibbon Orangutan Gorilla Human Chimp

Chimp

Human

Gorilla

Orangutan

Gibbon

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1

2

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Version 1 Version 2

b.

Version 3

Figure 20.3

• The root of a phylogenetic tree indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where two lineages diverged. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister taxa. A branch with more than two lineages is a polytomy.

Figure 20.4

• This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different characters are placed in different groups based on the characteristics they share.

Figure 20.5

• The taxonomic classification system uses a hierarchical model to organize living organisms into increasingly specific categories. The common dog, Canis lupus familiaris, is a subspecies of Canis lupus, which also includes the wolf and dingo. (credit “dog”: modification of work by Janneke Vreugdenhil)

Figure 20.6

• At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same species because they can breed and produce viable offspring, but they are different enough to be classified as different subspecies. (credit “plant”: modification of work by “berduchwal”/Flickr; credit “insect”: modification of work by Jon Sullivan; credit “fish”: modification of work by Christian Mehlfuhrer; credit “rabbit”: modification of work by Aidan Wojtas; credit “cat”: modification of work by Jonathan Lidbeck; credit “fox”: modification of work by Kevin Bacher, NPS; credit “jackal”: modification of work by Thomas A. Hermann, NBII, USGS; credit “wolf”: modification of work by Robert Dewar; credit “dog”: modification of work by “digital_image_fan”/Flickr)

Figure 20.7

• Bat and bird wings are homologous structures, indicating that bats and birds share a common evolutionary past. (credit a: modification of work by Steve Hillebrand, USFWS; credit b: modification of work by U.S. DOI BLM)

Figure 20.8

• The (c) wing of a honeybee is similar in shape to a (b) bird wing and (a) bat wing, and it serves the same function. However, the honeybee wing is not composed of bones and has a distinctly different structure and embryonic origin. These wing types (insect versus bat and bird) illustrate an analogy—similar structures that do not share an evolutionary history. (credit a: modification of work by Steve Hillebrand, USFWS; credit b: modification of work by U.S. DOI BLM; credit c: modification of work by Jon Sullivan)

Similarity may not accurately predict evolutionary relationships

– Early systematists relied on the assumption that the greater the time since two species diverged from a common ancestor, the more different they would be.

– That concept works sometimes, but we also know that:

– Rates of evolution vary– Evolution is not unidirectional

(fish-> tetrapod ->whale)– Convergent evolution may mislead us

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Cladistics

• Derived trait (or character)– Similarity that is inherited from the most

recent common ancestor of an entire group, and defines that clade

• Ancestral trait (or character)– Similarity that arose prior to the common

ancestor of the group

• In cladistics, only shared derived characters are considered informative about evolutionary relationships

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• Traits (or characters) can be any aspect of the phenotype– Morphology – Physiology– Behavior – DNA

• Characters should exist in recognizable character states– Example: Character “teeth” in amniote

vertebrates has two states, present in most mammals and reptiles, and absent in birds and turtles

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17“1” = possession of derived character state“0” = possession of ancestral character state


Traits:Organism

Jaws Lungs AmnioticMembrane

Hair No Tail Bipedal

Lamprey

Shark

Salamander

Lizard

Tiger

Gorilla

Human

0 0 0 0 0 0

1

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0

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1 1 1

1 1 0

1 0 0

0 0 0

0

0 0 0

0 0

a.

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The derived characters between the cladogram branch points are shared by all organisms above the branch points and are not

present in any below them. The outgroup (in this case, the lamprey) does not possess any of the derived characters.


Lamprey Shark Salamander Lizard Tiger Gorilla Human

Jaws

Lungs

Amnioticmembrane

Hair

Tail loss

Bipedal

b.

Figure 20.10

• Lizards, rabbits, and humans all descend from a common ancestor that had an amniotic egg. Thus, lizards, rabbits, and humans all belong to the clade Amniota. Vertebrata is a larger clade that also includes fish and lamprey.

Figure 20.11

• All the organisms within a clade stem from a single point on the tree. A clade may contain multiple groups, as in the case of animals, fungi and plants, or a single group, as in the case of flagellates. Groups that diverge at a different branch point, or that do not include all groups in a single branch point, are not considered clades.

Manual cladistic analysis

• First step is to determine if the characters are ancestral or derived (a.k.a to “polarize” the character)

– Example: to polarize “teeth” means to determine presence or absence in the most recent common ancestor

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– Outgroup comparison is used• Species or group of species that is closely

related to, but not a member of, the group under study is designated as the “outgroup”

• When the group under study exhibits multiple character states, and one of those states is exhibited by the outgroup, then that state is ancestral and other states are derived

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Manual cladistic analysis (continued)

• Simple cladogram is a nested set of clades• Amniotes are a clade for which the evolution of an

amniotic membrane is a synapomorphy (derived trait)• Within that clade, mammals are a clade, with hair as

a synapomorphy (derived trait)23


Lamprey Shark Salamander Lizard Tiger Gorilla Human

Jaws

Lungs

Amnioticmembrane

Hair

Tail loss

Bipedal

b.

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Based on the principle of parsimony, the cladogram that requires the fewest number of evolutionary changes is favored; in this case the cladogram in (a) requires four changes, whereas that in (b) requires five


Salamander Frog Lizard Tiger Gorilla Human Salamander Lizard Tiger Frog Gorilla Human

Tail loss

Amnioticmembrane

Hair

Tail loss

Amnioticmembrane

Hair

Tail loss

Amnioticmembrane

loss

Hair loss

a. b.

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G

Site

Species A

Species B

Species C

Species D

Outgroup

DNA Sequence

1 2 3 4 5 6 7 8 9 10

A T A T C C G T A T

A C A G C C G C A T

A C A T C G G T G G

G C A T A G T G T

G C A T A G G C G T

• Systematists increasingly use DNA sequence data to construct phylogenies because of the large number of characters that can be obtained through sequencing

• Character states are polarized by reference to the sequence of an outgroup• Cladogram is constructed that minimizes the amount of character evolution

required

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Outgroup Species B Species D Species A Species C

Homologousevolutionarychanges

Homoplasticevolutionarychanges

2:T C

4:T8:T

GC

10:T G

8:T C

9:A6:C

GG

5:C A1:A G

• Statistical approach– Start with an assumption about the rate at which

characters evolve– Fit the data to these models to derive the

phylogeny that best accords (i.e., “maximally likely”) with these assumptions

• Molecular clock– Rate of evolution of a molecule is constant through

time– Divergence in DNA can be used to calculate the

times at which branching events have occurred

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Other Phylogenetic Methods

Comparative Biology• Most complex characters do not evolve in

one step, but rather through a sequence of evolutionary changes

• Initial stages of a character evolved as an adaptation to some environmental selective pressure, but later were selected for an entirely different function (this is the concept of “preadaptation”)

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• Preadaptation: the first featherlike structures evolved in the theropod phylogeny as modified scales– For insulation or perhaps decoration

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Other dinosaurs Coelophysis Tyrannosaurus Sinosauropteryx Velociraptor Caudipteryx Archaeopteryx Modern Birds

Light bones

Wishbone, breastbone,loss of fingers 4 and 5

Downy feathers

Long arms, highly mobile wrist, featherswith vanes, shafts, and barbs

Long, aerodynamicfeathers

Arms longer than legs

Loss of teeth andreduction of tail

Disease Evolution• AIDS first recognized in 1980s

• Current estimate: > 33 million people infected with human immunodeficiency virus (HIV); > 2 million die each year

• Simian immunodeficiency virus (SIV) found in 36 species of primates– Does not usually cause illness in monkeys

• Around for more than a million years as SIV in primates

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Phylogenetic analysis of HIV and SIV

1.HIV descended from SIV in other primates

2.Several different strains of HIV exist• Each human strain is more closely related to a strain

of SIV than to other HIV strains

3.Humans have acquired HIV from different host species

• Independent transfers from different primate species

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HIV

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SIV-

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HIV

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SIV-

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SIV-

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SIV-

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HIV

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Indicatestransmissionto humans

• HIV mutates so rapidly that a single HIV-infected individual often contains multiple genotypes in his or her body

• As a result, it is possible to create a phylogeny of HIV strains and to identify the source of infection of a particular individual

• In this case, the HIV strains of the victim (V) clearly are derived from strains in the body of another individual, the patient

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Vict

im

Patie

nt

Com

mun

ity

Horizontal Gene Transfer

• HGT: transfer of genes between unrelated species. – Common in Prokaryotes

• Bacteria and Archea

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Figure 20.13

• (a) Red aphids get their color from red carotenoid pigment. Genes necessary to make this pigment are present in certain fungi, and scientists speculate that aphids acquired these genes through HGT after consuming fungi for food. If genes for making carotenoids are inactivated by mutation, the aphids revert back to (b) their green color. Red coloration makes the aphids a lot more conspicuous to predators, but evidence suggests that red aphids are more resistant to insecticides than green ones. Thus, red aphids may be more fit to survive in some environments than green ones. (credit a: modification of work by Benny Mazur; credit b: modification of work by Mick Talbot)

Figure 20.14

• The theory that mitochondria and chloroplasts are endosymbiotic in origin is now widely accepted. More controversial is the proposal that (a) the eukaryotic nucleus resulted from the fusion of archaeal and bacterial genomes, and that (b) Gram-negative bacteria, which have two membranes, resulted from the fusion of Archaea and Gram-positive bacteria, each of which has a single membrane.

Figure 20.15

• Three alternate hypotheses of eukaryotic and prokaryotic evolution are (a) the nucleusfirst hypothesis, (b) the mitochondrion-first hypothesis, and (c) the eukaryote-first hypothesis.

Figure 20.16

• In the (a) phylogenetic model proposed by W. Ford Doolittle, the “tree of life” arose from a community of ancestral cells, has multiple trunks, and has connections between branches where horizontal gene transfer has occurred. Visually, this concept is better represented by (b) the multi-trunked Ficus than by the single trunk of the oak similar to the tree drawn by Darwin Figure 20.12. (credit b: modification of work by “psyberartist”/Flickr)

Ch.20 lecture presentation1

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