1 Systematics, Phylogenies, and Comparative Biology Chapter 23.

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Systematics,Phylogenies,

and Comparative Biology Chapter 23

Sec. 23.1 - SystematicsIntroduction:All organisms share many characteristics Ex:

Composed of one or more cellsCarry out metabolismTransfer energy with ATPEncode hereditary information in DNA

There is a tremendous diversity of lifeEx:

Bacteria, whales, sequoia treesBiologists group organisms based on shared characteristics and newer molecular sequence data

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Since fossil records are not complete, scientists rely on other types of evidence to establish the best hypothesis of evolutionary relationships

SystematicsReconstruction and study of evolutionary

relationships through phylogenyPhylogeny

Hypothesis about patterns of relationship among species using cladograms

CladogramA branching, treelike diagram in which the

endpoints of the branches represent specific species of organisms. It is used to illustrate phylogenetic relationships and show points at which various species have diverged from common ancestral forms.

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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

1

3

1

2

2

3

3

2

1

Version 1 Version 2

Version 3

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

He depicted this history of life as a branching tree

“Descent with modification”

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a.Reproduced by kind permission of the Syndics of Cambridge University Library, Darwin’s Notebook ‘B’,

‘Tree of Life’ Sketch, p. 36 from DAR.121 D312

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• Key to interpreting a phylogeny – look at how recently species share a common ancestor


Variations of a Cladogram

Gibbon Human Chimp Gorilla Orangutan Gibbon Orangutan Gorilla Human Chimp

Chimp

Human

Gorilla

Orangutan

Gibbon

1

3

1

2

2

3

3

2

1

Version 1 Version 2

b.

Version 3

Similarity may not accurately predict evolutionary relationshipsEarly systematists relied on the

expectation that the greater the time two species diverged from a common ancestor, the more different they would be Problems:

1. Rates of evolution varyEvolution may not be unidirectional

2. Evolution is not always divergentConvergent evolution

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CladisticsTechnique used for creating hierarchies of

organisms that represent true phylogenetic relationship and descent

Derived characteristicSimilarity that is inherited from the most

recent common ancestor of an entire groupAncestral

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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When using cladistics the character variation needs to be identified as ancestral or derived

When creating cladistics, data needs to be collected on various Characters for ex:Morphology – PhysiologyBehavior – DNA

Characters should exist in recognizable character statesEx: Character: “teeth” in amniote vertebrates

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

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

Cladistics (cont.)

To create a cladistics you need:1.Number of taxa (species or higher level groups)2.Determine the states for each character

Ex: Ancestral Vs. Derived Characters

Presence of hair is a shared derived feature of mammals

Presence of lungs in mammals is an ancestral feature; also present in amphibians and reptiles

Shared, derived feature of hair suggests that all mammal species share a common ancestor that existed more recently than the common ancestor of mammals, amphibians, and reptiles

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Examples of Ancestral Vs. Derived Characteristics

Determination of ancestral Vs. Derived1. Polarize the characters –

determine if states are ancestral or derived

2. Determine which state was exhibited by the most recent ancestor of the group

a) Outgroup comparison is used to assign character polarity.

b) If Outgroup, closely related but not a member, shares multiple character states, then state is considered to be ancestral, but outgroups also evolve from their ancestors, so outgroup will not always exhibit the ancestral condition.

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Polarity assignments are most reliable when using several different outgroups.

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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.

Cladogram Clade - a group of

species that share a common ancestor as indicated by the possession of shared derived characters Evolutionary units

and refer to a common ancestor and all descendants

Synapomorphy – derived character shared by clade members

Plesiomorphies – ancestral states

Symplesiomorphies – shared ancestral states

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Simple cladogram is a nested set of clades, each characterized by its own synapomorphies

Amniotes are a clade for which the evolution of an amniotic membrane is a synapomorphy

Within that clade, mammals are a clade, with hair as a synapomorphy

Character state: “presence of a tail”Exhibited by

lampreys, sharks, salamanders, lizards, and tigers

Are tigers more closely related to lizards and sharks than apes and humans?

Symplesiomorphies reflect character states inherited from a distant ancestor, they do not imply that species exhibiting that state are closely related

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Bipedal

Tail loss

Hair

Amnioticmembrane

Lungs

Jaws

No.

Homoplasy – a shared character state that has not been inherited from a common ancestor. It can result from:Convergent evolution – independent

development of similar structures in organisms that are not related

Evolutionary reversal Systematists rely on the principle of

parsimony, which favors the hypothesis that requires the fewest assumptions

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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


Traits:Organism

Jaws Lungs AmnioticMembrane

Hair No Tail Bipedal Lamprey Shark Salamander Lizard Tiger Gorilla Human

Lamprey

Shark

Salamander

Lizard

Tiger

Gorilla

Human

0 0 0 0 0 0

1

1

1

1

1

1

0

1

1

1

1

1

0

0

1

1

1

1

1 1 1

1 1 0

1 0 0

0 0 0

0

0 0 0

0 0

Jaws

Lungs

Amnioticmembrane

Hair

Tail loss

Bipedal

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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Other Phylogenetic MethodsSome characters evolve rapidly and

principle of parsimony may be misleadingFor example: parts of DNA that appear to have

no function. Can result in mutations and are not eliminated by

natural selection will thus have high rates of evolution of new character states as result of genetic drift

Because only 4 character states are possible (A, T, G,C), there is a high probability that two species will independently evolve the same derived character state at any particular base position

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1. Statistical approachRapid evolutionStart with an assumption about the rate at which

characters evolve and then Fit the data to these models to derive the phylogeny that best accords (i.e., “maximally likely”) with these assumptions

Advantage is that different assumptions of rate can be used for different models of evolution for different characters.

2. Molecular clockStates that the rate of evolution of a

molecule is constant through timeIn this model, Divergence in DNA can be

used to calculate the times at which branching events have occurred

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Systematics and ClassificationClassification

species and higher groups are placed into the taxonomic hierarchy

Genus, family, class, etc.

Monophyletic groupIncludes the most recent common ancestor of

the group and all of its descendants (clade)

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Monophyletic Group

Archosaurs

Systematics and ClassificationParaphyletic group

Includes the most recent common ancestor of the group, but not all its descendants

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Paraphyletic Group

Dinosaurs

Polyphyletic groupDoes not include the most recent common

ancestor of all members of the group

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Polyphyletic Group

Flying Vertebrates

Bats and birds could be classified in the same group, but their similarities reflect convergent evolution, not common ancestry.

Taxonomic hierarchies are based on shared traits, and should reflect evolutionary relationships, but do not fit the new understanding of phylogenetic relationships

Good example are BirdsTraditionally they were in the class Aves,

and dinosaurs in the class Reptilia but recent phylogenetic advances make clear that birds evolved from dinosaurs.

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Traditionally three major groups were recognized: green algae, bryophytes, and vascular plants

Recent research reveals that the green algae and bryophytes are not monophyletic:

Rather Bryophytes and are more closely related to vascular plants

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Red Algae Green Algae

Chlorophytes Charophytes Liverworts

Bryophytes

Hornworts Mosses

Vascular Plants

Biological species concept (BSC) Defines species as groups of

interbreeding populations that are reproductively isolated

Phylogenetic species concept (PSC)Species is a population or set of

populations characterized by one or more shared derived characters

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Species concepts

PSC solves 2 BSC problemsBSC cannot be applied to allopatric

populations – would they interbreed?PSC looks to the past to see if they have

been separated long enough to develop their own derived characters

BSC can be applied only to sexual speciesPSC can be applied to both sexual

and asexual species

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PSC still controversial Critics contend it will lead to the

recognition of even slightly different populations as distinct species

Paraphyly problem

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A B C D E

PhylogeneticsBasis for all comparative biologyHomologous structures

Derived from the same ancestral sourceDolphin flipper and horse leg

Homoplastic structures are notWings of birds and dragonflies

Phylogenetic analysis can help determine which a structure is

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Parental care in dinosaurs initially treated as unexpected

Examination of phylogenetic comparison of dinosaurs indicates they are most closely related to crocodiles and birds – both show parental care

Parental care in 3 groups not convergent but homologous behaviors

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a.a: Image #5789, photo by D. Finnin/American Museum of Natural History


b.b: © Roger De La Harpe/Animals Animals

Homoplastic convergence: saber teeth Evolved independently in different

clades of extinct carnivoresSimilar body proportions (cat)Similar predatory lifestyleMost likely evolved independently at

least 3 times

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Monotremes

MarsupialsPlacentals

Phylogeny of Mammals

Car

niv

ore

s

Sab

er-t

oo

thed

m

arsu

pia

l

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Nimravids are a now-extinct group of catlike carnivores


Carnivores

Felines

Nimravids

Sab

er-t

oo

thed

cat

Hye

nas

Civ

ets

Mo

ng

oo

ses

Sab

er-t

oo

thed

n

imra

vid

Phylogeny of CarnivoresB

ears

, se

als

,w

ease

ls,

can

ids

,an

d r

acco

on

s

Sab

er-t

oo

thed

nim

rav

id

Homoplastic convergence: plant conducting tubesSieve tubes facilitate long-distance

transport of food and other substances in tracheophytesEssential to the survival of tall plants on

landBrown algae also have sieve elementsClosest ancestor a single-celled

organism that could not have had a multicellular transport system

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µm 2 µm

Stramenopiles Alveolates Red Algae Chlorophytes Chlorophytes Liverworts Hornworts Mosses Tracheophytes

Brown Alga

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Angiosperms

(left): © Lee W. Wilcox; (right): © Dr. Richard Kessel & Dr. Gene Shih/Visuals Unlimited

Comparative BiologyMost complex characters do not evolve in one

stepEvolve through a sequence of evolutionary

changesModern-day birds exquisite flying machines

Wings, feathers, light bones, breastboneInitial stages of a character evolved as an

adaptation to some environmental selective pressure

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First featherlike structure evolved in theropod phylogenyInsulation 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

Phylogenetic methods can be used to distinguish between competing hypotheses

Larval dispersal in marine snailsSome snails produce microscopic larvae

that drift in the ocean currentsSome species have larvae that settle to

the ocean bottom and do not disperse

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• Fossils show increase in nondispersing snails

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Eocene

Percentage of species withnondispersing larvae

40 MYA

45 MYA

50 MYA

55 MYA

60 MYA

65 MYA

0 10050

Two processes could produce an increase in nondispersing larvaeEvolutionary change from dispersing to

nondispersing occurs more often than change in the opposite direction

Species that are nondispersing speciate more frequently, or become extinct less frequently than dispersing species

The two processes would result in different phylogenetic patterns

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In this hypothetical example, the evolutionary transition from dispersing to nondispersing larvae occurs more frequently (four times) than the converse (once)

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a.

Dispersing larvae

Nondispersing larvae

By contrast, clades that have nondispersing larvae diversify to a greater extent due to higher rates of speciation or lower rates of extinction (assuming that extinct forms are not shown)

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b.

Dispersing larvae


Phylogeny for Conus, a genus of marine snails. Nondispersing larvae have evolved eight separate times from dispersing larvae, with no instances of evolution in the reverse direction. This phylogeny does not show all species, however; nondispersing clades contain on average 3.5 times as many species as dispersing clades.

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c.

Dispersing larvaeNondispersing larvae

Dispersing larvae


Analysis indicates:Evolutionary increase in nondispersing

larvae through time may be a result of both a bias in the evolutionary direction and an increase in rate of diversification

Lack of evolutionary reversal not surprising – evolution of non-dispersing larvae a one-way street

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Loss of larval stage in marine invertebratesEggs develop directly into adultsNonreversible evolutionary changeMarine limpets: show direct development

has evolved many times3 cases where evolution reversed and larval

stage re-evolved

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a.

Larval stage

Direct development

Less parsimonious interpretation of evolution in the clade in the light blue box is that, rather than two evolutionary reversals, six instances of the evolution of development occurred without any evolutionary reversal

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b.

Larval stage

Direct development


Phylogenetics helps explain species diversification

Use phylogenetic analysis to suggest and test hypotheses

Insight into beetle diversificationCorrespondence between phylogenetic

position and timing of plant origins suggests beetles are remarkably conservative in their diet

Beetle families that specialize on conifers have the deepest branches

Beetles specialize on Angiosperms have shorter branches

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Tertiary

Cretaceous

Jurassic

Triassic AngiospermCycadConifer

Number of Species

85 2000

24 1500

41,6

02

10 20 750

78 25,0

00

3 400

8 18 33,4

00

Phylogenetic explanations for beetle diversificationNot the evolution of herbivorySpecialization on angiosperms a

prerequisite for diversificationRisen 5 times independently within

herbivorous beetlesAngiosperm specializing clade is more

species-rich than the clade most closely related

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Disease EvolutionAIDS first recognized in 1980sCurrent estimate: > 33 million people

infected with human immunodeficiency virus (HIV); > 2 million die each year

Simian immunodeficiency virus (SIV) found in 36 species of primatesDoes not usually cause illness in

monkeysAround for more than a million years as SIV

in primates

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Phylogenetic analysis of HIV and SIV1. HIV descended from SIV

All strains of HIV are nested within clades of SIV

2. Number of different strains of HIV exitIndependent transfers from different

primate speciesEach human strain is more closely related

to a strain of SIV than to other HIV strainsSeparate origins for HIV strains

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3. Humans have acquired HIV from different host species

HIV-1, which is the virus responsible for the global epidemic, has three subtypesEach of these subtypes is most closely related

to a different strain of chimpanzee SIV, indicating that the transfer occurred from chimps to humans

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Subtypes of HIV-2, which is much less widespread, are related to SIV found in West African monkeys, primarily the sooty mangabey (Cercocebus atys) Moreover, the subtypes of HIV-2 also

appear to represent several independent cross-species transmissions to humans

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HIV

- 1

gro

up

M

HIV

- 1

gro

up

N

SIV

- c

him

pa

nze

e

HIV

- 1

gro

up

O

SIV

- d

rill

SIV

- ta

nta

lus

SIV

- s

oo

ty m

an

ga

be

y

HIV

- 2

gro

up

A

SIV

- c

him

pa

nze

e

SIV

- c

him

pa

nze

e

SIV

- c

him

pa

nze

e

SIV

- c

him

pa

nze

e

HIV

- 1

gro

up

P

SIV

- c

him

pa

nze

e

SIV

- re

d-c

ap

pe

d m

an

ga

be

y

SIV

- g

ori

lla

SIV

- v

erv

et

mo

nk

ey

HIV

- 2

gro

up

B

SIV

- s

yk

e’s

mo

nk

ey

SIV

- D

e B

razz

as

mo

nk

ey

SV

- s

oo

ty m

an

ga

be

y

SV

- g

rea

ter

sp

ot-

na

sa

l m

on

ke

y

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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Vic

tim

Pat

ien

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Co

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1 Systematics, Phylogenies, and Comparative Biology Chapter 23.

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