25- Phylogeny Text

8/14/2019 25- Phylogeny Text

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Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

PowerPoint Lectures for

Biology, Seventh Edition

Neil Campbell and Jane Reece

Lectures by Chris Romero

Chapter 25

Phylogeny and Systematics


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Overview: Investigating the Tree of Life

This chapter describes how biologists trace

phylogeny

The evolutionary history of a species or group

of related species


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Biologists draw on the fossil record

Which provides information about ancientorganisms

Figure 25.1


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Biologists also use systematics

As an analytical approach to understanding thediversity and relationships of organisms, both

present-day and extinct


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Currently, systematists use

Morphological, biochemical, and molecularcomparisons to infer evolutionary relationships

Figure 25.2


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Concept 25.1: Phylogenies are based on

common ancestries inferred from fossil,morphological, and molecular evidence


7/54Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Fossil Record

Sedimentary rocks

Are the richest source of fossils

Are deposited into layers called strata

Figure 25.3

1 Rivers carry sediment to the

ocean. Sedimentary rock layerscontaining fossils form on the

ocean floor.

2 Over time, new strata are

deposited, containing fossils

from each time period.

3 As sea levels change and the seafloor

is pushed upward, sedimentary rocks are

exposed. Erosion reveals strata and fossils.

Younger stratum

with more recent

fossils

Older stratum

with older fossils



The fossil record

Is based on the sequence in which fossils haveaccumulated in such strata

Fossils reveal

Ancestral characteristics that may have been

lost over time



Though sedimentary fossils are the most

common Paleontologists study a wide variety of fossils

Figure 25.4ag

(a) Dinosaur bones being excavated

from sandstone

(g) Tusks of a 23,000-year-old mammoth,

frozen whole in Siberian ice

(e) Boy standing in a 150-million-year-old

dinosaur track in Colorado

(d) Casts of ammonites,

about 375 millionyears old

(f) Insects

preserved

whole in

amber

(b) Petrified tree in Arizona, about

190 million years old

(c) Leaf fossil, about 40 million years old



Morphological and Molecular Homologies

In addition to fossil organisms

Phylogenetic history can be inferred fromcertain morphological and molecular

similarities among living organisms

In general, organisms that share very similarmorphologies or similar DNA sequences

Are likely to be more closely related than

organisms with vastly different structures orsequences



Sorting Homology from Analogy

A potential misconception in constructing a

phylogeny Is similarity due to convergent evolution, called

analogy, rather than shared ancestry



Convergent evolution occurs when similar

environmental pressures and natural selection Produce similar (analogous) adaptations in

organisms from different evolutionary lineages

Figure 25.5



Analogous structures or molecular sequences

that evolved independently Are also called homoplasies



Evaluating Molecular Homologies

Systematists use computer programs and

mathematical tools

When analyzing comparable DNA segments from

different organisms

Figure 25.6

C C A T C A G A G T C C




G T A

Deletion

Insertion

C C A T C A A G T C C

C C A T G T A C A G A G T C C

C C A T C A A G T C C

C C A T G T A C A G A G T C C

1 Ancestral homologous

DNA segments are

identical as species 1

and species 2 begin to

diverge from theircommon ancestor.

2 Deletion and insertion

mutations shift whathad been matching

sequences in the two

species.

3 Homologous regions

(yellow) do not all align

because of these mutations.

4 Homologous regions

realign after a computer

program adds gaps in

sequence 1.

1

2

1

2

1

2

1

2

A C G G A T A G T C C A C T A G G C A C T A

T C A C C G A C A G G T C T T T G A C T A G

Figure 25.7


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Concept 25.2: Phylogenetic systematics

connects classification with evolutionary history Taxonomy

Is the ordered division of organisms into

categories based on a set of characteristics

used to assess similarities and differences


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Binomial Nomenclature

Binomial nomenclature

Is the two-part format of the scientific name ofan organism

Was developed by Carolus Linnaeus


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The binomial name of an organism or scientific

epithet Is latinized

Is the genus and species


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Hierarchical Classification

Linnaeus also introduced a system

For grouping species in increasingly broadcategories

Figure 25.8

Panthera

pardus

Panthera

Felidae

Carnivora

Mammalia

Chordata

Animalia

EukaryaDomain

Kingdom

Phylum

Class

Order

Family

Genus

Species


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Linking Classification and Phylogeny

Systematists depict evolutionary relationships

In branching phylogenetic trees

Figure 25.9

Pantherapardus(leopard)

Mephitismephitis

(striped skunk)

Lutra lutra(European

otter)

Canisfamiliaris

(domestic dog)

Canislupus(wolf)

Panthera Mephitis Lutra Canis

Felidae Mustelidae Canidae

CarnivoraOrder

F

amily

Genus

Species


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Each branch point

Represents the divergence of two species

Leopard Domestic cat

Common ancestor


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Deeper branch points

Represent progressively greater amounts ofdivergence

Leopard Domestic cat

Common ancestor

Wolf


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Concept 25.3: Phylogenetic systematics informs the

construction of phylogenetic trees based on shared

characteristics

A cladogram

Is a depiction of patterns of shared characteristics

among taxa

A clade within a cladogram

Is defined as a group of species that includes an

ancestral species and all its descendants

Cladistics

Is the study of resemblances among clades


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Cladistics

Clades

Can be nested within larger clades, but not allgroupings or organisms qualify as clades


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A valid clade is monophyletic

Signifying that it consists of the ancestorspecies and all its descendants

Figure 25.10a

(a) Monophyletic. In this tree, grouping 1,

consisting of the seven species BH, is a

monophyletic group, or clade. A mono-

phyletic group is made up of an

ancestral species (species B in this case)

and allof its descendant species. Only

monophyletic groups qualify as

legitimate taxa derived from cladistics.

Grouping 1

D

C

E G

F

B

A

J

I

KH


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A paraphyletic clade

Is a grouping that consists of an ancestralspecies and some, but not all, of the

descendants

Figure 25.10b

(b) Paraphyletic. Grouping 2 does not

meet the cladistic criterion: It is

paraphyletic, which means that it

consists of an ancestor (A in this case)

and some, but not all, of that ancestors

descendants. (Grouping 2 includes the

descendants I, J, and K, but excludes

BH, which also descended from A.)

D

C

E

B

GH

F

J

I

K

A

Grouping 2


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A polyphyletic grouping

Includes numerous types of organisms thatlack a common ancestor

Figure 25.10c

(c) Polyphyletic. Grouping 3 also fails the

cladistic test. It is polyphyletic, which

means that it lacks the common ancestor

of (A) the species in the group. Further-

more, a valid taxon that includes the

extant species G, H, J, and K would

necessarily also contain D and E, which

are also descended from A.

D

C

B

E G

F

H

A

J

I

K

Grouping 3

Sh d P i i i d Sh d D i d Ch i i


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Shared Primitive and Shared Derived Characteristics

In cladistic analysis

Clades are defined by their evolutionarynovelties


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A shared primitive character

Is a homologous structure that predates thebranching of a particular clade from other

members of that clade

Is shared beyond the taxon we are trying todefine


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A shared derived character

Is an evolutionary novelty unique to aparticular clade

O


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Outgroups

Systematists use a method called outgroup

comparison

To differentiate between shared derived and

shared primitive characteristics


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As a basis of comparison we need to designate

an outgroup

which is a species or group of species that is

closely related to the ingroup, the various

species we are studying

Outgroup comparison

Is based on the assumption that homologies

present in both the outgroup and ingroup mustbe primitive characters that predate the

divergence of both groups from a common

ancestor


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The outgroup comparison

Enables us to focus on just those charactersthat were derived at the various branch points

in the evolution of a clade

Figure 25.11a, b

SalamanderTAXA

T

urtle

Leopard

T

una

Lamprey

L

ancelet

(o

utgroup)

Hair

Amniotic (shelled) egg

Four walking legs

Hinged jaws

Vertebral column (backbone)

Leopard

Hair

Amniotic egg

Four walking legs

Hinged jaws

Vertebral column

Turtle

Salamander

Tuna

Lamprey

Lancelet (outgroup)

(a) Character table. A 0 indicates that a character is absent; a 1

indicates that a character is present.

(b) Cladogram. Analyzing the distribution of these

derived characters can provide insight into vertebrate

phylogeny.

CHARACTERS

Ph l ti T d Ti i


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Phylogenetic Trees and Timing

Any chronology represented by the branching

pattern of a phylogenetic tree

Is relative rather than absolute in terms of

representing the timing of divergences

Ph l


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Phylograms

In a phylogram

The length of a branch in a cladogram reflects the number of

genetic changes that have taken place in a particular DNA orRNA sequence in that lineage

Figure 25.12

Dros

ophil

a

Lanc

elet

Amphibian

Fish

Bird

Human

Rat

Mouse

Ult t i T


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Ultrametric Trees

In an ultrametric tree

The branching pattern is the same as in a phylogram, but all the

branches that can be traced from the common ancestor to thepresent are of equal length

Figure 25.13

Drosophil

a

Lancele

t

Amphibian

Fish

Bird

Hum

an

Rat

Mouse

Cenozoic

Mesozoic

Paleozoic

Proterozoic

542

251

65.5

Millionsof

yearsago

Maximum Parsimony and Maximum Likelihood


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Maximum Parsimony and Maximum Likelihood

Systematists

Can never be sure of finding the single besttree in a large data set

Narrow the possibilities by applying the

principles of maximum parsimony andmaximum likelihood


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Among phylogenetic hypotheses

The most parsimonious tree is the one thatrequires the fewest evolutionary events to

have occurred in the form of shared derived

characters


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Applying parsimony to a problem in molecular

systematics

Figure 25.14

Human Mushroom Tulip

40%

40%

0

30%0Human

Mushroom

Tulip

(a) Percentage differences between sequences

0


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Applying parsimony to a problem in molecular

systematics

Figure 25.14

Tree 1: More likely

(b) Comparison of possible trees

Tree 2: Less likely

15%

5%

15% 20%

5%

10%

15%

25%


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APPLICATION In considering possible phylogenies for a group of species, systematists compare molecular data for the species. Th e most efficient way to study the various phylogenetic

hypotheses is to begin by first considering the most parsimoniousthat is, which hypothesis requires the fewest total evolutionary events (molecular changes) to ha ve occurred.

TECHNIQUE Follow the numbered steps as we apply the principle of parsimony to a hypothetical phylogenetic problem involving four closely related bird spe cies.

SpeciesI

SpeciesII

SpeciesIII

SpeciesIV

I II III IV I III II IV I IV II III

Sites in DNA sequence

Three possible phylogenetic hypothese

1 2 3 4 5 6 7

A G G G G G T

G G G A G G G

G A G G A A T

G G A G A A G

I

II

III

IV

I II III IV

A G G G

GG

G

Bases atsite 1 foreach species

Base-changeevent

1 First, draw the possible phylogenies for the species(only 3 of the 15 possible trees relating these four

species are shown here).

2 Tabulate the molecular data for the species (in this simplified

example, the data represent a DNA sequence consisting of

just seven nucleotide bases).

3 Now focus on site 1 in the DNA sequence. A single base-

change event, marked by the crossbar in the branch leading

to species I, is sufficient to account for th e site 1 data.

Species

The principle of maximum likelihood

States that, given certain rules about how DNAchanges over time, a tree can be foundthat reflects

the most likely sequence of evolutionary events

Figure 25.15a


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GG GG AA AA

GG AA

GG

GG AA GG AA

GG GG

GG

GG AA GG AA

GG GG

GG

T G T G

T T

T

T T G G

T G

T

T G G T

T T

T

10 events9 events8 events

4 Continuing the comparison of bases at sites 2, 3, and 4reveals that each of these possible trees requires a total offour base-change events (marked again by crossbars).Thus, the first four sites in this DNA sequence do not helpus identify the most parsimonious tree.

5 After analyzing sites 5 and 6, we find that the first tree requiresfewer evolutionary events than the other two trees (two basechanges versus four). Note that in these diagrams, we assumethat the common ancestor had GG at sites 5 and 6. But even ifwe started with an AA ancestor, the first tree still would requireonly two changes, while four changes would be required to make

the other hypotheses work. Keep in mind that parsimony onlyconsiders the total number of events, not the particular nature ofthe events (how likely the particular base changes are to occur).

6 At site 7, the three trees also differ in the number of

evolutionary events required to explain the DNA data.

RESULTS To identify the most parsimonious tree, we total

all the base-change events noted in steps 36 (dont forget to

include the changes for site 1, on the facing page). We conclude

that the first tree is the most parsimonious of these three possible

phylogenies. (But now we must complete our search by

investigating the 12 other possible trees.)

Two base

changes

Figure 25.15b

Phylogenetic Trees as Hypotheses


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Phylogenetic Trees as Hypotheses

The best hypotheses for phylogenetic trees

Are those that fit the most data: morphological,molecular, and fossil


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Sometimes there is compelling evidence

That the best hypothesis is not the mostparsimonious

Figure 25.16a, b

Lizard

Four-chambered

heart

Bird Mammal

Lizard

Four-chambered

heart

Bird Mammal

Four-chambered

heart

(a) Mammal-bird clade

(b) Lizard-bird clade


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Concept 25.4: Much of an organisms

evolutionary history is documented in its

genome

Comparing nucleic acids or other molecules to

infer relatedness Is a valuable tool for tracing organisms

evolutionary history

Gene Duplications and Gene Families


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Gene Duplications and Gene Families

Gene duplication

Is one of the most important types of mutationin evolution because it increases the number

of genes in the genome, providing further

opportunities for evolutionary changes


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Orthologous genes

Are genes found in a single copy in thegenome

Can diverge only once speciation has taken

place

Figure 25.17a

Ancestral gene

Speciation

Orthologous genes(a)


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Paralogous genes

Result from gene duplication, so they arefound in more than one copy in the genome

Can diverge within the clade that carries them,

often adding new functions

Figure 25.17b

Ancestral gene

Gene duplication

Paralogous genes(b)

Genome Evolution


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Genome Evolution

Orthologous genes are widespread

And extend across many widely varied species

The widespread consistency in total gene

number in organisms of varying complexity

Indicates that genes in complex organisms are

extremely versatile and that each gene can

perform many functions


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Concept 25.5: Molecular clocks help track

evolutionary time


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Neutral Theory


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Neutral Theory

Neutral theory states that

Much evolutionary change in genes andproteins has no effect on fitness and therefore

is not influenced by Darwinian selection

And that the rate of molecular change in thesegenes and proteins should be regular like a

clock

Difficulties with Molecular Clocks


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Difficulties with Molecular Clocks

The molecular clock

Does not run as smoothly as neutral theorypredicts

Applying a Molecular Clock: The Origin of HIV


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Applying a Molecular Clock: The Origin of HIV

Phylogenetic analysis shows that HIV

Is descended from viruses that infectchimpanzees and other primates

A comparison of HIV samples from throughout

the epidemic

Has shown that the virus has evolved in a

remarkably clocklike fashion

The Universal Tree of Life


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The Universal Tree of Life

The tree of life

Is divided into three great clades called domains: Bacteria,

Archaea, and Eukarya

The early history of these domains is not yet clear

Figure 25.18

Bacteria Eukarya Archaea

4 Symbiosis of

chloroplast

ancestor with

ancestor of greenplants

3 Symbiosis of

mitochondrial

ancestor with

ancestor of

eukaryotes

2 Possible fusion

of bacterium

and archaean,

yielding

ancestor of

eukaryotic cells

1 Last common

ancestor of all

living things

4

3

2

1

Billionyearsago

Origin of life

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