copyright © 2005 pearson education, inc. publishing as benjamin cummings evolutionary biology is...

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Evolutionary biology is about both process and history.

• The processes of evolution are natural selection and other mechanisms that change the genetic composition of populations and can lead to the evolution of new species.

• A major goal of evolutionary biology is to reconstruct the history of life on earth.


Overview: Investigating the Tree of Life

• Phylogeny is the evolutionary history of a species or group of related species

• Biologists draw on the fossil record, which provides information about ancient organisms


• Systematics is an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct

• Systematists use morphological, biochemical, and molecular comparisons to infer evolutionary relationships

• Molecular systematics, which uses comparisons of nucleotide sequences in DNA and RNA to help identify evolutionary relationships between individual genes or even entire genomes.


Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence

• To infer phylogenies, systematists gather information about morphologies, development, and biochemistry of living organisms

• They also examine fossils to help establish relationships between living organisms

• Fossils are the preserved remnants or impressions left by organisms that lived in the past. In essence, they are the historical documents of biology.


• Sedimentary rocks form from layers of sand and silt that are carried by rivers to seas and swamps, where the minerals settle to the bottom along with the remains of organisms.

• As deposits pile up, they compress older sediments below them into layers called strata.

• The fossil record is the ordered array in which fossils appear within sedimentary rock strata.

• These rocks record the passing of geological time.


• Fossils can be used to construct phylogenies only if we can determine their ages.

• The majority of living things were not captured as fossils upon their death.

• Of those that formed fossils, later geological processes destroyed many.

• Only a fraction of existing fossils have been discovered.


Morphological and Molecular Homologies

• Similarities due to shared ancestry are called homologies.

• In addition to fossils, phylogenetic history can be inferred from morphological and molecular similarities in living organisms

• Organisms with very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences


Sorting Homology from Analogy

• In constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy

• Homology is similarity due to shared ancestry

• Analogy is similarity due to convergent evolution


• Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages

• Similar analogous adaptations may evolve in such organisms.

• Analogies are not due to shared ancestry.


• Distinguishing homology from analogy is critical in the reconstruction of phylogeny.

• For example, both birds and bats have adaptations that allow them to fly.

• However, a close examination of a bat’s wing shows a greater similarity to a cat’s forelimb that to a bird’s wing.


• Fossil evidence also documents that bat and bird wings arose independently from walking forelimbs of different ancestors.

• Thus a bat’s wing is homologous to other mammalian forelimbs but is analogous in function to a bird’s wing.

• Analogous structures or molecular sequences that evolved independently are also called homoplasies.


• In general, the more points of resemblance that two complex structures have, the less likely it is that they evolved independently.

• For example, the skulls of a human and a chimpanzee are formed by the fusion of many bones. The two skulls match almost perfectly, bone for bone.

• It is highly unlikely that such complex structures have separate origins. More likely, the genes involved in the development of both skulls were inherited from a common ancestor.


• Systematists compare long stretches of DNA and even entire genomes to assess relationships between species.

• If genes in two organisms have closely similar nucleotide sequences, it is highly likely that the genes are homologous.


Evaluating Molecular Homologies

• Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

• Deletions or insertions may shift the remaining sequences, making it difficult to recognize closely matching nucleotide sequences.

LE 25-6

1

2

1

2

Deletion

Insertion

1

2

1

2


Phylogenetic systematics connectsclassification with evolutionary history

• Taxonomy is the ordered division of organisms into categories based on characteristics used to assess similarities and differences

• In 1748, Carolus Linnaeus published a system of taxonomy based on resemblances.

• Two key features of his system remain useful today: two-part names for species and hierarchical classification


Binomial Nomenclature

• The two-part scientific name of a species is called a binomial nomenclature

• The first part of the name is the genus

• The second part, called the specific epithet, is unique for each species within the genus

• The first letter of the genus is capitalized, and the entire species name is latinized

• Both parts together name the species (not the specific epithet alone)


Hierarchical Classification

• Linnaeus introduced a system for grouping species in increasingly broad categories

• Linneaus’s classification was not based on evolutionary relationships but simply on resemblances between organisms.

• Each taxonomic level is more comprehensive than the previous one.

• As an example, all species of cats are mammals, but not all mammals are cats.


• The named taxonomic unit at any level is called a taxon.

• Example: Panthera is a taxon at the genus level, and Mammalia is a taxon at the class level that includes all of the many orders of mammals.

LE 25-8

Species

Pantherapardus

PantheraGenus

FamilyFelidae

CarnivoraOrder

MammaliaClass

PhylumChordata

KingdomAnimalia

EukaryaDomain


Linking Classification and Phylogeny

• Systematists depict evolutionary relationships in branching phylogenetic trees

• The branching of the tree reflects the hierarchical classification of groups nested within more inclusive groups.

• Methods for tracing phylogeny began with Darwin, who realized the evolutionary implications of Linnaean hierarchy.

LE 25-9

Carnivora

Pantherapardus

(leopard)

Mephitismephitis

(striped skunk)

Lutra lutra(European

otter)

Canisfamiliaris

(domestic dog)

Canislupus(wolf)S

pec

ies

Gen

us

Fam

ilyO

rder

Felidae Mustelidae Canidae

Panthera Mephitis Lutra Canis


• Each branch point represents the divergence of two species

• “Deeper” branch points represent progressively greater amounts of divergence


Concept 25.3: Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics

• If shared characteristics are homologous and, thus, explained by common ancestry, then the cladogram forms the basis of a phylogenetic tree.

• A cladogram depicts patterns of shared characteristics among taxa

• A clade is a group of species that includes an ancestral species and all its descendants

• Cladistics studies resemblances among clades


• A shared derived character is an evolutionary novelty unique to a particular clade

• The presence of a backbone can qualify as a shared derived character, but at a deeper branch point that distinguishes all vertebrates from other mammals.

• Among vertebrates, the backbone is a shared primitive character because it evolved in the ancestor common to all vertebrates.

LE 25-10a

Grouping 1

Monophyletic

A valid clade is monophyletic, signifying

that it consists of the ancestor species and all

its descendants

LE 25-10b

Paraphyletic

Grouping 2

A paraphyletic grouping consists of an ancestral species

and some, but not all, of the descendants

LE 25-10c

Polyphyletic

Grouping 3

A polyphyletic grouping consists of various species that lack a common ancestor


Outgroups

• An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied

• Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared primitive characteristics


• Outgroup comparison assumes that homologies shared by the outgroup and ingroup must be primitive characters that predate the divergence of both groups from a common ancestor

• It enables us to focus on characters derived at various branch points in the evolution of a clade

LE 25-11

Hair

Amniotic (shelled) egg

Four walking legs

Hinged jaws

Vertebral column(backbone)

Character table

CH

AR

AC

TE

RS

TAXA

La

nc

ele

t(o

utg

rou

p)

La

mp

rey

Tu

na

Sa

lam

an

de

r

Tu

rtle

Le

op

ard

Turtle Leopard

Hair

Amniotic egg

Four walking legs

Hinged jaws

Vertebral column

Salamander

Tuna

Lamprey

Lancelet (outgroup)

Cladogram


Phylogenetic Trees and Timing

• Any chronology represented by the branching of a phylogenetic tree is relative rather than absolute in representing timing of divergences

• 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 or RNA sequence in that lineage

LE 25-12

Droso

phila

Lanc

elet

Fish

Amph

ibia

nBird

Human

Rat

Mou

se


Ultrametric Trees

• Branching in an ultrametric tree is the same as in a phylogram, but all branches traceable from the common ancestor to the present are equal length

LE 25-13

Droso

phila

Lanc

elet

Fish

Amph

ibia

nBird

Human

Rat Mou

se

Ce

no

zoic

Me

so

zoic

Pa

leo

zoic

65

.52

51

54

2

Ne

op

rote

rozo

ic

Mil

lio

ns

of

ye

ars

ag

o


Maximum Parsimony and Maximum Likelihood

• Systematists can never be sure of finding the best tree in a large data set

• They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood


• The most parsimonious tree requires the fewest evolutionary events to have occurred in the form of shared derived characters

• The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events

LE 25-14Human

0

Mushroom

30%

0

Tulip

40%

40%

Human

Mushroom

0Tulip

Percentage differences between sequences

Comparison of possible trees

15% 15% 20%

5% 5%

10%

15%

25%

Tree 1: More likely Tree 2: Less likely


• In considering possible phylogenies for a group of species, systematists compare molecular data for the species.

• The most efficient way to study hypotheses is to consider the most parsimonious hypothesis, the one requiring the fewest evolutionary events (molecular changes)

LE 25-15ab

Sites in DNA sequence

I

Species

1

Base-changeevent

Bases atsite 1 foreach species

2 3 4 5 6 7

II

III

IV

I II III IV


Phylogenetic Trees as Hypotheses

• The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil

• Sometimes the best hypothesis is not the most parsimonious

LE 25-16

Lizard Bird Mammal

Four-chamberedheart

Mammal-bird clade

Lizard Bird Mammal

Four-chamberedheart

Four-chamberedheart

Lizard-bird clade

• Orthologous genes are genes found in a single copy in the genome

• They can diverge only after speciation occurs

LE 25-17a

Ancestral gene

Speciation

Orthologous genes

• Paralogous genes result from gene duplication, so are found in more than one copy in the genome

• They can diverge within the clade that carries them, often adding new functions

LE 25-17b

Ancestral gene

Gene duplication

Paralogous genes

Genome Evolution

• Orthologous genes are widespread and extend across many widely varied species

• The widespread consistency in total gene number in organisms indicates genes in complex organisms are very versatile and that each gene can perform many functions


Much of an organism’s 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 duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes


Concept 25.5: Molecular clocks help track evolutionary time

• To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time

• The molecular clock is a yardstick for measuring absolute time of evolutionary change based on the observation that some genes and other regions of genomes seem to evolve at constant rates


Neutral Theory

• Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection

• It states that the rate of molecular change in these genes and proteins should be regular like a clock


Difficulties with Molecular Clocks

• The molecular clock does not run as smoothly as neutral theory predicts

• Irregularities result from natural selection in which some DNA changes are favored over others

• Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty


Applying a Molecular Clock: The Origin of HIV

• Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates

• Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way


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

copyright © 2005 pearson education, inc. publishing as benjamin cummings evolutionary biology is...

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