Lecture 4: Phylogeny and the Tree of Life Campbell: Chapter 26

Lecture 4: Phylogeny and the Tree of Life

Campbell:

Chapter 26

HumansRattlesnakePine treeAmoebaBacterium

All life is interconnected by descent

How to determine the pattern of descent?

Systematics - field of biology dealing with diversity and evolutionary history of life

Includes Taxonomy: DINCDescription Identification NomenclatureClassification

Goal:– Determine Evolutionary History (Phylogeny) of Life

Description

= assign features

Character = a feature (e.g., “petal color”)

Character states = two or more forms of a character (e.g., “red,” “white”).

Identification

= associate an unknown with a knownHow? One way: Taxonomic Key, e.g.,

Tree Leaves simple …….………………………… Species A Leaves pinnate …….………..…..…..…… Species B

Herb Flowers red …….…………………………… Species C Flowers white …….…………………..…… Species D

Nomenclature

Naming, according to a formal system.

Binomial: Species are two names (Linnaeus):

E.g., Homo sapiensHomo = genus namesapiens = specific epithetHomo sapiens = species name

Nomenclature

Hierarchical Ranks:Domain

KingdomPhylum

ClassOrder

FamilyGenus

Species

Classification

• Placing objects, e.g., life, into some type of order.

• Taxon = a taxonomic group (plural = taxa).

How to classify life

• Phenetic classification

– Based on overall similarity

– Those organisms most similar are classified more “closely” together.

Problem with phenetic classification:• Can be arbitrary,

e.g., classify these:

Phylogenetic classification

• Based on known (inferred) evolutionary history.

• Advantage:– Classification reflects pattern of evolution– Classification not ambiguous

= representation of the history of life

Ingroup – group studied

Outgroup – group not part of ingroup, used to “root” tree

Fig. 26-5

Sistertaxa

ANCESTRALLINEAGE

Taxon A

PolytomyCommon ancestor oftaxa A–F

Branch point(node)

Taxon B

Taxon C

Taxon D

Taxon E

Taxon F

Apomorphy (derived trait)

= a new, derived feature= a new, derived featureE.g., for this evolutionary transformationE.g., for this evolutionary transformation

scales --------> feathers scales --------> feathers(ancestral feature)(ancestral feature) (derived feature) (derived feature)

Presence of feathers is an Presence of feathers is an apomorphyapomorphy for birds.for birds.

Taxa are grouped by apomorphies

Apomorphies are the result of evolution.

Taxa sharing apomorphies underwent same evolutionary history should be grouped together.

Principle of ParsimonyThat cladogram (tree) having the fewest number

of “steps” (evolutionary changes) is the one accepted.

Okham’s razor: the simplest explanation, with fewest number of “ad hoc” hypotheses, is accepted.

Other methods of phylogeny reconstruction:

• Maximum Likelihood or Bayesian analysis– Uses probabilities– Advantage: can use evolutionary models.

Fig. 26-11

TAXA

Lan

cele

t(o

utg

rou

p)

Lam

pre

y

Sal

aman

der

Leo

par

d

Tu

rtle

Tu

na

Vertebral column(backbone)

Hinged jaws

Four walking legs

Amniotic (shelled) egg

CH

AR

AC

TE

RS

Hair

(a) Character table

Hair

Hinged jaws

Vertebralcolumn

Four walking legs

Amniotic egg

(b) Phylogenetic tree

Salamander

Leopard

Turtle

Lamprey

Tuna

Lancelet(outgroup)

0

0 0

0

0

0

0 0

0

0

0 0

0 0 0 1

11

111

1

11

1

1

11

11

Sequentially group taxa by shared derived character states (apomorphies)

Fig. 26-8a

Deletion

Insertion

1

2

DNA sequence data – most important type of data

Fig. 26-8b

3

4

DNA sequence data - alignment

Each nucleotide position = CharacterCharacter states = specific nucleotide

Homology

• Similarity resulting from common ancestry.

– E.g., the forelimb bones of a bird, bat, and cat.

Homoplasy (analogy)

• Similarity not due to common ancestry

• Reversal – loss of new (apomorphic) feature, resembles ancestral (old) feature.

• Convergence (parallelism) – gain of new, similar features independently.

Convergent evolution:spines of cacti & euphorbs

Cactus EuphorbEuphorb

euphorb spines cactus spines

Convergent evolution:spines of cacti & euphorbs

Both examples of reversal within Tetrapods: loss of a derived feature – forelimbs.

Leg-less lizards Snake

Example of convergence relative to one another!Independently evolved.

snakesleg-lesslizards

leggedlizards

**

*= loss of legs

gain of legs (Tetrapods)

Convergent evolution:wings of some animals evolved independently

Fig. 26-7

Convergent evolution:Australian “mole” and N. Am. “mole”

Fig. 26-18

(b) Paralogous genes

(a) Orthologous genes

Ancestral gene

Paralogous genes

Ancestral species

Speciation withdivergence of gene

Gene duplication and divergence

Species A after many generations

Species A Species B

Species A

Orthologous genes

Orthology – genes homologous

Paralogy – genes not homologous

Gene Duplicationcan occur!

Monophyletic Group

• a group consisting of: – a common ancestor +– all descendents of that common ancestor

C B F E D A

Cladograms can be “flipped” at nodes, show same relationships

Fig. 26-13

Drosophila

Lancelet

Zebrafish

Frog

Human

Chicken

Mouse

CENOZOIC

Present65.5

MESOZOIC

251

Millions of years ago

PALEOZOIC

542

One can date divergence times with molecular clock and fossils

Relationship

• = recency of common ancestry

i.e., taxa sharing a common ancestor more recent in time are more closely related than those sharing common ancestors more distant in time.

Example:

• Are fish more closely related to sharks or to humans?

Example:

• Are crocodyles more closely related to lizards or to birds?

Lizards &Turtles Snakes Crocodiles Birds


C B F E D A

Is “E” more closely related to “D” or to “F”?Is “E” more closely related to “B” or to “A”?Is “E” more closely related to “B” or to “C”?

C B F E D A

Is “E” more closely related to “D” or to “F”?Is “E” more closely related to “B” or to “A”?Is “E” more closely related to “B” or to “C”?

Answers: F, B, neither (equally to “B” & “C”)

Paraphyletic group

• Consist of common ancestor but not all descendents

• Paraphyletic groups are unnatural, distort evolutionary history, and should not be recognized.


“Reptilia” here paraphyletic


Re-defined Reptilia monophyletic


Lizards &Turtles Snakes Crocodiles

Dinosaurs

Birds

Importance of a name:Did humans evolve from apes?

Orangutan Gorilla Chimpanzees Humans

HominidaePongidae

“Great Apes”Orangutan Gorilla Chimpanzees Humans

Pongidae“Great Apes”Pongidae orHominidae


Pongidae orHominidae


Pongidae orHominidae


We are human, butwe are also apes.

• We share unique human features.

• We also share features with other apes (and with other animals, plants, fungi, bacteria, etc.).

• Humans didn’t evolve from apes, humans are apes.

All of life is interconnectedby descent.

There are no “higher” or “lower” species.

Importance of systematics & evolution:

1) Foundation of biology - study of biodiversity2) Basis for classification of life3) Gives insight into biological processes:

speciation processesadaptation to environment

4) Can be aesthetically/intellectually pleasing!

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Lecture 4: Phylogeny and the Tree of Life Campbell: Chapter 26