phylogeny.ppt

7/27/2019 Phylogeny.ppt

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HumansRattlesnakePine treeAmoebaBacterium

All life is interconnected by descent

How to determine the pattern of descent?


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Systematics - field of biology dealing withdiversity and evolutionary history of life

Includes Taxonomy: DINC

Description

Identification

Nomenclature

Classification

Goal: Determine Evolutionary History (Phylogeny) of Life


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Description

= assign features

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

Character states = two or more forms of a

character (e.g., red, white).


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Identification

= associate an unknown with a known

How? One way:

Taxonomic Key, e.g.,Tree . SpeciesA

Leaves simple . Species B

Leaves pinnate ....... Species CHerb

Flowers red . Species D

Flowers white ... Species E


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Nomenclature

Naming, according to a formal system.

Binomial: Species are two names (Linnaeus):

E.g., Homo sapiens

Homo = genus namesapiens = specific epithet

Homo sapiens = species name


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Nomenclature

Hierarchical Ranks:Domain

Kingdom

Phylum

Class

Order

Family

Genus

Species


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Classification

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

order.

Taxon = a taxonomic group (plural = taxa).


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How to classify life

Phenetic classification

Based on overall similarity

Those organisms most similar are classified more

closely together.


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Problem with phenetic classification:

Can be arbitrary,e.g., classify these:


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Phylogenetic classification

Based on known (inferred) evolutionary

history.

Advantage:

Classification reflects pattern of evolution

Classification not ambiguous


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A B C D E F

TIME

lineage

or clade

Cladogram or Phylogenetic Tree

TAXA


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A B C D E F

TIME

speciation


TAXA


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Ingroup group studied

Outgroup group not part ofingroup, used to root tree

Fig 26 5


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Fig. 26-5

Sistertaxa

ANCESTRALLINEAGE

Taxon A

PolytomyCommon ancestor oftaxa AF

Branch point

(node)

Taxon B

Taxon C

Taxon D

Taxon E

Taxon F


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Apomorphy (derived trait) = a new, derived feature

E.g., for this evolutionary transformation

scales --------> feathers

(ancestral feature) (derived feature)

Presence of feathers is an apomorphy

for birds.


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Taxa are grouped by apomorphies

Apomorphies are the result of evolution.

Taxa sharing apomorphies

underwent same evolutionary history

should be grouped together.


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Principle of Parsimony

That cladogram (tree) having the fewest number

of steps (evolutionary changes) is the one

accepted.

Okhams razor: the simplest explanation, with

fewest number of ad hoc hypotheses, is

accepted.


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Other methods of phylogeny

reconstruction:

Maximum Likelihood or Bayesian analysis

Uses probabilities

Advantage: can use evolutionary models.


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apomorphies

(for Taxa B & C)

apomorphy(for Taxon D)

apomorphy(for Taxa B,C,D,E,F)

A B C D E F

TIME


TAXA


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Fig. 26-11

TAXA

Leopard

Tuna

Vertebral column

(backbone)

Hinged jaws

Four walking legs

Amniotic (shelled) egg

Hair

(a) Character table

Hair

Hinged jaws

Vertebral

column

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)


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Fig. 26-8a

Deletion

Insertion

1

2

DNA sequence datamost important type of data


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Fig. 26-8b

3

4

DNA sequence data - alignment

Each nucleotide position = Character

Character states = specific nucleotide


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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.


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Convergent evolution:

spines of cacti & euphorbs

Cactus Euphorb

C l i


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euphorb spines cactus spines


spines of cacti & euphorbs


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Both examples ofreversal within Tetrapods:

loss of a derived feature forelimbs.

Leg-less lizards Snake

Example ofconvergence relative to one another!Independently evolved.

snakesleg-less

lizards

legged

lizards

**

*= loss of legs

gain of legs (Tetrapods)


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wings of some animals evolved independently

Fig. 26-7


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Convergent evolution:Australian mole and N. Am. mole

A t l


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Fig. 26-18(b) Paralogous genes

(a) Orthologous genes

Ancestral gene

Paralogous genes

Ancestral species

Speciation with

divergence 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 Duplication

can occur!


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A B C D E F

TIME


TAXA

common ancestor(of taxon A & taxa B-F)

common ancestor(of taxon D, E, & F)

Common ancestry


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Monophyletic Group

a group consisting of:

a common ancestor + all descendents of that common ancestor


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monophyleticgroup

A B C D E F

TIME


TAXA




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monophyleticgroup

A B C D E F

TIME


TAXA




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monophyleticgroup

A B C D E F

TIME


TAXA




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monophyleticgroup

A B C D E F

TIME


TAXA




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monophyleticgroup

A B C D E F

TIME


TAXA




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A B C D E F

TIME

speciation


TAXA


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C B F E D A

Cladograms can be flipped at nodes, show same

relationships

Fig. 26-13


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Drosophi la

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


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Relationship

= recency of common ancestry

i.e., taxa sharing a common ancestor

more recent in time are more closely relatedthan those sharing common ancestors more

distant in time.


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Example:

Are fish more closely related to sharks or to

humans?


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Shark Fish Humans

TIME


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Shark Fish Humans

TIME

common ancestor ofFish and Humans

common ancestor ofSharks, Fish, and Humans


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monophyleticgroup

OsteichthyesVertebrata

Shark Fish Humans

TIME

common ancestor ofFish and Humans

common ancestor ofSharks, Fish, and Humans


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Example:

Are crocodyles more closely related to lizards

or to birds?


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Lizards &Snakes Crocodyles BirdsTurtles


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"Reptilia"


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Paraphyletic group

Consist of common ancestor but not all

descendents

Paraphyletic groups are unnatural, distort

evolutionary history, and should not be

recognized.


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"Reptilia"


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"Reptilia"

Reptilia here paraphyletic


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Reptilia

Re-defined Reptilia monophyletic


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Dinosaurs

Reptilia


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Importance of a name:

Did humans evolve from apes?


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Gorilla Chimpanzees HumansOrangatan


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HominidaePongidae

Great Apes


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Hominidae


Pongidae

Great Apes

Pongidae or

Hominidae


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Hominidae


Pongidae or

Hominidae


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Hominidae


Pongidae or

Hominidae


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We are human but


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We are human, but

we are also apes.

We share unique human features.

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

Humans didnt evolve from apes, humansare apes.


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Importance of systematics & evolution:

1) Foundation of biology - study of biodiversity

2) Basis for classification of life

3) Gives insight into biological processes:

speciation processes

adaptation to environment

4) Can be aesthetically/intellectually pleasing!

i i i


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E.g., schistosomiasis


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Schistosomiasis:

knowledge of species

diversity and evolutionary

history of primary host can

aid in controlling parasite

(Schistosoma, a fluke)

Phylogeny ofOncomelania

snails

All of life is interconnected


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All of life is interconnected

by descent.

A B C D E F

TIME

lineageor clade


TAXA

There are no higher or


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There are no higher or

lower species.

A B C D E F

TIME

lineageor clade


TAXA

phylogeny.ppt

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