BIS2C. Biodiversity and the Tree of Life. 2014. L3. Characters, Traits and States

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Lecture 3

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Lecture 3: !

Characters, Traits and States !!!

BIS 002C Biodiversity & the Tree of Life

Spring 2014 !

Prof. Jonathan Eisen

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Where we are going and where we have been

• Previous Lecture: !Trees, Taxa and Groups.

• Current Lecture: !Characters, Traits and States

• Next Lecture: ! Inferring trees.

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Lecture 2 Outline

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• Groupings in trees !Monophyletic groups !Non monophyletic groups !Relatedness ! Ingroups and outgroups ! “Sisters”


a b c d e h g f

Sister groups: two clades or species that are each other’s closest relatives (the two descendants of a single node)

Key Concept: Sister groups

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a b c d e h g f

g and h are “sisters” or “sister taxa”

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a b c d e h g f

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The group “g and h” is sister to f

f is sister to the group “g and h”6



Lecture 3: Key Concept

Using a phylogenetic tree to trace and infer the history of traits.

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Lecture 3: Outline

• Knowing history

• Character traits and states

• State changes

• Synapomorphies

• Homoplasy

• Character state reconstruction

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Lecture 3: Outline

• Knowing history


• State changes

• Synapomorphies

• Homoplasy


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Computer Simulation http://www.life10e.com/at22.02.html

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http://www.life10e.com/at22.02.html


Computer Simulation http://www.life10e.com/at22.02.html

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http://www.life10e.com/at22.02.html


Lab Simulation

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In the laboratory, researchers produced an unambiguous phylogeny of nine viral lineages, enhancing the mutation rate to increase variation among the lineages.

Outgroup lineageA lineage

D lineage

C lineage

E lineage

F lineage

H lineage

B lineage

G lineage

Growth in presence of mutagen

400 400 400

Generations


Thought Simulation

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Dog Breed Geneology (imperfect record)

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http://www.macwebguru.com/2010/09/11/the-dog/


Lenski Long Term E. coli evolution 1988 ——

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Lenski Long Term E. coli evolution 1988 ——

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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 16


Lecture 3: Outline

• Knowing history


• State changes

• Synapomorphies

• Homoplasy


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Key Concept: Character Traits and States

• Character: !A heritable feature of an organism. !Also known as a character trait or trait.

• Character state: !The particular form that a character takes.

• Example: !Character = heart !Character state = present/absent !Character state = # of chambers

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Character trait = fur; Character state = different colors

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a b c d e h g f

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Model Tree


a b c d e h g f

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Character Evolution Example 1

Character Trait: Face Character State: Happy


a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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Character Evolution from Tree of Life video


Key Concept: Homologous characters

Characters (e.g., a face) that are inherited from a common ancestor are homologous.

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Lecture 3: Outline

• Knowing history


• State changes

• Synapomorphies

• Homoplasy


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Key Concept: Divergence

• Species change over time

• Known (generally) as divergence, or divergent evolution.

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Character trait = fur; Character state = different colors

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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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Character State: Frowny


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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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a b c d e h g f

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Key Concept: Ancestral and Derived States

• A character with the same form as in the ancestor of a group has an ancestral state.

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• A character with a different form as in the ancestor of a group has a derived state.

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a b c d e h g f

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Which state is ancestral? !a) Smiley Face b) Frowny Face c) Both d) Neither

Clicker Question


Key Concept: Ancestral & Derived Status is Relative

• A trait may be ancestral or derived, depending on the point of reference.

• Example: feathers are an ancestral trait for any group of modern birds.

• But in a phylogeny of all vertebrates, feathers would be a derived trait, showing the relationship between birds and their theropod dinosaur relatives.

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a b c d e h g f

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Character Trait: Face Ancestral State: Happy Derived State: Frowny

For This Clade


Lecture 3: Outline

• Knowing history


• State changes

• Synapomorphies

• Homoplasy


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Key Concept: Synapomorphy

• Derived traits that are shared among a group and are viewed as evidence of the common ancestry of the group are known as synapomorphies.

• The vertebral column is a synapomorphy of all vertebrates.

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a b c d e h g f

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Synapomorphy Example


Synapomorphy

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Key Concept: Synapomorphy

• Synapomorphy = a shared derived trait

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• Derivation: Greek !Syn ~ with (a.k.a. shared) !Apo ~ away from (a.k.a. derived) !Morphy ~ shape (a.k.a. character trait or state

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a b c d e h g f

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3 45

Which traits are synapomorphies for fgh?

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8 9

A: 7,8,9 B: 4,5,6,7 C: 6

D: 6,7,8,9 E: 7

Clicker Question


a b c d e Birds Dinos f


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Mammals Reptiles



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34

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Mammals Reptiles



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3

hairmilk

mammary glandsfour-chambered heart 4

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Mammals Reptiles



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3

hairmilk

mammary glandsfour-chambered heart 4

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Mammals Reptiles



12

34

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Mammals Reptiles

hairmilk

mammary glandsfour-chambered heart


Lecture 3: Outline

• Knowing history


• State changes

• Synapomorphies

• Homoplasy


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Key Concept: Homoplasy

Traits that are similar for reasons other than inheritance from a common ancestor are called homoplastic traits or homoplasies.

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a b c d e h g f

Homoplasy Example

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a b c d e h g f

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Homoplasy Example


a b c d e h g f

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Homoplasy Example


a b c d e h g f

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Homoplasy Example


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Homoplasy Example


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Homoplasy Example


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Homoplasy Example


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Homoplasy Example


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Homoplasy Example


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Homoplasy Example

Frowny face is homoplasious


Key Concept: Convergence

Similar traits can develop in unrelated groups of organisms:

Convergent evolution—independently evolved traits subjected to similar selection pressures may become superficially similar.

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Example: the wings of bats and birds

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Figure 22.4 The Bones Are Homologous, the Wings Are Not

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Convergence

a Bats c d e Birds g f

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can fly

can’t fly

Mammals Reptiles


Lecture 3 Outline

• Knowing history


• State changes

• Synapomorphies

• Homoplasy


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Key Concept: Character State Reconstruction

Character state reconstruction methods allow one to infer history of states and state changes

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Character State Reconstruction

can fly

can’t fly

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Mammals Reptiles



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In theory, each node could have either of the two states

can fly

can’t fly

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Mammals Reptiles



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can fly

can’t fly

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Mammals Reptiles



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can fly

can’t fly

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Mammals Reptiles



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can fly

can’t fly

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Mammals Reptiles



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can fly

can’t fly

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Mammals Reptiles



Which pattern is the most plausible?

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Pattern 1 Pattern 2 Pattern 3


Key Concept: Principle of parsimony

The Principle of Parsimony: the simplest of two (or more) competing theories is to be preferred (assuming all else is equal).

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Key Concept: Principle of parsimony

The Principle of Parsimony: the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). !

Which character state pattern requires the fewest changes in states?

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Principle of parsimony

How many “steps” (state changes) required for each?

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+++Pattern 1 Pattern 2 Pattern 3



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can fly

can’t fly

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Pattern 1: How many steps?

Mammals Reptiles



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can fly

can’t fly

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Mammals Reptiles



Mammals Reptiles

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Note you could have more changes but seven is the minimum needed. We focus on the minimum needed.

Pattern 1: Seven Steps is the minimum needed.

can fly

can’t fly

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can fly

can’t fly

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Mammals Reptiles



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Pattern 2: Two steps

can fly

can’t fly

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Mammals Reptiles



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can fly

can’t fly

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Mammals Reptiles



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Pattern 3: Six steps

can fly

can’t fly

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Mammals Reptiles



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Pattern 1 Pattern 2 Pattern 3




+++Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps

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Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps



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Pattern 2: Flight in birds and bats arose separately and is homoplasious.

can fly

can’t fly

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Mammals Reptiles



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ASSUMPTIONS …

can fly

can’t fly

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Mammals Reptiles


Figure 22.4 The Bones Are Homologous, the Wings Are Not

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Figure 22.10 The Origin of a Sexually Selected Trait

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SIVsyk (Sykes monkeys)

HIV-1 (humans)

SIVcpz (chimpanzees)

SIVhoest (L’Hoest monkeys)SIVsun (sun-tailed monkeys)

SIVmnd (mandrills)

SIVagm (African green monkeys)SIVsm (sooty mangabeys)

HIV-2 (humans)

Common ancestor

Where did HIV Come From?


Common ancestor



Common ancestor



Common ancestor


Virus transferred from simian host to humans


Which Came First Red or Green Fluorescent Protein

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Kinds of Phylogenetic Trees

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A B C D

A

BC

D

A B C D

Units of character divergence

Units of time

Cladogram Phylogram Chronogram

Different kinds of trees

Only the relative branching order is depicted. No meaning to branch lengths.

Branch length is proportional to the amount of character change

Branch length is proportional to time


Next Lecture: Phylogenetic Tree Inference

What if you did not know the phylogeny and only knew the traits and the organisms? How would you infer homology, convergence, homoplasy, etc?

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Table 22.1

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22.2 How Are Phylogenetic Trees Constructed?

The root of the tree is located between the ingroup and the outgroup.

A trait present in both ingroup and outgroup must have evolved before the ingroup and thus must be ancestral for the ingroup.

Lampreys (jawless fishes) arose before the lineage leading to other vertebrates—they are the outgroup.

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22.2 How Are Phylogenetic Trees Constructed?

Chimpanzees and mice share two derived traits—fur and mammary glands. They are synapomorphies for this group.

Keratinous scales are a synapomorphy of the crocodile, pigeon, and lizard.

Information about the synapomorphies allows construction of the tree.

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Figure 22.5 Constructing a Phylogenetic Tree

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Figure 22.5 Constructing a Phylogenetic Tree

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Science

BIS2C. Biodiversity and the Tree of Life. 2014. L3. Characters, Traits and States