eeob 400: lecture 13 phylogeny outgroupaagcttcataggagcaaccattctaataataagcctcataaagcc species...

EEOB 400: Lecture 13

Phylogeny

Outgroup AAGCTTCATAGGAGCAACCATTCTAATAATAAGCCTCATAAAGCCSpecies A AAGCTTCACCGGCGCAGTTATCCTCATAATATGCCTCATAATGCCSpecies B GTGCTTCACCGACGCAGTTGTCCTCATAATGTGCCTCACTATGCCSpecies C GTGCTTCACCGACGCAGTTGCCCTCATGATGAGCCTCACTATGCA

Extra credit

Using genetic markers to examine spatial and temporal variation in Ohio Canada Goose harvest composition

Dr. Kristin MylecraineThe Ohio State University

and Ohio Division of Natural Resources

Thursday November 912:00 PM, Lazenby 21

Why is phylogeny important?

Understanding and classifying the diversity of life on Earth

Testing evolutionary hypotheses: - trait evolution - coevolution - mode and pattern of speciation - correlated trait evolution - biogeography - geographic origins - age of different taxa - nature of molecular evolution - disease epidemiology

…and many more applications!

Tree of life

http://www.tolweb.org/tree/home.pages/aboutoverview.html

Phylogeny

What is a phylogeny?

Branching diagram showing relationships between species (or higher taxa) based on their shared common ancestors

Species: A B C D

Tim

e

A

B

C

DTime

A and B are most closely related because they share a common ancestor ( call the ancestor “E”) that C and D do not share

E

E

F

F

A+B+C are more closely related to each other than to D because they share a common ancestor (“F”) that D does not share

Phylogeny

Terminal nodes = contemporary taxa

Internal nodes = ancestral taxa

Phylogeny and classification

Hierarchy

All taxonomic classifications are hierarchical – how does phylogeny differ?

Class

Order

Family Family

Genus

Species 1Species 2Species 3Species 4

Species 1Species 2Species 3

Genus

Genus

Species 1Species 2

Order

Family

Genus

Species 1Species 2Species 3Species 4Species 5Species 6Species 7Species 8Species 9

Genus

Species 1Species 2

Species 1Genus

Species 1Species 2Species 3

Genus

Hierarchy

Phylogenetic (cladistic) classification reflects evolutionary history

The only objective form of classification – organisms share a true evolutionary history regardless of our arbitrary decisions of how to classify them


Class

Order

Order

Family

Family

Family

Genus

Genus

Genus

Genus

Genus

Genus

FamilyGenus

Genus

PhylogenyClassification


Classification

Note that taxa are nestedon the basis of sharedcommon ancestors

e.g., All tetrapods share a common ancestor withlegs, but other chordatesoutside of Tetrapoda donot share this commonancestor

The traits mapped ontothe phylogeny aresynapomorphies – we will return to them later


Monophyletic group

Includes an ancestorall of its descendants

A B C D

Paraphyletic group

Includes ancestor and some, but not all of its descendants

A B C D

Polyphyletic group

Includes two convergentdescendants but not theircommon ancestor

A B C D

Taxon A is highly derivedand looks very differentfrom B, C, and ancestor

How could this happen? Taxon A and C sharesimilar traits throughconvergent evolution

Only monophyletic groups (clades) are recognized in cladistic classification


Monophyly

Each of the colored lineagesin this echinoderm phylogenyis a good monophyletic group

Asteroidea

Ophiuroidea

Echinoidea

Holothuroidea

Crinoidea Each group shares a commonancestor that is not shared by any members of another group

Lindblad-Toh et al. (2005) Nature 438: 803-819

Paraphyletic groups

Paraphyly

“Foxes” are paraphyletic with respect to dogs, wolves, jackals, coyotes, etc.

This is a trivial example because “fox” and “dog” are not formal taxonomic units, but it does show that a dog or a wolf is just a derived fox in the phylogenetic sense

Foxes

Lindblad-Toh et al. (2005) Nature 438: 803-819

Paraphyletic groups

Monophyly

Note that canids are still a good monophyletic clade within Mammalia

Each of the colored lineages withincanids is also a monophyletic clade

Canids

Paraphyletic groups

Fry et al. (2006) Nature 439: 584-588

Paraphyly

“Lizards” (Sauria) areparaphyletic with respectto snakes (Serpentes)

Serpentes is a monophyleticclade within lizards

Squamata (lizards + snakes)is a monophyletic cladesister to sphenodontida

Snakes are just derived,limbless lizards

Lizards

Paraphyletic groups

Paraphyly

Birds are more closely relatedto crocodilians than to otherextant vertebrates

Archosauria = Birds + Crocs

We think of reptiles as turtles,lizards, snakes, and crocodiles

But Reptilia is a paraphyleticgroup unless it includes Aves

Reptilia

What does this mean?

It means that“reptiles” don’t

exist!

No, it means that you’re one

of us!

What it means is that “reptile” is only a valid clade if it includes birds

Birds are still birds, but Aves cannot be considered a “Class” equivalent toClass Reptilia because it is evolutionarily nested within Reptilia

Reptilia

Aves(birds)

Turtles

Crocodiles

Lizards and snakes

Tuataras

Blood squirting? No Yes

Mapping evolutionary transitions

Some horned lizards squirt blood from their eyes when attacked by canids

How many times has blood-squirting evolved?

Testing evolutionary hypotheses

Blood squirting? No Yes


Some horned lizards squirt blood from their eyes when attacked by canids

How many times has blood-squirting evolved? This phylogeny suggests a single evolutioary gain and a single lossof blood squirting


Leaché and McGuire. Molecular Phylogenetics and Evolution 39: 628-644

But a new phylogeny using multiple characters suggests that blood squirting has been lost many times in the evolution of this group

Our interpretation of these evolutionary scenarios depends on phylogeny



Leaché and McGuire. Molecular Phylogenetics and Evolution 39: 628-644


Reconstructing ancestral characters

This phylogeny also shows how we can usedata from living species to infer character states in ancestral taxa

??

Ancestral state could be blue, purple, or intermediate…outgroup comparisonindicates blue is most parsimonious

Fry et al. (2006) Nature 439: 584-588



How many times has venom evolved in squamate reptiles?

Once in the large “venom clade”

Groups within this clade thenevolved different venom types

e.g., different proteins found in Snakes versus Gila monsters

Even non-venomous lizards in thisclade (Iguania) share ancestral toxins


Convergence and modes of speciation

What can this phylogeny tell us about homology/analogy and speciation?

Lake Tanganyika Lake Malawi

1. Similarities between each pair arethe result of convergence

2. Sympatric speciation more likely than allopatric speciation


Clark et al. (2000)

Coevolution

Aphids and bacteria are symbiotic

Given this close relationship, we might expect that speciation in an aphid would cause parallel speciation in the bacteria

When comparing phylogenies for each group we see evidence for reciprocal cladogenesis (but also contradictions)

Matsuoka et al. (2002)

A

B


Geographic origins

Where did domestic corn (Zea mays maize) originate?

Populations from Highland Mexico are at the base of each maize clade


Geographic origins

Where did humans originate?

Each tip is one of 135 different mitochondrial DNA types found among 189 individual humans

African mtDNA types are clearly basal on the tree, with the non-African types derived

Suggests that humans originated in Africa

Vigilant et al. (1991) Science

Reconstructing evolutionary history

Phenetic methods

Based on overall difference between taxa = “distance” methods

Only considers shared characters; not shared, derived characters

Suppose you use DNA hybridizationto compare DNA of 4 species

A differs from B by 4%A differs from C by 10%A differs from D by 10%…for all pairs

Use algorithm to find shortest tree

“Quick and dirty” method

Distance method will often recovertrees that are similar to cladistic trees,but it requires constant rate of evolutionor it will give erroneous groupings

Reconstructing evolutionary history

Cladistic methods (Willi Hennig 1966)

Based on shared, derived characters = synapomorphies

Similarity is not enough – requires similarity reflecting descent with modification

Requires characters that can be assigned a particular character state

Characters and character states

Character: eye color Character states: blue, brown, green

mammary glands present, absent

number of legs 0, 2, 4, 6, 8, etc.

Molecular Characters nucleotide bases A, C, T, G

amino acid codons ACC, CGT, GAT, etc.

Terminology

Polarity Distinguishing ancestral (0) from derived (1) = assigning polarity - polarity can be assessed by outgroup comparison

“Blue” and “square” are plesiomorphic A B C D

Plesiomorphy Character state found in ancestor of group

Apomorphy Derived character state in descendants of group

Symplesiomorphy Shared, ancestral character state

Synapomorphy Shared, derived character state (indicates homology)

“Small size” is an apomorphy for A

“Red” is a synapomorphy for A + B

“Circle” is a synapomorphy for A + B + C …but a symplesiomorphy for A + B

Synapomorphy

Each character shown inpink is a synapomorphy

Shared - by all descendantsin the clade

e.g., all chordates share anotochord

Derived – not present in ancestral taxa

e.g., ancestral deuterostomelacks a notochord

Any clade must share at least one synapomorphy

Synapomorphy

Synapomorphy

Many synapomorphies = stronger support

Few synapomorphies = weaker support

How can we tell how wella clade is supported?

In part, by the number ofsynapomorphies

Homoplasy

Homoplasy

Taxa share a character, but not by descent from a common ancestor

Equivalent to analogy, homoplasy is a product of convergent evolution

Homoplasy gives the impression of homology (synapomorphy) and thereforemisleads phylogenetic analyses by supporting polyphyletic taxa

True phylogeny

Recovered phylogeny

Homoplasy

Lake Tanganyika Lake Malawi

StripesSpotted caudal fin Yellow color

Recoveredphylogeny

Homoplasies that look likehomologies:

True phylogeny:Malawi cichlidsmonophyletic

Morphological characters

Examples

Skull structure in cetaceans Genitalia in ants

Morphological characters

Character: Pattern

Striped

Barred

Barred

Barred

Caudal Shape

Round

Forked

Forked

Round

Caudal Pattern

Spot

None

None

None

ForeheadBulge?

No

No

No

Yes

Constructing a character matrix

Suppose we want to know the phylogeny of cichlids A, B, C using an Outgroup

First, we need characters that are variable within this group

Out

A

B

C

Synapomorphies

Apomorphy

Parsimony

How do we decide the “best” phylogeny?

Parsimony – the simplest explanation is preferred (Occam’s razor)

A trivial example (much more complicated with real datasets)

Round forked tail

No bump forehead bump

Round forked tail

Stripe barredSpot plain tail

Round forked tail

No bump forehead bump

Requires 5 steps Requires only 4 steps

Most parsimonious:

Stripe barredSpot plain tail

1. Extract

OutgroupSpecies ASpecies BSpecies C

Molecular characters

2. Sequence

AAGCTTCATAGGAGCAACCATTCTAATAATAAGCCTCATAAAGCCAAGCTTCACCGGCGCAGTTATCCTCATAATATGCCTCATAATGCCGTGCTTCACCGACGCAGTTGTCCTCATAATGTGCCTCACTATGCCGTGCTTCACCGACGCAGTTGCCCTCATGATGAGCCTCACTATGCA

3. Align

AAGCTTCATAGAGCTTCACAGTGCTTCACGGTGCTTCACG



Out

A

B

C

Invariable sites

These are not usefulphylogenetic characters

Out

A

B

C




Out

A

B

C

AG TC

Any mutations atthis time would affectA, B and C because they have not yet diverged

Synapomorphiessupporting A+B+C

Out

A

B

C

AAGCTTCATAGAGCTTCACAGTGCTTCACGGTGCCTCACG



Out

A

B

C

AG TC

Any mutations at this time would affect A and B


AT AG

Synapomorphiessupporting B+C

Out

A

B

C

AAGCTTCATAGAGCTTCACAGTGCTTCACGGTGCCTCACG



Out

A

B

C

AG TC


AT AG

Synapomorphiessupporting B+C

Out

A

B

C

Apomorphy for C

Any mutations at this time would only affect C TC


Homoplasy is still a problem

There are only 4 possible character states for nucleotides: A G C T

Homoplasy arises when nucleotide mutates back to ancestral state: ATA

Out

A

B

C


AG TC

AT AG


TA

AAGCTTCATAGAGCTTCACAGTGCTTCACGGAGCTTCACG

Back-mutation “erases”synapomorphy and produces homoplasy


Homoplasy is still a problem

There are only 4 possible character states for nucleotides: A G C T

Homoplasy arises when nucleotide mutates back to ancestral state: ATA


Out

A

B

C

AG TC

AT AG

TA


AAGCTTCATAGAGCTTAACAGTGCTTCACGGAGCTTAACG

Back-mutation “erases”synapomorphy and produces homoplasy

CA

CA

Homoplasy can also reflect

convergent mutations

Morphology vs molecules

Morphology

Homoplasy can be assessed from structure, development, etc. PRO

Characters may be subject to selection = convergence = homoplasy CON

Takes lots of time to identify and codecharacters for analysis CON

Requires parsimony analysis ?

Only someone familiar with taxon canidentify good characters PRO & CON

Nucleotides

Homoplasy can’t be assessed directly (an “A” is an “A”) CON

Characters may or may not be subject to selection – depends on the site ?

Sequencing yields lots of charactersif gene is sufficiently variable PRO

Can use either parsimony or likelihoodanalysis – stronger inference PRO

Any idiot can get sequence dataPRO & CON

With either approach, it all comes down to successfully identifying synapomorphies and distinguishing them from homoplasies

Character conflict

Character conflict

With either morphology or molecules,some characters will not “agree” onthe most parsimonious phylogeny

Some characters support monophyleticReptilia exclusive of birds

These are not synapomorphies for “reptiles”, they are ancestral traits

Feathers, two legs, and endothermy are apomorphic in birds

Other characters reflect synapomorphy and recover the true relationships

But in many cases it is more difficult toresolve character conflict

Consensus

When multiple phylogenies are supported…

A consensus tree shows only those relationships common to all trees

The lower tree is a “compromise” between conflicting upper phylogenies

Consensus trees will always have at least one polytomy - a branching event that is not a bifurcation

Better to have an incompletely resolved tree than an incorrect tree

Examples:

- two equally parsimonious trees- two trees from different genes- morphological vs. molecular tree- parsimony vs. likelihood tree

Consensus

An example of a consensus tree for loons

The middle tree is a “compromise” between conflicting left and right trees

Polytomy

Are polytomies real?

Usually not - they reflect inability to reconstruct the true bifurcating phylogeny

We often encounter polytomies in cases of rapid speciation when an ancestor rapidly diverged into many new forms

ABCD

EFG

HIJK

Truephylogeny

= Change in character state

= 1 million years

Inferredphylogeny

We can only recover those branches on which we “see” characters change

Different genes for different questions

Molecular stopwatch Molecular hourglass

Deepest root: 35 mya (use mtRNA) 600 mya (use nuclear rRNA)

Different genes, different trees

Gene 1 Gene 2Species A Species B Species C Species A Species B Species C

A B C

Incorrect

A B C

Correct

Because genes are inherited as a single unit, all of the nucleotides in a gene cansupport the same phylogeny, and it could still not reflect true speciation sequence

Red and blueindicate different alleles for a particular gene (gene 1 or 2)

eeob 400: lecture 13 phylogeny outgroupaagcttcataggagcaaccattctaataataagcctcataaagcc species...

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