Phylogeography Phylogenetics oUnderstanding phylogenetic trees oMajor approaches to determining...

Phylogeography

Phylogenetics

o Understanding phylogenetic trees

o Major approaches to determining phylogenies

Phylogeography

Phylogenetics Study of the evolutionary relationships among

individuals, groups, or species

Relationships often represented as dichotomous branching tree

Extremely common approach for detecting and displaying relationships among genotypes

Important in evolution, systematics, and ecology (phylogeography)

A

B M

K

IJ

N

L

H

G

F

E

D

C

ZYXWVUT

PQ

SR

O

Ç

Evolution

What is a phylogeny?

ZYXWVUT

PQ

SR

O

Ç Homology: similarity that is the result of inheritance from a common ancestor

Phylogenetic Tree Terms

A B C D E F G H I J

ROOT

interior branches

node

terminal branches

Leaves, Operational Taxonomic Units (OTUs)

Group, cluster, clade

Bacteria 1

Bacteria 3

Bacteria 2

Eukaryote 1

Eukaryote 4

Eukaryote 3

Eukaryote 2

Tree Topology

(Bacteria1,(Bacteria2,Bacteria3),(Eukaryote1,((Eukaryote2,Eukaryote3),Eukaryote4)))

Bacteria 1

Bacteria 3Bacteria 2

Eukaryote 1

Eukaryote 4Eukaryote 3

Eukaryote 2

http://helix.biology.mcmaster.ca

How about these?

Are these trees different?

Rooted versus Unrooted Trees

archaea

archaea

archaea

eukaryote

eukaryote

eukaryote

eukaryote

Unrooted tree

Rooted by outgroup

bacteria outgroup

root

eukaryote

eukaryote

eukaryote

eukaryote

archaea

archaea

archaea

Monophyletic group

Monophyleticgroup

D

C

B

AG

E

F

C

B

A

F

E

G

D

Rooting with D as outgroup

D

C

B

AG

E

F

C

B

A

F

E

G

D

C

B

A

F

E

G

D

Now with C as outgroup

Which of these four trees is different?

Baum et al.

Phenetics (distance) vs Cladistics (character state

based) Lowe, Harris, and Ashton 2004

Choosing Phylogenetic Trees MANY possible trees can

be built for a given set of taxa

Very computationally intensive to choose among these

Lowe, Harris, and Ashton 2004

)!3(2

)!52(3

n

nU

nN nnN Unn

nR )32(

)!2(2

)!32(2

7

9

8

9

9

9

9

5

8

10

11

11

Felsenstein 2004

Choosing Phylogenetic Trees Many algorithms exist for

searching tree space

Local optima are problem: need to traverse valleys to get to other peaks

Heuristic search: cut trees up systematically and reassemble

Branch and bound: search for optimal path through tree space

Phylogeography

The study of evolutionary relationships among individuals based on phylogenetic analysis of DNA sequences in geographic context

Can be used to infer evolutionary history of populations

Migrations Population subdivisions Bottlenecks/Founder Effects

Can provide insights on current relationships among populations

Connectedness of populations Effects of landscape features on gene flow

Phylogeography Topology of tree provides

clues about evolutionary and ecological history of a set of populations

Dispersal creates poor correspondence between geography and tree topology

Vicariance (division of populations preventing gene flow among subpopulations) results in neat mapping of geography onto haplotypes

Example: Pocket gophers (Geomys pinetis)

Fossorial rodent that inhabits 3-state area in the U.S.

RFLP for mtDNA of 87 individuals revealed 23 haplotypes

Parsimony network reveals geographic relationships among haplotypes

Haplotypes generally confined to single populations

Major east-west split in distribution revealed

Avise 2004

Avise 2004

I

II

III

IV

V

Example: Brown Bears (Ursus arctos) Reduced to <1%

of original range in North America

Sequence mtDNA control region of bears from worldwide distribution

Notice unique haplotype F in ABC islands of Alaska

Notice position of polar bear

Lowe, Harris, and Ashton 2004

Brown Bear Surprise Subsequent study of samples from ice cores

(36,000-43,000 years old) found all four haplotypes

How do you explain the modern distribution?

Current Ancient

Brown Bears in North America (Ursus arctos) Diversity assessed

based on 8 microsatellite loci

Reduced diversity for more isolated sites (Kodiak, Yellowstone)

Brown Bear Nuclear Differentiation Assessed differentiation based

on 17 nuclear microsatellite loci

Strong differentiation between Kodiak and Admiralty islands

Lowe, Harris, and Ashton 2004

Brown Bear Nuclear Differentiation Less differentiation for

nuclear than mitochondrial markers

Degree of differentiation driven by distances between islands: Admiralty much more divergent than Chicagof or Baranof

Why?

Lowe, Harris, and Ashton 2004

T

SST H

HG 1

SH1

Also, maternal inheritance of mitochondrion

Smaller effective population size of mitochondrion

Mitochondrion is one locus: selective sweeps!

Ursus arctos in Europe Highly degraded populations,

low genetic diversity

Haplotypes reveal 3 refugia during glaciation

Migration and admixture following deglaciation (“suture zones” in Scandinavia and central Europe)

Taberlet et al. 1998; Molecular Ecology

7:453

Human Phylogeography Most evidence points to origins in Africa and

subsequent migrations

Cavalli-Sforza 2003 Nature Genetics 33:266

Human Phylogeography: mtDNA Most ancient and diverse

haplotypes in Africa (dots)

Migration and admixture is evident from presence of African haplotypes in other clades

Human Phylogeography: X-chromosome genes Pyruvate dehydrogenase

E1 alpha subunit sequence

25 polymorphic sites, 23 of which were in African sample

African θ=6.9, non-African θ=0.57

Using chimp sequence as outgroup, estimated that divergence occurred 1.9 million years ago

Complexities to Human Phylogeography Some genes show evidence of Asian origin

Sequence of X-linked ribonucleotide reductase M2 pseudogene 4

Suggests single origin model is too simple: admixture and selection?

Garrigan 2007 Nature Reviews Genetics 7:669

Evidence of Admixture in Ancient Eurasians

Garrigan 2007 Nature Reviews Genetics 7:669

Evidence for Ancient Population Structure in Nuclear but not Mitochondrial Trees

Garrigan 2007 Nature Reviews Genetics 7:669

Evidence for Ancient Population Structure in Nuclear but not Mitochondrial Trees

Garrigan 2007 Nature Reviews Genetics 7:669

Alternative Models to Single Origin

Garrigan 2007 Nature Reviews Genetics 7:669

Human Phylogeography with SNP Assayed 500,000 SNP genotypes for 3,192 Europeans

Used Principal Components Analysis to ordinate samples in space

High correspondence betweeen sample ordination and geographic origin of samples

Individuals assigned to populations of origin with high accuracy

Nested Clade Analysis

Combines spatial and temporal tests of association

Can be used to distinguish ongoing population processes from historical events

Dc – Clade distance (measures geographic range of a particular clade)Dn – Nested clade distance (geographic relationship to other same level categories)I-T – average distance between interior and tip clades within nested group

Branco et al 2002 Evolution 56:792–803

Use random permutation testing to test significance of associations

Templeton AR 1998 Molecular Ecology 7:381-397

Nested Clade Analysis - critique and summary (reflections of a colleague)

Hardly anyone believes in it anyway (ie Wayne Maddison is strongly against it, because it is too conjectural - not statistically sound)

All you need to know is that people use it to make conclusions about range expansions and historical vicariant events, based on molecular data

The method replies on this inference key, which ultimately tells you nothing in the end