Lecture 17 phylogenetics and phylogeography
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Lecture 17: Phylogenetics and Phylogeography. October 22, 2012. Announcements. Exam Next Wednesday (Oct 31) Review on Monday Bring questions Covers material from genetic drift (Sept 28) through Coalescence (Friday) I will be gone Monday, Oct 29 (after office hours) through Oct 31

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Lecture 17 phylogenetics and phylogeography

Announcements

  • Exam Next Wednesday (Oct 31)

  • Review on Monday

    • Bring questions

  • Covers material from genetic drift (Sept 28) through Coalescence (Friday)

  • I will be gone Monday, Oct 29 (after office hours) through Oct 31

  • Bring questions on Monday!


Lecture 17 phylogenetics and phylogeography

Last Time

  • Using FST to estimate migration

  • Direct estimates of migration: parentage analysis

  • Introduction to phylogenetic analysis


Lecture 17 phylogenetics and phylogeography

Today

  • Phylogeography

  • Limitations of phylogenetic analysis

  • Coalescence introduction

  • Influence of demography on coalescence time


Upgma method
UPGMA Method

  • Use all pairwise comparisons to make dendrogram

  • UPGMA:Unweighted Pairwise Groups Method using Arithmetic Means

  • Hierarchically link most closely related individuals

Read the Lab 9 Introduction!



Lecture 17 phylogenetics and phylogeography

Parsimony Methods

  • Based on underlying genealogical relationships among alleles

  • Occam’s Razor: simplest scenario is the most likely

  • Useful for depicting evolutionary relationships among taxa or populations

  • Choose tree that requires smallest number of steps (mutations) to produce observed relationships


Lecture 17 phylogenetics and phylogeography

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


Lecture 17 phylogenetics and phylogeography

Choosing Phylogenetic Trees

9

8

9

10

9

11

9

8

7

11

9

5

Felsenstein 2004

  • 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


Lecture 17 phylogenetics and phylogeography

Choosing Phylogenetic Trees

E

A

F

Felsenstein 2004

D

C

B

60

60

60

Lowe, Harris, and Ashton 2004

  • If multiple trees equally likely, select majority rule or consensus

  • Strict consensus is most conservative approach

  • Bootstrap data matrix (sample with replacement) to determine robustness of nodes


Phylogeography
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


Phylogeography1
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

Avise 2004

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


Problems with using phylogenetics for inferring evolution
Problems with using Phylogenetics for Inferring Evolution

  • It’s a black box: starting from end point, reconstructing past based on assumed evolutionary model

  • Homologs versus paralogs

  • Hybridization

  • Differential evolutionary rates

  • Assumes coalescence


Lecture 17 phylogenetics and phylogeography

Gene Orthology

  • Phylogenetics requires unambiguous identification of orthologous genes

  • Paralogous genes are duplicated copies that do not share a common evolutionary history

  • Difficult to determine orthology relationships

Lowe, Harris, Ashton 2004


Lecture 17 phylogenetics and phylogeography

Gene Trees vs Species Trees

Gene Tree

B

C

A

  • Genes (or loci) evolve at different rates

    • Why?

  • Topology derived by a single gene may not match topology based on whole genome, or morphological traits


Lecture 17 phylogenetics and phylogeography

Gene Trees vs Species Trees

  • Failure to coalesce within species lineages drives divergence of relationships between gene and species trees

Divergent Gene Tree:

b is closer to c than to a

Concordant Gene Tree

b is closer to a than to c

a

b

c

a

b

c


Coalescence
Coalescence

  • Retrospective tracing of ancestry of individual alleles

  • Allows explicit simulation of sequence evolution

  • Incorporation of factors that cause deviation from neutrality: selection, drift, and gene flow


Lecture 17 phylogenetics and phylogeography

9 generations in the history of a population of 14 gene copies

Time

present

Individual alleles

Slide courtesy of Yoav Gilad



Lecture 17 phylogenetics and phylogeography

Modeling from Theoretical Ancestors: Forward Evolution copies

  • Can model populations in a forward direction, starting with theoretical past

  • Fisher-Wright model of neutral evolution

  • Very computationally intensive for large populations


Lecture 17 phylogenetics and phylogeography

Alternative: Start at the end and work your way back copies

Most recent common ancestor (MRCA)

Time

present

Individual alleles

Slide courtesy of Yoav Gilad


Lecture 17 phylogenetics and phylogeography

The genealogy of a sample of 5 gene copies copies

Most recent common ancestor (MRCA)

Time

present

individuals

Slide courtesy of Yoav Gilad


Lecture 17 phylogenetics and phylogeography

The genealogy of a sample of 5 gene copies copies

Most recent common ancestor (MRCA)

Time

present

Individual alleles

Slide courtesy of Yoav Gilad


Examples of coalescent trees for a sample of 6
Examples of coalescent trees for a sample of 6 copies

Time

Individual alleles

Slide courtesy of Yoav Gilad


Coalescence advantages
Coalescence Advantages copies

  • Don’t have to model dead ends

  • Only consider lineages that survive to modern day: computationally efficient

  • Based on actual observations

  • Can simulate different evolutionary scenarios to see what best fits the observed data


Coalescent tree example
Coalescent Tree Example copies

  • Coalescence: Merging of two lineages in the Most Recent Common Ancestor (MRCA)

  • Waiting Time: time to coalescence for two lineages

    • Increases with each coalescent event


Probability of coalescence
Probability of Coalescence copies

  • For any two lineages, function of population size

  • Also a function of number of lineages

where k is number of lineages


Probability of coalescence1
Probability of Coalescence copies

  • Probability declines over time

    • Lineages decrease in number

  • Can be estimated based on negative exponential

where k is number of lineages





Applications of the coalescent approach
Applications of the Coalescent Approach copies

  • Framework for efficiently testing alternative models for evolution

  • Inferences about effective population size

  • Detection of population structure

  • Signatures of selection (coming attraction)