phylogeography

traditional summary statistics and phylogeography

mathematical approach using population genetic models.  examine patterns of DNA sequence variation and allele frequencies 

phylogenetic approach (building phylogenetic trees of individuals and comparing to trees to geography)

discipline concerned with relationships between gene genealogies, phylogenetics, and geography

recognition that mtDNA lineages in natural populations often display distinct geographic orientations (expand to nuclear genes) 

mitochondrial DNA markers 

as time since isolation incr., degree of agreement among characters within a gene incre.

geographyic placement of phylogenetic gaps agree across codistributed species 

genealogical concordance and regional concordance. 

• wide varity of phylogeographic outsomes, 
• smalll mammals: strong population differentation
• large: less population differentation 
• marine: moderate popu. differentiation 

display wide variety of phylogeographic outcomes 

• sedentary and show strong population differentiation
• marine turtles: highly mobile, but show population differentiation 

• freshwater: strong differentiation 
• marine: minimal differentiation 

display wide variety of phylogeographic outcomes 

• fewer phylogeographic than animals 
• lack useful genetic markers and technical limitations 
• complex xbreeding system 
• dispersal via seeds and pollen
• comlicated cuz of hybridization and introgression with other species 
• hybrid zones common in nature 

• insufficient polymorphism
• coexistence of ancestor and descendants 
• rejoining of lineages 

• distance or parismony based. 
• seize of circle represent frequency of haplotype 
• hatch marks on connection represnt mutational steps 

- a common way of representing the inferred genealogythe number of mutational changes among alleles is minimizedby parsimony.

- if homoplasy (mutational convergence or reversal) is infrequent,then a single minimum spanning tree can be inferred bymaximum parsimony searches

Extant alleles (haplotypes) on a gene tree are oftenseparated by more than one mutational step.

Why are intermediate alleles missing and need to be inferred?

-links haplotypes to one another through a series ofevolutionary steps.

- algorithm estimates (at 95% statistical confidence) themaximum number of base pair differences betweenhaplotypes [= the parsimony limit].

-Haplotypes that differ by a single mutation are connected,followed by two mutations, then three . . … ..

End product: a single network showing interrelationshipsof haplotypes that requires the smallest number of mutations. The connections represent coalescent events.

Haplotypes that exceed the parsimony limit are not connected.

1. High frequency haplotypes are likely to be old alleles.

2. Old alleles are interior to the network, new are peripheral.

3. Haplotypes with lots of connections likely to be old.

4. Old haplotypes likely to be broad ranging (long time fordispersal).

5. Haplotypes with one connection (singletons) likely to beconnected to haplotypes from their own population (not along time for dispersal).

used to identify historical and geographical factors behind distribution of haplotypes.  tests specific hypotheses

• first step: estimate haplotype network
• ea. step long network represents one mutation change that was observed in data

next: nested groups of haplotypes (clades) that are spearated from one another by one or more mutational steps are identified

then: superimpose geography over clades 

whether samples from same population are closer to each other in haplotype network than would be xpected by chance

if evidence of geographic structure is found, relationships between mutational distance and geographical distance among haplotypes are interpreted using inference key of possible demographic factors 

• Dc - clade distance 
• Dn- nested clade distance

looks for non-random association of haplotypes and geography

geographical range of a clade or avg distance of ea. member of a clade from its geographic center

avg geographic distance of all members of a clade from geographical centre of its higher-level nesting clade

• expected patterns of geographical assoicaton
• restricted gene flow, range expansion and allopatric fragmentation