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Phylogeography

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Phylogeography

John Brookfield

Ecology Club

11th February 2010

Circular DNAs derived from bacterial symbionts

16kb, 37 genes (in humans)

Rapid evolutionary rates in warm blooded vertebrates (particularly in “D loop”)

Maternally transmitted and non-recombining

2Nf

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2Nf

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Nor Nor Nor Nor Sou Sou Sou Sou

Sou Nor Sou Nor Sou Nor Sou Nor

MRCA

MRCA

Nor Nor Nor Nor Nor Sou Sou Sou Sou Sou

- Hardy-Weinberg Formula: q=1-p
- AA: p2
- Aa: 2pq
- aa: q2
Random Mating

Inbreeding (specified by F ), when homozygotes exceed p2 +q2

p=0.8

q=0.2

p=0.2

q=0.8

- FST=(p1-p2)2/4(p(1-p))
- -scaled squared difference in allele frequency between the populations
- -averaged over alleles and loci

p=0.8

q=0.2

p=0.2

q=0.8

FST = (0.8-0.2)2/(4x0.5x0.5)=0.36

- FST=(p1-p2)2/4(p(1-p))
=(0.8-0.2)2/(4x0.5X0.5)=0.36

How many heterozygotes expected (Hardy-Weinberg)=2p(1-p)=0.50

How many seen=

2p1(1-p1)/2

+2p2(1-p2)/2

=0.8x0.2+0.2x0.8 =0.32

p=0.9

q=0.1

p=0.1

q=0.9

FST = (0.9-0.1)2/(4x0.5x0.5)=0.64

p=1.0

q=0.0

p=0.0

q=1.0

FST = (1.0-0.0)2/(4x0.5x0.5)=1.00

p=0.6

q=0.4

p=0.4

q=0.6

FST = (0.6-0.4)2/(4x0.5x0.5)=0.04

pA=0.6

qa=0.4

pB=0.7

qb=0.3

pA=0.4

qa=0.6

pB=0.3

qb=0.7

Linkage Disequilibrium: Association of A and B and association of a and b

- AMOVA-Laurent Excoffier ARLEQUIN
- http://cmpg.unibe.ch/software/arlequin3/
- Designed for mtDNAs initially
- Takes various levels-populations and subpopulations, etc. molecular variation between them as a proportion of total molecular variance

- Dc: Clade distance: Geographical separation of individuals within a clade
- Dn: Nested clade distance: Distance from the centre of a clade and the mean location of individuals in related clades (all those within the same higher level of nesting)
- Isolation by distance: A clade-defining mutation arises in a single location, and its spread will increase with age. Clades within that clade (nested clades) will have a geographic distribution within that of the ancestral clade.
- Fragmentation: Strict correlation of clades with geography-which breaks down as older clades are considered.
- Range Expansion: Subclades can be more widespread geographically than their ancestral clades.

Samples individuals and genotypes at many loci

Creates subpopulations where there are Hardy-Weinberg proportions and linkage equilibrium within subpopulations

Assigns individuals to subpopulations

http://pritch.bsd.uchicago.edu/structure.html

G. Guillot, Estoup, A., Mortier, F. Cosson, J.F. A spatial statistical model for landscape genetics. Genetics, 170, 1261-1280, 2005.

http://www2.imm.dtu.dk/~gigu/Geneland/

Selective Sweeps

Complete or partial

Locus-specific

- Effects on FST
- Balanced polymorphism throughout species range gives low FST
- Geographically localised selection gives high FST