John BrookfieldEcology 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

Phylogeography (Avise 1994*)Molecular Markers, Natural History and Evolution. Chapman and Hall

2Nf

Mutations enable the tree to be estimated-Average divergence=2NfN

2Nf*

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Nor Nor Nor Nor Sou Sou Sou Sou

Animals from Northern and Southern Populations (complete migration and mixing)

Sou Nor Sou Nor Sou Nor Sou Nor

Nor Nor Nor Nor Nor Sou Sou Sou Sou Sou

MRCA

MRCA

Hardy-Weinberg Formula: q=1-p AA: p2

Aa: 2pq aa: q2

Random Mating

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

p=0.8q=0.2

p=0.2q=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=0.8q=0.2

p=0.2q=0.8

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

What does FST mean

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=0.9q=0.1

p=0.1q=0.9

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

p=1.0q=0.0

p=0.0q=1.0

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

p=0.6q=0.4

p=0.4q=0.6

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

pA=0.6qa=0.4pB=0.7qb=0.3

pA=0.4qa=0.6pB=0.3qb=0.7

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

The Island Model: FST =1/(1+4Nem)

Mixed Migrant Pool

m m m m m m m m

Infinite Number

of Populations of size Ne

Linear Stepping Stone Model

Isolation By Distance

0

0.05

0.1

0.15

0.2

0.25

0.3

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8

Distance

FST/(

1-F

ST)

Table of FST Values

Populations B C D E

A 0.0256 0.0453 0.0220 0.0465

B 0.0562 0.0110 0.0375

C 0.0504 0.0321

D 0.0634

Interpretation 1-Gene FlowInferred Migration Rates- Nem

Populations B C D E

A 9.51 5.28 11.11 5.13

B 4.20 22.48 6.42

C 4.71 7.54

D 3.69

Table of FST Values

Populations B C D E

A 0.0256 0.0453 0.0220 0.0465

B 0.0562 0.0110 0.0375

C 0.0504 0.0321

D 0.0634

Interpretation 2-Ancestral Population SplittingUPGMA Tree of Population Ancestry

B D A C E

0.011

0.0238 0.0321

0.0479

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

Methods-Nested Clade Analysis (1)Templeton, A. (2006) Population genetics and microevolutionary theory. Wiley

Nested Clade Analysis (2) 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

Methods: STRUCTURE- Jonathan Pritchard

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/

Methods-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