View
220
Download
4
Tags:
Embed Size (px)
Citation preview
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*
*
*
* *
*
**
*
*
*
*
*
*
*
*
*
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