John Brookfield Ecology Club 11 th February 2010.
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Transcript of John Brookfield Ecology Club 11 th February 2010.
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John BrookfieldEcology Club
11th February 2010
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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
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Phylogeography (Avise 1994*)Molecular Markers, Natural History and Evolution. Chapman and Hall
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2Nf
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Mutations enable the tree to be estimated-Average divergence=2NfN
2Nf*
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Nor Nor Nor Nor Sou Sou Sou Sou
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Animals from Northern and Southern Populations (complete migration and mixing)
Sou Nor Sou Nor Sou Nor Sou Nor
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Nor Nor Nor Nor Nor Sou Sou Sou Sou Sou
MRCA
MRCA
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Hardy-Weinberg Formula: q=1-p AA: p2
Aa: 2pq aa: q2
Random Mating
Inbreeding (specified by F ), when homozygotes exceed p2 +q2
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p=0.8q=0.2
p=0.2q=0.8
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FST=(p1-p2)2/4(p(1-p))
-scaled squared difference in allele frequency between the populations
-averaged over alleles and loci
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p=0.8q=0.2
p=0.2q=0.8
FST = (0.8-0.2)2/(4x0.5x0.5)=0.36
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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
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p=0.9q=0.1
p=0.1q=0.9
FST = (0.9-0.1)2/(4x0.5x0.5)=0.64
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p=1.0q=0.0
p=0.0q=1.0
FST = (1.0-0.0)2/(4x0.5x0.5)=1.00
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p=0.6q=0.4
p=0.4q=0.6
FST = (0.6-0.4)2/(4x0.5x0.5)=0.04
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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
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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
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Linear Stepping Stone Model
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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)
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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
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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
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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
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Interpretation 2-Ancestral Population SplittingUPGMA Tree of Population Ancestry
B D A C E
0.011
0.0238 0.0321
0.0479
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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
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Methods-Nested Clade Analysis (1)Templeton, A. (2006) Population genetics and microevolutionary theory. Wiley
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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.
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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
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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
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Selective Sweeps
Complete or partial
Locus-specific
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Effects on FST
◦ Balanced polymorphism throughout species range gives low FST
◦ Geographically localised selection gives high FST