1. John Brookfield Ecology Club 11 th February 2010

2.  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

4. 2Nf

5. * * * * * * * * * * * * * * * * *

6. Nor Nor Nor Nor Sou Sou Sou Sou

7. Animals from Northern and Southern Populations (complete migration and mixing) Sou Nor Sou Nor Sou Nor Sou Nor

8. Nor Nor Nor Nor Nor Sou Sou Sou Sou Sou MRCA

9.  Hardy-Weinberg Formula: q=1-p  AA: p 2  Aa: 2pq  aa: q 2 Random Mating Inbreeding (specified by F ), when homozygotes exceed p 2 +q 2

10. p=0.8 q=0.2 p=0.2 q=0.8

11.  F ST =(p 1 -p 2 ) 2 /4(p(1-p))  -scaled squared difference in allele frequency between the populations  -averaged over alleles and loci

12. p=0.8 q=0.2 p=0.2 q=0.8 F ST = (0.8-0.2) 2 /(4x0.5x0.5)=0.36

13. What does F ST mean  F ST =(p 1 -p 2 ) 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= 2p 1 (1-p 1 )/2 +2p 2 (1-p 2 )/2 =0.8x0.2+0.2x0.8 =0.32

14. p=0.9 q=0.1 p=0.1 q=0.9 F ST = (0.9-0.1) 2 /(4x0.5x0.5)=0.64

15. p=1.0 q=0.0 p=0.0 q=1.0 F ST = (1.0-0.0) 2 /(4x0.5x0.5)=1.00

16. p=0.6 q=0.4 p=0.4 q=0.6 F ST = (0.6-0.4) 2 /(4x0.5x0.5)=0.04

17. 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

18. The Island Model: F ST =1/(1+4N e m)

20. Isolation By Distance

21. PopulationsBCDE A0.02560.04530.02200.0465 B0.05620.01100.0375 C0.05040.0321 D0.0634

22. PopulationsBCDE A9.515.2811.115.13 B4.2022.486.42 C4.717.54 D3.69

23. PopulationsBCDE A0.02560.04530.02200.0465 B0.05620.01100.0375 C0.05040.0321 D0.0634

25.  AMOVA-Laurent Excoffier ARLEQUIN  http://cmpg.unibe.ch/software/arlequin3/ 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

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

27.  D c : Clade distance: Geographical separation of individuals within a clade  D n : 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.

28.  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 http://pritch.bsd.uchicago.edu/structure.html Methods: STRUCTURE - Jonathan Pritchard

29.  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.d k/~gigu/Geneland/ http://www2.imm.dtu.d k/~gigu/Geneland/ Methods-GENELAND

30.  Selective Sweeps  Complete or partial  Locus-specific

31. Natural Selection  Effects on F ST ◦ Balanced polymorphism throughout species range gives low F ST ◦ Geographically localised selection gives high F ST