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Phylogeography

Phylogeography. John Brookfield Ecology Club 11 th 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. Mitochondrial DNAs.

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Phylogeography

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  1. Phylogeography John Brookfield Ecology Club 11th 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 Mitochondrial DNAs

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

  4. Mitochondrial DNAs in an undivided population 2Nf

  5. Mutations enable the tree to be estimated-Average divergence=2NfN * * 2Nf * * * * * * * * * * * * * * *

  6. Animals from Northern and Southern Populations 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. Animals from Northern and Southern Populations MRCA MRCA Nor Nor Nor Nor Nor Sou Sou Sou Sou Sou

  9. A complementary approach- FST • Hardy-Weinberg Formula: q=1-p • AA: p2 • Aa: 2pq • aa: q2 Random Mating Inbreeding (specified by F ), when homozygotes exceed p2 +q2

  10. Two Islands p=0.8 q=0.2 p=0.2 q=0.8

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

  12. Two Islands p=0.8 q=0.2 p=0.2 q=0.8 FST = (0.8-0.2)2/(4x0.5x0.5)=0.36

  13. 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

  14. Two Islands p=0.9 q=0.1 p=0.1 q=0.9 FST = (0.9-0.1)2/(4x0.5x0.5)=0.64

  15. Two Islands p=1.0 q=0.0 p=0.0 q=1.0 FST = (1.0-0.0)2/(4x0.5x0.5)=1.00

  16. Two Islands p=0.6 q=0.4 p=0.4 q=0.6 FST = (0.6-0.4)2/(4x0.5x0.5)=0.04

  17. Two Islands-Two Loci, A and B 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: FST =1/(1+4Nem)

  19. Linear Stepping Stone Model

  20. Isolation By Distance

  21. Table of FST Values

  22. Interpretation 1-Gene FlowInferred Migration Rates- Nem

  23. Table of FST Values

  24. Interpretation 2-Ancestral Population SplittingUPGMA Tree of Population Ancestry

  25. Methods • 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

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

  27. 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.

  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 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.dk/~gigu/Geneland/ Methods-GENELAND

  30. Selective Sweeps Complete or partial Locus-specific Natural Selection

  31. Natural Selection • Effects on FST • Balanced polymorphism throughout species range gives low FST • Geographically localised selection gives high FST

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