2. Restriction enzyme analysis

3. The new(ish) population genetics Old view New view Allele frequency change looking forward in time; alleles either the same or different Shape of gene tree looking backward in time; alleles are related phylogenetically

4. The first ‘gene tree’, 1979

5. Diploid individualsDissolved individuals

7. Wright, Kingman and the coalescent Sewell Wright J. F. C. Kingman Probability of common ancestry of two Randomly chosen alleles in previous generation

8. Probability that 10 sequences have j ancestors in previous generation

9. Probability that all k copies from a sample came from different copies in the preceding generation So, the time it takes for two copies from a sample to come from the same copy in the preceding generation is: And, the total time it takes for all copies from a sample to come from a common ancestral copy is: With large k (units in generations) 4N generations

10. Expected fixation time of neutral allele in population of size N (Kimura)

11. Shape of gene trees from a random mating population

12. How to draw a coalescent tree 1.Sample k copies from a population of 2N chromosomes 2.Go back in time, drawing from an exponential distribution, with the average being 3. Combine two lineages 4. Decrease k by 1 5. If k-1, stop; otherwise, go back to step 1, using k-1 as a starting point

13. Root of a gene tree captured in very few samples

14. Stochastic nature of the coalescent process

15. Estimating genetic diversity within populations  = 4N  average number of differences between two randomly sampled sequences from a population “Watterson’s theta” or  = observed number of differences between all pairs of sequences from a population. Also called “  ”

16. past present Genetic diversity (  ) or population size Signatures of stable and expanding populations Long internal branches Short external branches Short internal branches Long external branches Stable population Expanding population

17. Mycoplasma is transmitted horizontally, often at bird feeders Expanded throughout the eastern US in just five years Has now crossed the Rockies and is spreading south through California. Rapid spread of Mycoplasma in House Finch populations Courtesy Cornell Lab of Ornithology

18. Serially-sampled phylogeny of 12 Mycoplasma strains Years before present 30 20 10 0 Estimated coalescence of chicken and finch strains, (611 yrs.) (95 % c.i. 484-753 yrs.) Numerous fixed SNP and indel differences, including CRISPR deletion Estimated mutation rate: ~9.3 x 10 -10 per site per year; 24 homoplasious sites suggest recombination Phylogeny obtained using BEAST, strict clock, 10 million cycles, sampling every 1000 cycles 743,011 aligned sites

19. Shape (node depths) of higher level trees depend on extrinsic factors Interordinal molecular phylogeny of mammals

21. “Lucky Mother” concept for mtDNA