Pattern of similarity between Europeans and Neanderthals

1. Pattern of similarity between Europeans and Neanderthals Green et al. Science 328, 710 (2010)

2. Summary of recent human history Reich et al. Nature 468, 1053 (2010)

3. Adaptive evolution in human brain development genes

5. Effect of selection on Tajima’s D balancing selection neutral selective sweep  Many low frequency variants and singletons, D negative =  D = 0   Pairwise differences (k) increase faster than S D positive

6. Sampling localities of babblers temporalis rubeculus Carpentarian barrier

7. Tajima’s test of neutrality for 12populations (A-K) Tajima’s D =  (or k) - ; Ho: D = 0 (K same as ) • In this diagram, each letter represents a different population • Under neutrality, k and s should be equal, as they estimate the same quantity (Edwards, 1997)

8. The site frequency spectrum under selection and neutrality Nielsen, Annu. Rev. Genet. 2005. 39:197–218

9. Neutral polymorphism and divergence Polymorphism  = 4Nm high  N Polymorphism  = 4Nm low m, N Ratio D/q = 2mt /4Nm = t/2N Divergence D = 2 (low m ) D = 2 (high ) t (in generations)  

10. The HKA test of selection • Compares the level of polymorphism within species with the level of divergence between species • Expected level of polymorphism is estimated from the level of divergence • Ratio of polymorphism to divergence should be the same for all neutral loci and is set by the mutation rate for a locus • Level of neutral divergence should be unaffected by occasional selective sweeps

11. Hudson Kreitman Aguadé test

12. The “footprint” of balancing selection at Adh in Drosophila Adapted from Kreitman and Hudson (1991) Genetics 127:565-82 polymorphism Adh-dup Adh locus Fast/Slow polymorphism Adjacent silent sites in linkage disequilibrium Fast F Fast F Adh Adh-dup 16 20 Fast F Fast F Slow S 50 13 Slow S Slow S Slow S Distant sites in Linkage Equiluilibrium P < 0.02

13. Effect of selective sweep on linked sites

14. Behavior of selection statistics around the target of selection Nielsen, Annu. Rev. Genet. 2005. 39:197–218

15. Selective sweep in Microcephalin

16. N=12 N=8 N=8 N=8 N=8 Zebra Finch: a population genomics model system 10 kb 2kb Seven ‘locus trios’ Locus 1 Locus 2 Locus 3 Balakrishnan, C.B. & Edwards, S. V. 2009. Genetics 181: 645-660

17. Reduced polymorphism in island finches Australian mainland Timor (island) 0.03 p = 0.01 p = 0.003 0.025 0.02 Nucleotide diversity 0.015 0.01 0.005 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Austosomes Z chromosome 13 monomorphic loci in island finches Balakrishnan, C.B. & Edwards, S. V. 2009. Genetics 181: 645-660

18. Low levels of linkage disequilibrium in mainland birds LD measured in r2

19. Enhanced LD in island zebra finches Balakrishnan, C.B. & Edwards, S. V. 2009. Genetics 181: 645-660

20. The effect of selection and mutation on levels of variability within and between species Nielsen, Annu. Rev. Genet. 2005. 39:197–218

21. A plethora of statistical tests of departures from neutrality