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 selective sweep balancing selection neutral  D = 0  Many low frequency variants and singletons, D negative  Pairwise differences (k) increase faster than S D positive

6. Sampling localities of babblers Carpentarian barrier temporalis rubeculus

7. Tajima’s test of neutrality for 12 populations (A-K) 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) Tajima’s D =  (or k) -  D  (K same as 

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

9. Neutral polymorphism and divergence D = 2   (low  ) t (in generations)   Divergence Polymorphism  = 4N  low  Polymorphism  = 4N  high  D = 2   (high  ) Ratio D/  2  t / 4N  t 

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

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

17. 0 0.005 0.01 0.015 0.02 0.025 0.03 1234567891011121314151617181920212223242526 Nucleotide diversity Balakrishnan, C.B. & Edwards, S. V. 2009. Genetics 181: 645-660 Reduced polymorphism in island finches 13 monomorphic loci in island finches Australian mainlandTimor (island) AustosomesZ chromosome  = 0.01  = 0.003

18. Low levels of linkage disequilibrium in mainland birds LD measured in r 2

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