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

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

Adaptive evolution in human brain development genes

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

Sampling localities of babblers Carpentarian barrier temporalis rubeculus

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 

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

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 

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

Hudson Kreitman Aguadé test

Fast/Slow polymorphism Adh locus Adh-dup polymorphism 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

Effect of selective sweep on linked sites

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

Selective sweep in Microcephalin

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 Genetics 181:

Nucleotide diversity Balakrishnan, C.B. & Edwards, S. V Genetics 181: Reduced polymorphism in island finches 13 monomorphic loci in island finches Australian mainlandTimor (island) AustosomesZ chromosome  = 0.01  = 0.003

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

Enhanced LD in island zebra finches Balakrishnan, C.B. & Edwards, S. V Genetics 181:

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

A plethora of statistical tests of departures from neutrality