Sequence signatures of selection and demography
Chapter 8, “Molecular deviants: sequence signatures of selection and demography,” dives into the logic and mechanics of some of the most common tests of neutrality to show how and why data can reveal differences from the predictions of the standard neutral model. It introduces approaches based on skewed patterns of polymorphism alone, including Tajima’s D test, and on differentiation or divergence alone, like the Lewontin-Krakauer, Population Branch Statistic (PBS), and KA / KS relative-rates tests. Chapter 8 also covers tests of neutrality that integrate information from both within and between species, including the HKA-test and McDonald-Kreitman (MK) test. The logic for other tests of neutrality also is introduced, including ABBA-BABA, Composite Likelihood Ratio (CLR), Extended Haplotype Homozygosity (EHH), and other approaches. Practical implications of ancestral polymorphism and slightly deleterious polymorphisms are discussed, for example, in calculating and interpreting the neutrality index and fraction of positively selected sites (α). The goal of this chapter is to explain the logic of methods applied to molecular population genetic data to read the story of evolutionary history from the genome.
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