Bruce Walsh and Michael Lynch
- Published in print:
- 2018
- Published Online:
- September 2018
- ISBN:
- 9780198830870
- eISBN:
- 9780191868986
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/oso/9780198830870.003.0010
- Subject:
- Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology
This chapter examines the search for a pattern of repetitive adaptive substitutions over evolutionary time. In contrast with the previous chapter, only a modest number of tests toward this aim have ...
More
This chapter examines the search for a pattern of repetitive adaptive substitutions over evolutionary time. In contrast with the previous chapter, only a modest number of tests toward this aim have been proposed. The HKA and McDonald-Kreitman tests contrast the polymorphism to divergence ratio between different genomic classes (such as different genes or silent versus replacement sites within the same gene). These approaches can detect an excess of substitutions, which allows one to estimate the fraction of adaptive sites. This chapter reviews the empirical data on estimates of this fraction and discusses some of the sources of bias it its estimation. Over an even longer time scale, one can contrast the rate of change of sites in a sequence over a phylogeny. These tests require a rather special type of selection, wherein the same specific site (usually a codon) experiences multiple adaptive substitutions over a phylogeny, such as might occur in arms-race genes.Less
This chapter examines the search for a pattern of repetitive adaptive substitutions over evolutionary time. In contrast with the previous chapter, only a modest number of tests toward this aim have been proposed. The HKA and McDonald-Kreitman tests contrast the polymorphism to divergence ratio between different genomic classes (such as different genes or silent versus replacement sites within the same gene). These approaches can detect an excess of substitutions, which allows one to estimate the fraction of adaptive sites. This chapter reviews the empirical data on estimates of this fraction and discusses some of the sources of bias it its estimation. Over an even longer time scale, one can contrast the rate of change of sites in a sequence over a phylogeny. These tests require a rather special type of selection, wherein the same specific site (usually a codon) experiences multiple adaptive substitutions over a phylogeny, such as might occur in arms-race genes.
Asher D. Cutter
- Published in print:
- 2019
- Published Online:
- August 2019
- ISBN:
- 9780198838944
- eISBN:
- 9780191874826
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/oso/9780198838944.003.0008
- Subject:
- Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology
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 ...
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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.Less
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.
