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Evolution and Selection of Quantitative Traits$
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Bruce Walsh and Michael Lynch

Print publication date: 2018

Print ISBN-13: 9780198830870

Published to Oxford Scholarship Online: September 2018

DOI: 10.1093/oso/9780198830870.001.0001

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Using Molecular Data to Detect Selection: Signatures from Multiple Historical Events

Using Molecular Data to Detect Selection: Signatures from Multiple Historical Events

Chapter:
(p.343) 10 Using Molecular Data to Detect Selection: Signatures from Multiple Historical Events
Source:
Evolution and Selection of Quantitative Traits
Author(s):

Bruce Walsh

Michael Lynch

Publisher:
Oxford University Press
DOI:10.1093/oso/9780198830870.003.0010

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.

Keywords:   codon-based models, fraction of adaptive substitutions, HKA test, Hudson-Kreitman-Aguade test, Ka to Ks ratio, McDonald-Kreitman test, Poisson random field model, rate of adaptive substitutions

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