Daniel L. Hartl
- Published in print:
- 2020
- Published Online:
- August 2020
- ISBN:
- 9780198862291
- eISBN:
- 9780191895074
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/oso/9780198862291.003.0007
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics
Chapter 7 is an introduction to molecular population genetics that includes the principal concepts of nucleotide polymorphism and divergence, the site frequency spectrum, and tests of selection and ...
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Chapter 7 is an introduction to molecular population genetics that includes the principal concepts of nucleotide polymorphism and divergence, the site frequency spectrum, and tests of selection and their limitations. Highlighted are rates of nucleotide substitution in coding and noncoding DNA, nucleotide and amino acid divergence between species, corrections for multiple substitutions, and the molecular clock. Discussion of the folded and unfolded site frequency spectrum includes the strengths and limitations of Tajima’s D, Fay and Wu’s H, and other measures. The chapter also discusses an emerging consensus to resolve the celebrated selection–neutrality controversy. It also includes examination of demographic history through the use of ancient DNA with special emphasis on the surprising findings in regard to the ancestral makeup of contemporary human populations. Also discussed are the population dynamics of transposable elements in prokaryotes and eukaryotes.Less
Chapter 7 is an introduction to molecular population genetics that includes the principal concepts of nucleotide polymorphism and divergence, the site frequency spectrum, and tests of selection and their limitations. Highlighted are rates of nucleotide substitution in coding and noncoding DNA, nucleotide and amino acid divergence between species, corrections for multiple substitutions, and the molecular clock. Discussion of the folded and unfolded site frequency spectrum includes the strengths and limitations of Tajima’s D, Fay and Wu’s H, and other measures. The chapter also discusses an emerging consensus to resolve the celebrated selection–neutrality controversy. It also includes examination of demographic history through the use of ancient DNA with special emphasis on the surprising findings in regard to the ancestral makeup of contemporary human populations. Also discussed are the population dynamics of transposable elements in prokaryotes and eukaryotes.
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.
