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A Primer of Population Genetics and Genomics$
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Daniel L. Hartl

Print publication date: 2020

Print ISBN-13: 9780198862291

Published to Oxford Scholarship Online: August 2020

DOI: 10.1093/oso/9780198862291.001.0001

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PRINTED FROM OXFORD SCHOLARSHIP ONLINE (oxford.universitypressscholarship.com). (c) Copyright Oxford University Press, 2021. All Rights Reserved. An individual user may print out a PDF of a single chapter of a monograph in OSO for personal use. date: 23 January 2022

Molecular Population Genetics

Molecular Population Genetics

(p.179) Chapter 7 Molecular Population Genetics
A Primer of Population Genetics and Genomics

Daniel L. Hartl

Oxford University Press

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.

Keywords:   nucleotide substitution, nucleotide divergence, molecular clock, site frequency spectrum, codon usage bias, Poisson random field, MacDonald–Kreitman test, demographic history, ancient DNA, transposable elements

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