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A Primer of Molecular Population Genetics$
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Asher D. Cutter

Print publication date: 2019

Print ISBN-13: 9780198838944

Published to Oxford Scholarship Online: August 2019

DOI: 10.1093/oso/9780198838944.001.0001

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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: 06 May 2021

Genealogy in evolution

Genealogy in evolution

(p.85) Chapter 5 Genealogy in evolution
A Primer of Molecular Population Genetics

Asher D. Cutter

Oxford University Press

Chapter 5, “Genealogy in evolution,” introduces branching tree diagrams as an intuitive way to visualize the evolutionary relationships between alleles, haplotypes, individuals, and species. It describes the nomenclature of gene tree topologies, the stochasticity in tree shape across genes, and the notion of a most recent common ancestor. This chapter also covers reverse-time genealogical thinking with coalescent theory and how it integrates with predictions about nucleotide polymorphism and the site frequency spectrum. An overview of how phylogenies show between-species genealogical relationships is used to highlight the concepts of orthology and homoplasy, how to calculate and interpret different metrics of DNA sequence divergence, the role of ancestral polymorphism in creating distinct gene trees, the multiple mutational hits problem, and factors that influence calculations of the time to the most recent common ancestor for species trees versus gene trees. This chapter surveys how to think of evolution in terms of genealogies that relate gene copies within a species or among species, and how to connect ideas about gene trees to other ideas in molecular population genetics.

Keywords:   genealogy, phylogeny, coalescent theory, species trees, substitution rates, sequence divergence, orthology, multiple mutational hits, incomplete lineage sorting

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