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Ancestral Population Genomics

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Evolutionary Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 856))

Abstract

The full genomes of several closely related species are now available, opening an emerging field of investigation borrowing both from population genetics and phylogenetics. Providing we can properly model sequence evolution within populations undergoing speciation events, this resource enables us to estimate key population genetics parameters, such as ancestral population sizes and split times. Furthermore, we can enhance our understanding of the recombination process and investigate various selective forces. We discuss the basic speciation models for closely related species, including the isolation and isolation-with-migration models. A major point in our discussion is that only a few complete genomes contain much information about the whole population. The reason being that recombination unlinks genomic regions, and therefore a few genomes contain many segments with distinct histories. The challenge of population genomics is to decode this mosaic of histories in order to infer scenarios of demography and selection. We survey different approaches for understanding ancestral species from analyses of genomic data from closely related species. In particular, we emphasize core assumptions and working hypothesis. Finally, we discuss computational and statistical challenges that arise in the analysis of population genomics data sets.

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Acknowledgments

The authors would like to thank Thomas Mailund for providing useful comments on this chapter. This publication is contribution 2011-035 of the Institut des Sciences de l’Évolution de Montpellier (UMR 5554—CNRS). This work was supported by the French Agence Nationale de la Recherche “Domaines Emergents” (ANR-08-EMER-011 “PhylAriane”).

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Authors and Affiliations

  1. Institut des Sciences de l’Évolution Montpellier (ISE-M), UMR 5554, CNRS, Unversité Montpellier, Montpellier, France

    Julien Y. Dutheil

  2. Bioinformatics Research Center (BiRC), Aarhus University, Aarhus, Denmark

    Asger Hobolth

Authors
  1. Julien Y. Dutheil
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  2. Asger Hobolth
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Corresponding author

Correspondence to Julien Y. Dutheil .

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Editors and Affiliations

  1. Department of Computer Science, ETH Zürich, Universitätsstr. 6, Zürich, 8092, Switzerland

    Maria Anisimova

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Dutheil, J.Y., Hobolth, A. (2012). Ancestral Population Genomics. In: Anisimova, M. (eds) Evolutionary Genomics. Methods in Molecular Biology, vol 856. Humana Press. https://doi.org/10.1007/978-1-61779-585-5_12

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  • DOI: https://doi.org/10.1007/978-1-61779-585-5_12

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-584-8

  • Online ISBN: 978-1-61779-585-5

  • eBook Packages: Springer Protocols

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