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Going down the rabbit hole: a review on methods for population genomics in natural populations

Yann X.C. Bourgeois, Khaled M. Hazzouri
doi: https://doi.org/10.1101/052761
Yann X.C. Bourgeois
New York University Abu Dhabi, PO Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates
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Khaled M. Hazzouri
New York University Abu Dhabi, PO Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates
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Abstract

  1. Characterizing species history and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The ongoing and constant improvement of next-generation sequencing (NGS) techniques has facilitated the production of an increasingly growing amount of genetic markers across genomes of non-model species.

  2. The study of variation at these markers across natural populations has deepened the understanding of how population history and selection act on genomes. However, this improvement has come with a burst of analytical tools that can confuse users.

  3. This confusion can limit the amount of information effectively retrieved from complex genomic datasets. In addition, the lack of a unified analytical pipeline impairs the diffusion of the most recent analytical tools into fields like conservation biology.

  4. This requires efforts be made in providing introduction to these methods. In this paper we describe possible analytical protocols and list more than 70 methods dealing with genome-scale datasets, clarify the strategy they use to infer demographic history and selection, and discuss some of their limitations.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 16, 2017.
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Going down the rabbit hole: a review on methods for population genomics in natural populations
Yann X.C. Bourgeois, Khaled M. Hazzouri
bioRxiv 052761; doi: https://doi.org/10.1101/052761
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Going down the rabbit hole: a review on methods for population genomics in natural populations
Yann X.C. Bourgeois, Khaled M. Hazzouri
bioRxiv 052761; doi: https://doi.org/10.1101/052761

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