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An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes
Molecular Ecology ( IF 4.9 ) Pub Date : 2021-05-19 , DOI: 10.1111/mec.15989
Yann X C Bourgeois 1 , Ben H Warren 2
Affiliation  

Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.

中文翻译:

当前用于分析真核生物全基因组重测序数据的群体基因组学方法概述

表征一个物种的种群历史并确定潜在的局部适应位点在功能生态学、进化生物学、保护和农学中至关重要。高通量测序技术的不断改进促进了广泛物种全基因组数据的产生。人口基因组学现在提供了将选择更好地整合到历史框架中的工具,并在重建人口历史时考虑到选择。然而,这种改进伴随着大量分析工具,这些工具可能会使用户感到困惑和沮丧。这种混淆限制了从复杂基因组数据集中有效检索的信息量,并损害了最新分析工具在保护生物学等领域的传播。它还可能导致方法之间的冗余。为了解决这些问题,我们提出了 100 多种可以处理全基因组数据的最先进方法的概述。我们总结了他们用来推断人口历史和选择的策略,并讨论了它们的一些局限性。可在 www.methodspopgen.com 上找到列出这些方法的网站。
更新日期:2021-05-19
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