Abstract
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.
Highlights
Comprehensive analyses of species history and selection contribute to our understanding of causation in biology, an effort that has included genetics, developmental science and ecology (Laland et al, 2011)
Investigating variation across multiple genomes sampled across populations or closely related species is a common task for teams studying evolutionary processes, who can rely on a diverse array of methods to infer demography and selection
| 29 inference of loci under selection and quantification of demographic dynamics is of crucial importance in fields such as landscape genomics or the study of ongoing speciation
Summary
Comprehensive analyses of species history and selection contribute to our understanding of causation in biology, an effort that has included genetics, developmental science and ecology (Laland et al, 2011). Increased data production has been accompanied by a drive to develop efficient computational methods to interpret patterns of genetic variation at the genomic scale These interconnected developments have allowed species histories to be inferred even when little preliminary knowledge is available. Investigating variation across multiple genomes sampled across populations or closely related species is a common task for teams studying evolutionary processes, who can rely on a diverse array of methods to infer demography and selection. While large-scale collaborations and sharing of skills between researchers allow for detailed analyses, a global summary of methods that can handle whole-genome resequencing data would be valuable for smaller research teams, so they can quickly start new projects and evaluate their experimental design It would facilitate communication between different subfields of evolutionary biology, by providing a common resource that can be used to identify methodological convergence and possible synergies. Pedigrees can assist phasing for short-read data (useful for reconstructing haplotypes and estimate recombination rates)
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