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 ever-increasing number of genetic markers across genomes of non-model species. 2. The study of variation in these markers across natural populations has deepened the understanding of how population history and selection act on genomes. 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 burst of analytical tools that can confuse users. 3. Such 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. To address this need, we describe possible analytical protocols and link these with more than 70 methods dealing with genome-scale datasets. We summarise 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.
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