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.
