Abstract
Abstract Identifying genomic regions underlying adaptation in extant lineages is key to understanding the trajectories along which biodiversity evolves. However, this task is complicated by evolutionary processes that obscure and mimic footprints of positive selection. Particularly, the long-term effects of linked selection remain underappreciated and difficult to account for. Based on patterns emerging from recent research on the evolution of differentiation across the speciation continuum, I illustrate how long-term linked selection affects the distribution of differentiation along genomes. I then argue that a comparative population genomics framework that exploits emergent features of long-term linked selection can help overcome shortcomings of traditional genome scans for adaptive evolution, but needs to account for the temporal dynamics of differentiation landscapes.
Highlights
Background selectionA process by which purifying selection against deleterious variants results in a loss of neutral genetic diversity at linked sites
While genomic regions of accentuated differentiation have commonly been interpreted as a footprint of ecological adaptation or selection against gene flow, awareness is increasing that such an approach is naïve towards the vast recombination rate variation found in many species, the long-term effects of linked selection associated therewith, and the contribution of BGS therein
Long-term linked selection in heterogeneous recombination landscapes leads to the evolution of highly heterogeneous differentiation landscapes
Summary
Identifying genomic regions underlying adaptation in extant lineages is key to understand the trajectories along which biodiversity evolves This task is complicated by evolutionary processes that obscure and mimic footprints of positive selection. I argue that a comparative population genomics framework that exploits emergent features of long-term linked selection can help overcome shortcomings of traditional genome scans for adaptive evolution, but needs to account for the temporal dynamics of differentiation landscapes. The past years have seen an unprecedented quest for such regions (Haasl & Payseur 2016) that assumed accentuated differentiation to evolve trough processes related to adaptation or speciation, in particular positive selection of beneficial variants (Maynard Smith & Haigh 1974; Kaplan et al 1989) or selection against gene flow (Turner et al 2005) in extant populations or species (in the following referred to as ‘extant lineages‘, see Glossary). Outlining how emergent features of long-term linked selection can be exploited to empirically take into account the long-term effects of linked selection in a comparative population genomics framework that takes into account the temporal dynamics of differentiation landscapes
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