Abstract
Identifying genomic regions underlying adaptation in extant lineages is key to understand 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.
Glossary
- Background selection
- A process by which purifying selection against deleterious variants results in a loss of neutral genetic diversity at linked sites.
- Extant lineages (extant populations, extant species)
- Non-ancestral lineages, i.e. lineages observed today including the time since the split from their ancestor.
- Genomic landscapes
- The distribution of parameters, such as diversity (‘diversity landscape’), differentiation (‘differentiation landscape’) or recombination rates (‘recombination landscape’) along chromosomes.
- Hitchhiking/recurrent hitchhiking
- A process by which positive selection for a beneficial variant leads to an increase in frequency of neutral variants at linked sites, and thus loss of neutral diversity at linked sites. If hitchhiking affects the same genomic region repeatedly, the process is referred to as recurrent hitchhiking.
- Linked selection
- The process by which neutral genetic diversity in the genome is lost as an effect of selection at a linked site. Both background selection and hitchhiking contribute to linked selection.
