Dissecting differentiation landscapes: a linked selection's perspective
Journal of Evolutionary Biology 30 (8): 1501-1505 (2017)

Eased on the assumption that locally accentuated dif- ferentiation within genomes represents a footprint of positive selection or barriers to gene flow, the last dec- ade’s quest for genomic regions involved in adaptation and speciation has led to the description of differentia- tion landscapes in numerous taxa (e.g. Ellegren et al., 2012; Jones et al., 2012; Renaut et al., 2013; Soria-Car- rasco et al., 2014). A major common pattern emerging from this research is a usually striking heterogeneity of differentiation along the genome, with regions of accentuated differentiation widespread across otherwise less differentiated genomes – as widespread and in sev- eral cases so markedly codistributed with genomic fea- tures (e.g. White et al., 2010; Burri et al., 2015), as to question these regions’ role in speciation (Noor & Ben- nett, 2009; Nachman & Payseur, 2012; Cruickshank & Hahn, 2014). In their review, Ravinet et al. (2017) discuss the com- plex evolution of differentiation landscapes, involving multiway interactions of diverse processes, and propose a road map through the challenge of disentangling the footprints of speciation from those of confounding pro- cesses. Here, I outline a few complementary angles from a linked selection’s perspective. (i) I revisit the effects of linked selection, suggesting that they may depend on the dynamics of recombination rate evolu- tion. (ii) I then emphasize the need for analyses to tar- get the most likely footprints of speciation given a system’s evolutionary history and its history of linked selection. (iii) Finally, I highlight how long-range sequencing will empower the characterization of geno- mic landscapes beyond differentiation.
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