Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

Abstract

The metaphor of 'genomic islands of speciation' was first used to describe heterogeneous differentiation among loci between the genomes of closely related species. The biological model proposed to explain these differences was that the regions showing high levels of differentiation were resistant to gene flow between species, while the remainder of the genome was being homogenized by gene flow and consequently showed lower levels of differentiation. However, the conditions under which such differentiation can occur at multiple unlinked loci are restrictive; additionally, essentially, all previous analyses have been carried out using relative measures of divergence, which can be misleading when regions with different levels of recombination are compared. Here, we test the model of differential gene flow by asking whether absolute divergence is also higher in the previously identified 'islands'. Using five species pairs for which full sequence data are available, we find that absolute measures of divergence are not higher in genomic islands. Instead, in all cases examined, we find reduced diversity in these regions, a consequence of which is that relative measures of divergence are abnormally high. These data therefore do not support a model of differential gene flow among loci, although islands of relative divergence may represent loci involved in local adaptation. Simulations using the program IMa2 further suggest that inferences of any gene flow may be incorrect in many comparisons. We instead present an alternative explanation for heterogeneous patterns of differentiation, one in which postspeciation selection generates patterns consistent with multiple aspects of the data.

Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

“…It is possible that differences in historical demography between these two species may contribute to different N eZ /N eA ratios. The lower genetic diversity of C. minimus reported here and elsewhere (Oyler-McCance et al, 1999, 2005b) is consistent with a genetic bottleneck or founder event and may inflate divergence estimates (F ST ) between species (Charlesworth, 1998;Cruickshank and Hahn, 2014). Both species have experienced significant population declines in recent history (Young et al, 2000;Schroeder et al, 2004) yet the demographic history of C. minimus may be much more severe with fewer than 5000 individuals remaining (Young et al, 2000) compared with an estimated 100 000-500 000 C. urophasianus (USFWS, 2010).…”

No evidence for maintenance of a sympatricHeliconiusspecies barrier by chromosomal inversions

“…We also calculated F ST , d XY , and f d (Cruickshank and Hahn 2014; Martin et al. 2015a) across inverted regions (Figs.…”

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

“…Several mechanisms could promote initial divergence at a few genomic regions while most of the genome remains homogenized through gene flow (Kondrashov and Kondrashov, 1999;Via, 2009;Feder and Nosil, 2010;Yeaman and Otto, 2011;Yeaman and Whitlock, 2011;Feder et al, 2012; see, however, Cruickshank and Hahn, 2014). Consequently, the distribution of divergence estimates across the genome is predicted to be L-shaped, with only a few loci showing high estimates, when population divergence is estimated at early stages of divergence.…”