Exploring the genomic architecture of species and populations divergence aids understanding how lineages evolve and adapt, and ultimately how repeatable evolution is. Yet, the genomic signatures associated with divergence are still relatively unexplored, leading to a knowledge gap on whether species divergence ultimately differs in its genetic architecture from divergence at other spatial scales (i.e. populations, ecotypes). Here we asked whether genomic islands of speciation are repeatedly more prone to harbor within-species differentiation due to genomic features, such as suppressed recombination, smaller effective population size and increased drift, across repeated hierarchically nested levels of divergence. We used two species of Phaseolus beans with strong genepool and population sub-structure and multiple independent domestications each. We genotyped 13,213 GBS-derived SNP markers in 209 individuals of wild and cultivated P. vulgaris and P. lunatus.
Results/Conclusions
We identified six regions for species-associated divergence. Out of these divergence peaks, 21% were recovered in the four within-species between-genepools comparisons and in the five within-genepool wild-cultivated comparisons (some of the latter did retrieve genuine signatures of the well described multiple domestication syndromes). However, regions with overall high relative differentiation (FST) coincided, independent of the scale of divergence, with sections of low SNP density, and for the between-genepools comparisons with regions of elevated delta divergence (ΔDiv). The divergence in chromosome Pv10 further coincided with a between-species pericentric inversion. These convergences suggests that shared variants are being recurrently fixed at replicated comparisons, and in a similar manner across different hierarchically nested levels of divergence, likely as result of genomic features that make certain regions more prone to accumulate islands of speciation as well as within-species divergence. In other words, neighboring signatures of speciation, adaptation and domestication in Phaseolus beans are influenced by ubiquitous genomic constrains, which may continue shaping, fortuitously, genomic differentiation at various others scales of divergence.