The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

Abstract

The analysis of introgression of genomic regions between divergent populations provides an excellent opportunity to determine the genetic basis of reproductive isolation during the early stages of speciation. However, hybridization and subsequent gene flow must be relatively common in order to localize individual loci that resist introgression. In this study, we used next-generation sequencing to study genome-wide patterns of genetic differentiation between two hybridizing subspecies of rabbits ( Oryctolagus cuniculus algirus and O. c. cuniculus) that are known to undergo high rates of gene exchange. Our primary objective was to identify specific genes or genomic regions that have resisted introgression and are likely to confer reproductive barriers in natural conditions. On the basis of 326,000 polymorphisms, we found low to moderate overall levels of differentiation between subspecies, and fewer than 200 genomic regions dispersed throughout the genome showing high differentiation consistent with a signature of reduced gene flow. Most differentiated regions were smaller than 200 Kb and contained very few genes. Remarkably, 30 regions were each found to contain a single gene, facilitating the identification of candidate genes underlying reproductive isolation. This gene-level resolution yielded several insights into the genetic basis and architecture of reproductive isolation in rabbits. Regions of high differentiation were enriched on the X-chromosome and near centromeres. Genes lying within differentiated regions were often associated with transcription and epigenetic activities, including chromatin organization, regulation of transcription, and DNA binding. Overall, our results from a naturally hybridizing system share important commonalities with hybrid incompatibility genes identified using laboratory crosses in mice and flies, highlighting general mechanisms underlying the maintenance of reproductive barriers.

Author Summary

A number of laboratory studies of speciation have uncovered individual genes that confer lower fitness when in a divergent genetic background. It is, however, unclear whether these genes were ever relevant to restricting gene flow in nature, or whether they are indirect consequences of functional divergence between species that in most cases can no longer hybridize in natural conditions. Analysis of introgression across the genome of divergent populations provides an alternative approach to determine the genetic basis of reproductive isolation. Using two subspecies of rabbits as a model for the early stages of speciation, we provide a genome-wide map of genetic differentiation. Our study revealed important aspects of the genetic architecture of differentiation in the early stages of divergence and allowed the identification of genomic regions that resist introgression and are likely to confer reproductive barriers in natural conditions. The gene content of these regions, which in several cases reached gene-level resolution, suggests an important role for epigenetic and transcription regulation in the maintenance of reproductive barriers. Some of the genes identified here in a natural system are similar in function to the hybrid male sterility genes identified in laboratory studies of speciation.