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.

Figure 1. Low to moderate overall genetic differentiation between the two subspecies of rabbits.

A) Histogram of F_ST values for all SNPs and SNPs showing a minor allele frequency (MAF) of 10%. B) Pie chart summarizing the proportion of fixed, shared and exclusive polymorphisms.

Figure 2. Levels of differentiation between subspecies varied greatly across the genome.

Chromosomal distribution of genetic differentiation for all rabbit chromosomes. Each data point is based on a sliding window analysis using 100 kb windows with 10 kb steps. The solid black line denotes a Z-score of three (three standard deviations departing from the median F_ST over all windows). The relative proportion of fixed (red) versus shared (gray) polymorphism for each window is indicated below the graph (F/S).

Figure 3. Regions of high differentiation are enriched for regions undergoing low rates of gene exchange.

Mean RND (A) and Fays and Wu's H values (B) for intronic fragments contained within and outside regions of differentiation. Regions of differentiated were defined both based on the proportion of fixed differences to shared polymorphisms and on a Z-score higher than three (three standard deviations departing from the median F_ST over all windows)). N.S. – non significant. Asterisks designate significant differences (t-test) for each comparison (*P<0.05; **P<0.01; ***P<0.001).

Figure 4. Highly heterogeneous size of differentiated regions.

Histogram summarizing the physical size (Kb) of independent regions of differentiation between rabbit subspecies.

Figure 5. Larger regions of differentiation were found close to centromeres.

Size of differentiated regions (Mb) relative to distance to the centromere (Mb) both for the autosomes (left panel) and X-chromosome (right panel).