Range expansion underlies historical introgressive hybridization in the Iberian hare

Abstract

Introgressive hybridization is an important and widespread evolutionary process, but the relative roles of neutral demography and natural selection in promoting massive introgression are difficult to assess and an important matter of debate. Hares from the Iberian Peninsula provide an appropriate system to study this question. In its northern range, the Iberian hare, Lepus granatensis, shows a northwards gradient of increasing mitochondrial DNA (mtDNA) introgression from the arctic/boreal L. timidus, which it presumably replaced after the last glacial maximum. Here, we asked whether a south-north expansion wave of L. granatensis into L. timidus territory could underlie mtDNA introgression, and whether nuclear genes interacting with mitochondria ("mitonuc" genes) were affected. We extended previous RNA-sequencing and produced a comprehensive annotated transcriptome assembly for L. granatensis. We then genotyped 100 discovered nuclear SNPs in 317 specimens spanning the species range. The distribution of allele frequencies across populations suggests a northwards range expansion, particularly in the region of mtDNA introgression. We found no correlation between variants at 39 mitonuc genes and mtDNA introgression frequency. Whether the nuclear and mitochondrial genomes coevolved will need a thorough investigation of the hundreds of mitonuc genes, but range expansion and species replacement likely promoted massive mtDNA introgression.

Figure 1

Geographic distribution of four hare species in the Iberian Peninsula (a,c) and Western Europe (b) (approximate distributions were based on Mitchel-Jones et al.57). (a) Localities sampled for L. granatensis (see Supplementary Table S1 for a detailed description); numbers indicate sample size, pie charts the proportion of STRUCTURE assignment to each of 3 clusters using the LOC prior and the complete SNP dataset (100 loci); the “X” marks the inferred origin of the range expansion; grey letters indicate specimens for which RNA was sequenced and used to build the transcriptome (“d-n” from Cahais et al. and Gayral et al., and “o” from this work). (b) Localities sampled for L. timidus, indicating the sample sizes; two sampling localities are not shown on this map (RUS – Russia; and FER – Far East Russia). (c) Proportion of the mitochondrial DNA lineages, native L. granatensis or introgressed from L. timidus, in the genotyped samples. Maps were generated in vectorial format using Inkscape v0.91 (https://inkscape.org).

Figure 2

Organization of genetic diversity in Lepus granatensis from the analysis of 100 SNP loci (see Supplementary Figs S2–S5 for a complete description of the results obtained with several subsets of the dataset): (a) Structure plots with individual assignment to 3 clusters, as determined using Evanno’s delta K method, and using the sample locations as priors of the admixture model; population codes as in Fig. 1; (b) coordinates of samples on the first two axes of variation determined with a Principal Component Analysis (PCA) (stars correspond to specimens from Northwestern Iberian population GAL; see Fig. 1); (c) Correlation between the first two PCA axes of variation and geographical coordinates of sample localities (Spearman rank correlation, p = 0.00 for both analyses; dashed line indicates a linear regression trendline); (d) correlation between genetic differentiation and geographic distance among pairs of populations (Spearman rank correlation, p = 0.00; dashed line indicates a linear regression trendline).