Iberian hares with anciently introgressed mitochondrial DNA express a marginal environmental niche

Aim The role of mitochondrial DNA (mtDNA) in local adaptation has been thoroughly debated, and the ancient pervasive mtDNA introgression from Lepus timidus into Lepus granatensis allows testing of this hypothesis. Here, we study the environmental niche of animals with introgressed mtDNA, to gain insights about the potential selective pressures maintaining the introgressed haplotypes. Location Iberian Peninsula. Taxon Lepus granatensis . Methods We modelled the frequency of the L. timidus mtDNA lineage within the L. granatensis distribution area. The response variable was the presence of the L. timidus lineage at the individual level. Finally, the variation in the introgression frequencies was plotted along the environmental gradients (identified by the models), after controlling for latitude. Results The results showed that (i) the niche of the introgressed populations occupy marginal environmental conditions relative to the complete niche of L . granatensis , (ii) both latitude and environment, and their overlaid effects, explain the variation in the introgression frequencies, and (iii) after controlling for latitude, clines in mtDNA introgression frequency are associated with transitions in the environmental gradients, even when the analyses were restricted to the territory where the introgressed haplotypes occur. Main Conclusions While the strict demographic explanation for mtDNA introgression in L. granatensis implies that geography, resulting from the post‐glacial expansion of the species, explains the gradients of introgression, our results show correlations with environmental gradients that are not geographically structured. Our results relate the prevalence of introgressed mtDNA with more extreme climatic conditions in the range of L . granatensis , suggesting that environmental selective pressures could have played a role in determining the spatial maintenance of mtDNA haplotypes originating from the cold‐adapted species. These results are thus relevant to understand the response of the species to the ongoing processes of global change, which will alter the selective pressures by reducing the specific niche of the introgressed mtDNA lineage.