Phylogenomics of the genus Alectoris: parapatry, introgression, and speciation in the Palearctic

Often regarded as an excellent model system for investigating the evolutionary history of Palaearctic vertebrates, the genus Alectoris comprises seven closely related polytypic species with allopatric or parapatric distributions: the red-legged partridge (A. rufa), the rock partridge (A. graeca), the chukar partridge (A. chukar), the rusty-necklaced partridge (A. magna), the Barbary partridge (A. barbara), the Arabian partridge (A. melanocephala), and Philby's partridge (A. philbyi). However, no genomic study has yet comprehensively examined the evolutionary dynamics of the genus as a whole. In this study, we re-sequenced the genomes of 25 Alectoris individuals and included re-sequencing data from 10 additional individuals. We recovered more than 3,700 ultraconserved elements (UCEs), identifying 21,706,368 SNPs at a genotyping rate of 94%. Our analyses revealed four major lineages: two basal lineages represented by the Afro-Arabian species A. melanocephala and A. barbara; a European lineage comprising A. rufa and A. graeca; and an Asian lineage including A. chukar, A. magna, and A. philbyi. The phylogenetic tree was supported by both concatenation and species tree based approaches. We detected multiple signatures of introgression with notable gene flow between eastern A. chukar populations with A. magna and A. philbyi with other Alectoris lineages. While some reflect the intensive management and translocation practices to which several species have been subjected and were therefore expected, others appear to preserve signals of historical connectivity among populations that are currently isolated. This is particularly evident in the case of A. chukar and A. philbyi, whose genomic patterns suggest past gene flow despite their present-day geographic separation. Comparison of regions of introgression across the genomes identified some areas to be more permeable to gene flow compared to others.