Genome-wide SNVs revealed reticulate evolutionary history of a Eurasian-African songbird radiation (Saxicola torquatus complex)

Phylogenomics has the power to reveal complex evolutionary hypotheses across taxa, thereby allowing important glimpses into the evolutionary history, such as incomplete lineage sorting (ILS) and introgression among closely related species. The Saxicola torquatus complex comprises several widely distributed insectivorous bird species across the Palearctic and Afrotropical realms. Nevertheless, the evolutionary history within this complex remains contentious, and previous findings suggest complications caused by cytonuclear discordance. Here, we conducted a phylogenomic analysis of nearly complete taxa within the complex using genome-wide single nucleotide variants to investigate potential causes of phylogenetic discordance across genomic regions and elucidate its evolutionary history. We detected multiple reticulate events during their diversification, leading to extensive phylogenetic discordance across the genome. The mitochondrial genome and non-recombining region of the W chromosome exhibited a consistent gene tree that conflicted with the species tree, with introgression being the most plausible explanation among several hypotheses. The Z chromosome was less affected by ILS/introgression and exhibited relatively stable local phylogenies compared to autosomes. Furthermore, we found that strongly introgressed regions were predominantly concentrated at the ends of smaller chromosomes, and the strength of introgression among species pairs showed consistently positive correlations, likely attributed to shared recombination hotspots in these regions. These findings stress the heterogeneous genomic landscape influenced by intricate evolutionary processes (e.g., ILS, introgression, and recombination) that endorse a reticulate evolution model for global speciation in the S. torquatus complex.