Integrating Mitochondrial, Genomic and Species Distribution Model Approaches in the Reconstruction of the Sardinian Warbler (Curruca melanocephala) Phylogeography

In the Western Palaearctic, ice ages played an important role in shaping the genetic diversity of birds, yet the phylogeography of species that persisted in the Mediterranean basin is understudied. Thus, we investigated the genetic diversity, phylogeography and demographic history of the Sardinian Warbler (Curruca melanocephala), a widespread Mediterranean songbird from the Canary Islands, North Africa, across southern Europe, to Turkey and the Middle East. Our study integrated mitochondrial (cytochrome C oxidase subunit I[(COI], cytochrome b [cytb]) and nuclear transforming growth factor-beta 2 (TGFB2) markers, single-nucleotide polymorphisms (SNPs) derived from a genotyping-by-sequencing (GBS) approach and species distribution models (SDMs). Both single markers and genomic SNPs identified four major clades. Several widespread haplotypes, extending from Iberia to Turkey and North Africa, indicate a panmictic pattern across the range of C. m. melanocephala. Among the remaining groups, one corresponds to C. m. momus, another includes individuals ascribable to subspeciesvalverdei and leucogastra, while the last consists of a highly divergent leucogastra haplotype. The ambiguity in subspecies range is further supported by nuclear markers and SNPs, which highlighted great levels of gene flow among populations. Phylogenetic reconstruction showed that the divergence of the clades within C. melanocephala occurred during the Pleistocene in the Middle East region. Demographic analyses suggest that the species maintained relatively stable effective population sizes (Ne) through time, findings supported by SDMs projections, which identify suitable habitats across the Mediterranean during the Last Glacial Maximum (LGM), implying broad persistence rather than contraction to isolated refugia. This study offers new insights into the historical processes that have shaped the apparent panmixia observed today in C. melanocephala and reveals that bird species originating in the Mediterranean may have partially escaped the constraints traditionally associated with glacial refugia along the region’s coasts. The findings also emphasise the value of combining molecular and ecological approaches to disentangle the complex evolutionary dynamics of avian biodiversity hotspots.