Phylogeography and Pleistocene refugia of the Little Owl (Athene noctua) as inferred from mtDNA sequence data

Pleistocene glaciations deeply affected the distribution of genetic diversity in animal populations. The Little Owl Athene noctua, is widely distributed in temperate regions and could have survived the last glaciations in southern refugia. To describe the phylogeographic structure of European populations, we sequenced the mitochondrial Cytochrome c Oxidase I (COI) and Control Region (CR1) in 326 individuals collected from 22 locations. Phylogenetic analyses of COI identified two deeply divergent clades: the Western haplogroup distributed in western and north-western countries, and the Eastern haplogroup distributed in south-eastern countries. Faster evolving CR1 sequences supported the divergence between these two main clades, and identified three sub-groups within the Eastern clade: Balkan, south Italian and Sardinian. Divergence times estimated from COI with fossil calibrations indicate that the Western and Eastern haplogroups split 2.01-1.71 Mya. Slightly different time splits were found using the standard 2% rate and 7.3% mtDNA neutral substitution rate. CR1 sequences dated the origin of endemic Sardinian haplotypes at 1.04-0.26 Mya and the split between southern Italian and Balkan haplogroups at 0.72-0.21 Mya, coincident with the onset of two Pleistocene glaciations. Admixture of mtDNA haplotypes was detected in northern Italy and in central Europe. These findings support a model of southern Mediterranean and Balkan refugia, with postglacial expansion and secondary contacts for Little Owl populations. Central and northern Europe was predominantly recolonized by Little Owls from Iberia, while expansion out of the Balkans was more limited. Northward expansion of the Italian haplogroup was likely prevented by the Alps, and the Sardinian haplotypes remained confined to the island. Results showed a clear genetic pattern differentiating putative subspecies. Genetic distances between haplogroups were comparable with the ones recorded between different avian species.