Cultural transmission and genomic co-divergence in the willow tit across the Palearctic

Cultural transmission of mating behaviour can both promote and constrain genetic divergence, yet its long-term population-genetic consequences remain unclear. In songbirds, learned song can generate behavioural isolation, but its potential to shape genome-wide differentiation at continental scales is rarely assessed. Willow tits provide a compelling system, as three culturally transmitted song types are largely allopatric across the Palearctic, while northern populations exhibit mixed repertoires. Here, we combined a chromosome-level reference genome, whole-genome resequencing of 88 willow tits ( Poecile montanus ) spanning all 14 subspecies, and palaeodistribution modelling to reconstruct the species’ evolutionary history across the Palearctic. Phylogenetic and demographic analyses indicate an origin in Asia during the Late Pliocene to Early Pleistocene, followed by expansions that yielded three deeply diverged genomic lineages in the Asian, Central European, and Northern Palearctic regions. The boundaries of these lineages coincide with major song-type divisions. Tests of historical allele sharing show that gene flow occurred preferentially among lineages that share the same or similar song types, even after accounting for geography, consistent with learned song contributing to prezygotic isolation. Peripheral, song-monotypic populations exhibit signatures of repeated bottlenecks associated with glacial isolation, whereas large northern populations retained broader song repertoires and signals of long-term connectivity. These results provide genome-wide continental evidence that culturally transmitted song mirrors and likely reinforces genomic structure through time in a widespread passerine bird.