Eroding species barriers: hybridising canids remain distinct around centromeres

Species barriers are shaped by variation in recombination coupled with natural selection [1–3]. Canids lost the Prdm9 gene 40–60 million years ago [4–6], stabilising low recombination at the centromeric ends [7] of acrocentric autosomes despite overall high recombination rates [6]. We predict canid recombination architecture will tend to maintain barriers to gene flow at one end of autosomes while eroding them at the other. Polarization [8] of 31 million single nucleotide variants (SNVs) across 980 canid genomes reveals elevated barriers to gene flow at pericentromeric regions between grey wolves, coyotes and golden jackals. Highly diagnostic SNVs are six-fold enriched in pericentromeric regions. The exception is the barrier to gene flow between dogs and wolves, which accumulated divergence differently from other comparisons: genomes of domesticated dogs preserve ancient genetic diversity lost in contemporary grey wolf populations, positioning them as reservoirs of ancestral alleles. Our results show that genome architecture modulates permeability of barriers to gene flow, pointing to pericentromeric regions as targets for reinforcement selection that may maintain canid taxa.