Evolution of genomic divergence across Prunella birds with different speciation times

Understanding how genomic differentiation accumulates during speciation is fundamental to elucidating the speciation process. Here, we compare whole-genome differentiation across six accentor species ( Prunella ) spanning different stages of speciation. Using species-specific PBS statistics, we identify genomic islands of elevated differentiation. These islands are wider in anciently divergent species than in recently divergent species, supporting their expansion over time via divergence hitchhiking. Across all six species, the islands consistently exhibit reduced nucleotide diversity, recombination rates, Tajima’s D , along with elevated codon sequence density and inbreeding. In recently divergent species, islands show reduced absolute divergence ( D XY ), whereas in anciently divergent species they show elevated D XY . This contrast indicates that initial island formation is driven by linked selection reducing ancestral diversity, while long-term maintenance and growth involve progressive accumulation of absolute divergence. Furthermore, the relative contributions of recombination and nucleotide diversity shift with divergence time: their interaction best explains differentiation in recently divergent species, whereas nucleotide diversity alone dominates in anciently divergent species. Thus, reduced nucleotide diversity, initially a consequence of linked selection and demographic decline such as inbreeding, later a driver of island expansion, becomes increasingly central as speciation proceeds. Together, these findings reveal that the interplay between nucleotide diversity and recombination landscape shapes expansion of genomic islands during speciation with gene flow.