Haploblocks are regions of the genome that coalesce to an ancestor as a single unit. Differentiated haplotypes in these regions can result from the accumulation of mutational differences in low-recombination chromosomal regions, especially when selective sweeps occur within geographically structured populations. We introduce a method to identify large well-differentiated haploblock regions (LHBRs), based on the variance in standardized heterozygosity (ViSHet) of single nucleotide polymorphism (SNP) genotypes among individuals, calculated across a genomic region (500 SNPs in our case). We apply this method to the greenish warbler (Phylloscopus trochiloides) ring species, using a newly assembled reference genome and genotypes at more than 1 million SNPs among 257 individuals. Most chromosomes carry a single distinctive LHBR, containing 4-6 distinct haplotypes that are associated with geography, enabling detection of hybridization events and transition zones between taxa. LHBRs have exceptionally low within-haplotype nucleotide variation and moderately low between-haplotype nucleotide distance, suggesting their establishment through recurrent selective sweeps at varying geographic scales. Meiotic drive is potentially a powerful mechanism of producing such selective sweeps, and the LHBRs are likely to often represent centromeric regions where recombination is restricted. Links between populations enable introgression of favored haplotypes and we identify one haploblock showing a highly discordant distribution compared to the rest of the genome, being present in two distantly separated geographic regions that are at similar latitudes in both east and west Asia. Our results set the stage for detailed studies of haploblocks, including their genomic location, gene content, and contribution to reproductive isolation.

Island ecosystems have emerged as vital model systems for evolutionary and speciation studies due to their unique environmental conditions and biodiversity. This study investigates the population divergence, hybridization dynamics, and evolutionary history of hybridizing golden-backed and red-backed Dinopium flameback woodpeckers on the island of Sri Lanka, providing insights into speciation processes within an island biogeographic context. Utilizing genomic analysis based on next-generation sequencing, we revealed that the Dinopium hybrid zone on this island is a complex three-way hybrid zone involving three genetically distinct populations: two cryptic populations of golden-backed D. benghalense in the north and one island-endemic red-backed population of D. psarodes in the south of Sri Lanka. Our findings indicate asymmetric introgressive hybridization, where alleles from the southern D. psarodes introgress into the northern D. benghalense genome while phenotype remains adapted to their respective northern arid and southern wet habitats. The discovery of two genetically distinct but phenotypically similar D. benghalense populations in northern Sri Lanka highlights the process of cryptic speciation within island ecosystems. These populations trace their ancestry back to a common ancestor, similar to the Indian form D. b. tehminae, which colonized Sri Lanka from mainland India during the late Pleistocene. Subsequent divergence within the island, driven by selection, isolation-by-distance, and genetic drift, led to the current three populations. Our findings provide evidence of cryptic speciation and within-island population divergence, highlighting the complexity of hybridization and speciation processes. These findings further emphasize the intricate nature of evolutionary dynamics in island ecosystems.