Data and code from: The distribution and dispersal of large haploblocks in a superspecies

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.