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 except..., This Dryad archive contains genotypes of 257 individual greenish warblers (Phylloscopus trochiloides / P. plumbeitarsus / P. nitidus) at more than 1 million loci located on a newly generated high-quality reference genome., , # Data and code from: The distribution and dispersal of large haploblocks in a superspecies

[https://doi.org/10.5061/dryad.8w9ghx3xr](https://doi.org/10.5061/dryad.8w9ghx3xr)

## Description of the data and file structure

This dataset is associated with this publication, which explains the research that produced the data:

Irwin, D., S. Bensch, C. Charlebois, G. David, A. Geraldes, S.K. Gupta, B. Harr, P. Holt, J.H. Irwin, V.V. Ivanitskii, I.M. Marova, Y. Niu, S. Seneviratne, A. Singh, Y. Wu, S. Zhang, T.D. Price. The distribution and dispersal of large haploblocks in a superspecies. *Molecular Ecology*, in press.

### Files and variables

#### File: GW\_haploblocks\_processing\_scripts\_Irwinetal2025.txt

**Description:** This text file contains the annotated code used in mapping GBS reads to the reference genome and calling genotypes of individuals.

#### File: GW2022ref.fa

**Description:** This fasta file contains the new *Phylloscopus trochiloides* reference genome in the format...,