DOI: 10.5061/dryad.8w9ghx3xr
title: Data and code from: The distribution and dispersal of large haploblocks in a superspecies

description: 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.
description: This Dryad archive contains genotypes of 257 individual greenish
 warblers (<em>Phylloscopus trochiloides</em> / <em>P.
 plumbeitarsus</em> / <em>P. nitidus</em>) at more than 1
 million loci located on a newly generated high-quality reference
 genome.
description: # 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 used in the analysis described in the script file above. #### File: GW2022\_all4plates.genotypes.SNPs\_only.whole\_genome.vcf **Description:** This file contains genotypic information from 310 individual genotyping-by-sequencing (GBS) runs and more than 5.5 million sites in the greenish warbler genome. The file is in standard Variant Call Format (VCF). This file contains all variant sites, prior to filtering. See the associated script file for details regarding how it was produced. #### File: GW2022\_all4plates.genotypes.SNPs\_only.whole\_genome.max2allele\_noindel.vcf.maxmiss60.MQ20.lowHet.tab.012minus1 **Description:** This file contains genotypes from 310 individual genotyping-by-sequencing (GBS) runs and 2,431,709 sites, following some filtering for biallelic single nucleotide polymorphisms (SNPs), less than 60% of individuals having missing genotypes, mapping quality (MQ) at least 20, and heterozygosity lower than 60. The format is a tab-delimited text file containing a matrix in which rows correspond to individual runs and columns correspond to sites in the genome. In each cell, `0` represents homozygous reference, `1` represents heterozygous, `2` represents homozygous alternate, and `-1` represents a missing genotype.  #### File: GW2022\_all4plates.genotypes.SNPs\_only.whole\_genome.max2allele\_noindel.vcf.maxmiss60.MQ20.lowHet.tab.012.indv **Description:** This text file contains the individual run IDs corresponding to the rows of the file above (the one ending in `012minus1`). #### File: GW2022\_all4plates.genotypes.SNPs\_only.whole\_genome.max2allele\_noindel.vcf.maxmiss60.MQ20.lowHet.tab.012.pos **Description:** This tab-delimited text file contains the genomic coordinates of the sites corresponding to the columns of the file above (the one ending in `012minus1`). There are two columns, with the first indicating the scaffold name and the second indicating the base number on that scaffold.  #### File: GW\_all4plates.Fst\_groups.txt **Description:** This file provides metadata for the samples used in the 310 individual GBS runs. Columns indicate the `ID` of the sample run, the `location` code of the sample, the `group` identifier of each sample, the `Fst_group` identifier of each sample, and the `plot_order` that determines the ordering of samples in genotype-by-individual plots. This file is used in the Julia scripts that process the data. #### File: GW\_all4plates.Fst\_groups.with\_dates\_etc.txt **Description:** This file is like the `GW_all4plates.Fst_groups.txt` file above, but with several columns added that indicate additional information about the samples: `previous_pub` lists if the sample is `new` with this 2025 publication or lists previous publications that used information from the sample; `sampling_date` provides the date of sampling; `otherID` and `otherID2` provide other identifiers for the individual samples (e.g. band numbers or color combinations); `providers_and_notes` provides that information when available. #### File: GW2022\_all4plates.genotypes.SNPs\_only.chrgwZ.max2allele\_noindel.vcf.maxmiss60.MQ20.lowHet.vcf.idepth **Description:** This file contains read depths of Z chromosome markers (used in the Julia scripts). #### File: GW2022\_all4plates.genotypes.SNPs\_only.chrgw2.max2allele\_noindel.vcf.maxmiss60.MQ20.lowHet.vcf.idepth **Description:** This file contains read depths of chromosome 2 markers (used in the Julia scripts). #### File: GW2022\_all4plates.genotypes.allSites.chrgw3.infoSites.max2allele\_noindel.maxmiss60.MQ20.lowHet.tab.012minus1 **Description:** This file contains genotypes for all sequenced sites on chromosome 3 (see the end of this page for its use: [https://darreni.github.io/GreenishWarblerGenomics2025/GW_Heterozygosity_Variance.html](https://darreni.github.io/GreenishWarblerGenomics2025/GW_Heterozygosity_Variance.html)). #### File: GW2022\_all4plates.genotypes.allSites.chrgw3.infoSites.max2allele\_noindel.maxmiss60.MQ20.lowHet.tab.012.indv **Description:** This file contains the individual run IDs corresponding to the rows of the chromosome 3 file above (the one ending in `012minus1`). #### File: GW2022\_all4plates.genotypes.allSites.chrgw3.infoSites.max2allele\_noindel.maxmiss60.MQ20.lowHet.tab.012.pos **Description:** This tab-delimited text file contains the genomic coordinates of the sites corresponding to the columns of the chromosome 3 file above (the one ending in `012minus1`). There are two columns, with the first indicating the scaffold name and the second indicating the base number on that scaffold. #### File: GW2022\_all4plates.genotypes.allSites.chrgw4A.infoSites.max2allele\_noindel.maxmiss60.MQ20.lowHet.tab.012minus1 **Description:** This file contains genotypes for all sequenced sites on chromosome 4A (see the end of this page for its use: [https://darreni.github.io/GreenishWarblerGenomics2025/GW_Heterozygosity_Variance.html](https://darreni.github.io/GreenishWarblerGenomics2025/GW_Heterozygosity_Variance.html)). #### File: GW2022\_all4plates.genotypes.allSites.chrgw4A.infoSites.max2allele\_noindel.maxmiss60.MQ20.lowHet.tab.012.indv **Description:** This file contains the individual run IDs corresponding to the rows of the chromosome 4A file above (the one ending in `012minus1`). #### File: GW2022\_all4plates.genotypes.allSites.chrgw4A.infoSites.max2allele\_noindel.maxmiss60.MQ20.lowHet.tab.012.pos **Description:** This tab-delimited text file contains the genomic coordinates of the sites corresponding to the columns of the chromosome 4A file above (the one ending in `012minus1`). There are two columns, with the first indicating the scaffold name and the second indicating the base number on that scaffold. ## Code/software Processing of the sequencing reads was done according to the file `GW_haploblocks_processing_scripts_Irwinetal2025.text`, which resulted in the production of the first files listed above ending in `012minus1`, `indv`, and `pos`. These three files were then imported into scripts written in the Julia programming language. These scripts are shown and described at [https://darreni.github.io/GreenishWarblerGenomics2025/](https://darreni.github.io/GreenishWarblerGenomics2025/) . The underlying Quarto files containing Julia code blocks are also provided in this repository, with these filenames (listed in order in which the code blocks in them should be run): **GreenishWarblerGenomics2025.qmd** **GW_Zchromosome_analysis.qmd** **GW_PCAplots.qmd** **GW_Heterozygosity_Variance.qmd** They above scripts use a new registered Julia package made available along with this paper: `GenomicDiversity.jl`, available at [https://github.com/darreni/GenomicDiversity.jl](https://github.com/darreni/GenomicDiversity.jl) and through the official Julia registry. ## Access information Associated data at other locations: * The new reference genome is provided at NCBI under PRJNA1210605. * New GBS reads have been deposited at NCBI SRA under accession PRJNA1207594; within this accession are data for 3 sets (i.e., plates) of samples: runs SRR31958018, SRR31958020, and SRR31958019. * This study also used GBS reads from a previously-sequenced set of samples, run SRR1176844 from NCBI accession PRJNA238841 (Alcaide et al., 2014, *Nature*). Associated software at other locations: * Julia functions used in data processing and graphing are provided in the new GenomicDiversity.jl package ([https://github.com/darreni/GenomicDiversity.jl](https://github.com/darreni/GenomicDiversity.jl)), and the complete analysis scripts that call these functions are available at [https://darreni.github.io/GreenishWarblerGenomics2025](https://darreni.github.io/GreenishWarblerGenomics2025) and at a Github repository ([https://github.com/darreni/GreenishWarblerGenomics2025](https://github.com/darreni/GreenishWarblerGenomics2025)).