DOI: 10.5061/dryad.jm63xsj7s
title: Heterogeneous histories of recombination suppression on stickleback sex chromosomes

description: How consistent are the evolutionary trajectories of sex chromosomes
 shortly after they form? Insights into the evolution of recombination,
 differentiation, and degeneration can be provided by comparing closely
 related species with homologous sex chromosomes. The sex chromosomes of
 the threespine stickleback (Gasterosteus aculeatus) and its sister
 species, the Japan Sea stickleback (G. nipponicus), have been well
 characterized. Little is known, however, about the sex chromosomes of
 their congener, the blackspotted stickleback (G. wheatlandi). We used
 pedigrees to obtain experimentally phased whole genome sequences from
 blackspotted stickleback X and Y chromosomes. Using multispecies gene
 trees and analysis of shared duplications, we demonstrate that Chromosome
 19 is the ancestral sex chromosome and that its oldest stratum evolved in
 the common ancestor of the genus. After the blackspotted lineage diverged,
 its sex chromosomes experienced independent and more extensive
 recombination suppression, greater X-Y differentiation, and a much higher
 rate of Y degeneration than the other two species. These patterns may
 result from a smaller effective population size in the blackspotted
 stickleback. A recent fusion between the ancestral blackspotted
 stickleback Y chromosome and Chromosome 12, which produced a neo-X and
 neo-Y, may have been favored by the very small size of the recombining
 region on the ancestral sex chromosome. We identify six strata on the
 ancestral and neo-sex chromosomes where recombination between the X and Y
 ceased at different times. These results confirm that sex chromosomes can
 evolve large differences within and between species over short
 evolutionary timescales.
description: Scripts and data used for comparative study of blackspotted
 stickleback (<em>Gasterosteus wheatlandi</em>) sex
 chromosomes.
 <strong>Scripts:</strong> <strong>ConstructFasta.wheatlandi.R</strong> - Takes a phased haploid vcf file and outputs a fasta file used to generate gene trees <strong>ExtractPaternalAllele.R </strong>- Takes a phased genotype file and extracts the alleles inherited by the father (i.e., blackspotted stickleback in this manuscript). <strong>IDautosomalpeaks.R </strong>- Identifies autosomal regions that duplicated onto the Y chromosome in the shared ancestor of blackspotted and Japan Sea stickleback <strong>phasescript.crosses.R </strong>- Phases sequences based on patterns of transmission in pedigree of parent-offspring quartets (used for analysis of blackspotted stickleback sex chromosomes) <strong>phasescriptXII.allSpecies.R -</strong> Phases sequences based on patterns of transmission in pedigree of parent-offspring quartets (used for gene tree analysis of Chr 12 neo-sex chromosome using data from blackspotted and Japan Sea stickleback quartets) <strong>phasescriptXIX.allSpecies.R -</strong> Phases sequences based on patterns of transmission in pedigree of parent-offspring quartets (used for gene tree analysis of Chr 19 ancestral sex chromosome using data from blackspotted and Japan Sea stickleback quartets) <strong>PopGenPlots.R</strong> - script used for basic population genetics analysis (<em>F</em><sub>ST</sub>, pi, Tajima's <em>D</em>) of blackspotted stickleback sex chromosomes, including creation of plots for manuscript <strong>ReadDepth.R </strong>- Analyzes male-to-female read depth ratio along sex chromosomes <strong>XYconsistency.R </strong>- Gene tree approach for detecting suppressed recombination between X and Y chromosomes <strong>Data:</strong> <strong>wheatlandi.pedigree<em> </em></strong>- pedigree file indicating identity of blackspotted stickleback father, threespine mother, son, and daughter for the 15 crosses used to obtain phased blackspotted X and Y chromosome sequences <strong>phasedchrXII.wheatlandi.masked.SibFilter.haploid.vcf</strong>- phased haploid vcf file for threespine x blackspotted stickleback parent-offspring quartets, mapped to Glazer et al. stickleback genome (Chr 12) <strong>phasedchrXIX.wheatlandi.masked.SibFilter.haploid.vcf</strong>- phased haploid vcf file for threespine x blackspotted stickleback parent-offspring quartets, mapped to Glazer et al. stickleback genome (Chr 19) <strong>wheatlandi.masked.chrXII.minQ999.mindepth26.maxdepth52.minGQ20.recode.vcf - </strong>unphased filtered vcf file for threespine x blackspotted stickleback parent-offspring quartets, mapped to Nath et al. 2021 stickleback genome (Chr 12) <strong>wheatlandi.masked.chrXIX.minQ999.mindepth26.maxdepth52.minGQ20.recode.vcf - </strong>unphased filtered vcf file for threespine x blackspotted stickleback parent-offspring quartets, mapped to Nath et al. 2021 stickleback genome (Chr 19) <strong>allspecies.pedigree<em> </em></strong>- pedigree file indicating identity of father, mother, son, and daughter for the 4 threespine x blackspotted stickleback crosses and 4 threespine x Japan Sea stickleback crosses used in multispecies gene tree analysis <strong>allspecies.masked.chrXII.phased.groves.haploid.vcf </strong>- phased haploid vcf file used for multispecies gene tree analysis of Chr 12 (mapped to Glazer et al. reference genome) <strong>allspecies.masked.chrXIX.phased.groves.haploid.vcf </strong>- phased vcf file used for multispecies gene tree analysis of Chr 19 (mapped to Glazer et al. reference genome) <strong>JS.wheatlandi.overlappingWindows.txt </strong>- all10kb autosomal windows that show outlier (top 2%) male-female <em>F</em><sub>ST</sub> in both blackspotted and Japan Sea stickleback <strong>JS.wheatlandi.overlappingSNPs.txt </strong>- SNPs falling within shared autosomal male-female <em>F</em><sub>ST </sub>outlier windows listed in above file