DOI: 10.5061/dryad.cfxpnvxmg
title: Data from: Persistence of an unusual triple sex chromosome system through allopolyploidization in African clawed frogs (<em>Xenopus</em>, subgenus <em>Silurana</em>)

description: This repository includes scripts and genotype files that were used in the
 associated manuscript. Genotype files (vcf) include Reduced representation
 genome sequence genotypes for 5 families from four species Whole genome
 sequence files from 15 X. tropicalis, 1 X. mellotropicalis, 3 X.
 calcaratus, and 1 X. tropicalis/X. calcaratus hybrid. Scripts include: A
 Perl script to perform simulations of genetic drift of a three sex
 chromosome system  A Perl script to quantify site patterns for
 "Analysis 1" described in the manuscript A Perl script to
 quantify site patterns for "Analysis 2" described in the
 manuscript  A Perl script to generate an artificial
 allotetraploid from two diploids Two Perl scripts to respectively (i)
 identify maternal and paternal heterozygous positions from a genotype
 (vcf) file and (ii) select from an angsd output file the associations of
 these positions with the phenotypic sex of offspring 
description: # Data from: Persistence of an unusual triple sex chromosome system
 through allopolyploidization in African clawed frogs (*Xenopus*, subgenus
 *Silurana*) Dataset DOI:
 [10.5061/dryad.cfxpnvxmg](https://doi.org/10.5061/dryad.cfxpnvxmg) ##
 Description of the data and file structure This repository includes
 genotype files and scripts that were used in Premachandra et al. 2025,
 that examined sex chromosome evolution and polyploidization of four
 species in the subgenus Silurana, genus Xenopus, and population structure
 of one species in this subgenus - *Xenopus tropicalis*. ### Files and
 variables #### File: C659_all_chromosomes.vcf.gz **Description:** This is
 a genotype file of previously published RRGS data for one of the two X.
 tropicalis used in this study mapped to the X. tropicalis genome. ####
 File: C660_all_chromosomes.vcf.gz **Description:** This is a genotype file
 of previously published RRGS data for the other of the two X. tropicalis
 used in this study mapped to the X. tropicalis genome. #### File:
 calc_all_combined.g.vcf.gz_genotyped.vcf.gz **Description:** This is a
 genotype file of new RRGS data for a X. calcaratus family used in this
 study mapped to the X. tropicalis genome. #### File:
 epi_all_combined.g.vcf.gz_genotyped.vcf.gz **Description:** This is a
 genotype file of new RRGS data for a X. epitropicalis family used in this
 study mapped to the X. tropicalis genome. #### File:
 mell_all_chromosomes.vcf.gz **Description:** This is a genotype file of
 previously published RRGS data for a X. mellotropicalis family used in
 this study mapped to the X. tropicalis genome. #### File:
 allsites_Chr1_1-217471166.g.vcf.gz_genotyped.vcf.gz **Description:** This
 is a genotype file of new WGS data from X. tropicalis, X. mellotropicalis,
 and X. calcaratus samples mapped to chromosome 1 of the X. tropicalis
 genome. #### File: allsites_Chr2_1-181034961.g.vcf.gz_genotyped.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis, X. mellotropicalis, and X. calcaratus samples mapped to
 chromosome 2 of the X. tropicalis genome. #### File:
 allsites_Chr4_1-153961319.g.vcf.gz_genotyped.vcf.gz **Description:** This
 is a genotype file of new WGS data from X. tropicalis, X. mellotropicalis,
 and X. calcaratus samples mapped to chromosome 4 of the X. tropicalis
 genome. #### File: allsites_Chr3_1-153873357.g.vcf.gz_genotyped.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis, X. mellotropicalis, and X. calcaratus samples mapped to
 chromosome 3 of the X. tropicalis genome. #### File:
 allsites_Chr10_1-52432566.g.vcf.gz_genotyped.vcf.gz **Description:** This
 is a genotype file of new WGS data from X. tropicalis, X. mellotropicalis,
 and X. calcaratus samples mapped to chromosome 10 of the X. tropicalis
 genome. #### File: allsites_Chr8_1-147241510.g.vcf.gz_genotyped.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis, X. mellotropicalis, and X. calcaratus samples mapped to
 chromosome 8 of the X. tropicalis genome. #### File:
 allsites_Scafs.g.vcf.gz_genotyped.vcf.gz **Description:** This is a
 genotype file of new WGS data from X. tropicalis, X. mellotropicalis, and
 X. calcaratus samples mapped to scaffolds of the X. tropicalis genome.
 #### File: allsites_Chr5_1-164033575.g.vcf.gz_genotyped.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis, X. mellotropicalis, and X. calcaratus samples mapped to
 chromosome 5 of the X. tropicalis genome. #### File:
 allsites_Chr9_1-91218944.g.vcf.gz_genotyped.vcf.gz **Description:** This
 is a genotype file of new WGS data from X. tropicalis, X. mellotropicalis,
 and X. calcaratus samples mapped to chromosome 9 of the X. tropicalis
 genome. #### File: allsites_Chr6_1-154486312.g.vcf.gz_genotyped.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis, X. mellotropicalis, and X. calcaratus samples mapped to
 chromosome 6 of the X. tropicalis genome. #### File:
 allsites_Chr7_1-133565930.g.vcf.gz_genotyped.vcf.gz **Description:** This
 is a genotype file of new WGS data from X. tropicalis, X. mellotropicalis,
 and X. calcaratus samples mapped to chromosome 7 of the X. tropicalis
 genome. #### File: XT_Lsubgenome_Chr1L_genotyped_filtered_removed.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis and previously published sequences from X. laevis samples
 mapped to chromsome 1L in subgenome L of the X. laevis genome. #### File:
 XT_Lsubgenome_Chr2L_genotyped_filtered_removed.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis and previously published sequences from X. laevis samples
 mapped to chromsome 2L in subgenome L of the X. laevis genome. #### File:
 XT_Lsubgenome_Chr3L_genotyped_filtered_removed.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis and previously published sequences from X. laevis samples
 mapped to chromsome 3L in subgenome L of the X. laevis genome. #### File:
 XT_Lsubgenome_Chr4L_genotyped_filtered_removed.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis and previously published sequences from X. laevis samples
 mapped to chromsome 4L in subgenome L of the X. laevis genome. #### File:
 XT_Lsubgenome_Chr5L_genotyped_filtered_removed.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis and previously published sequences from X. laevis samples
 mapped to chromsome 5L in subgenome L of the X. laevis genome. #### File:
 XT_Lsubgenome_Chr6L_genotyped_filtered_removed.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis and previously published sequences from X. laevis samples
 mapped to chromsome 6L in subgenome L of the X. laevis genome. #### File:
 XT_Lsubgenome_Chr7L_genotyped_filtered_removed.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis and previously published sequences from X. laevis samples
 mapped to chromsome 7L in subgenome L of the X. laevis genome. #### File:
 XT_Lsubgenome_Chr8L_genotyped_filtered_removed.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis and previously published sequences from X. laevis samples
 mapped to chromsome 8L in subgenome L of the X. laevis genome. #### File:
 XT_Lsubgenome_Chr9_10L_genotyped_filtered_removed.vcf.gz
 **Description:** This is a genotype file of new WGS data from X.
 tropicalis and previously published sequences from X. laevis samples
 mapped to chromsome 9_10L in subgenome L of the X. laevis genome. ##
 Code/software **File: 2025_Liberia_autapomorphy_windowz.pl**
 **Description:** **File: Does_block_jackknife_ABB_BAB.pl**
 **Description:** This script performs the block jackknife on the output of
 the "2025_Liberia_ABBA_BABA_windowz.pl" script **File:
 2025_Liberia_autapomorphy.pl** **Description:** This script performs
 Analysis 1 in the paper. **File: 2025_Liberia_ABBA_BABA_windowz.pl**
 **Description:** This script performs Analysis 1 in the paper but in
 genomic windows. **File: Does_block_jackknife_ABBA_BABA.pl**
 **Description:** This script performs the block jackknife on the output of
 the "2025_Liberia_ABBA_BABA_windowz.pl" script **File:
 2025_Liberia_ABBA_BABA.pl** **Description:** This script performs Analysis
 2 in the paper. **File: 2025_Liberia_ABBA_BABA_windowz.pl**
 **Description:** This script performs Analysis 2 in the paper but in
 genomic windows. **File: 2025_artificial_allotetraploid.pl**
 **Description:** This script generates an artificial allotetraploid using
 genotypes from two individuals in a genotype file. **File:
 Gets_matpat_positions_from_vcf_file.pl** **Description:** This script
 identifies maternal and paternal variants from a vcf file that includes
 both parents and their offspring. **File:
 Makes_a_mat_and_pat_from_angsdoutput.pl** **Description:** This script
 uses output of the "**Gets_matpat_positions_from_vcf_file.pl**"
 script to filter the output of angsd for associations of maternal and
 paternal variants **File: WZY_sims.pl** **Description:** This script
 performs the simulations described in the paper ## Access information
 Reduced representation genome sequencing from *X. mellotropicalis* and *X.
 tropicalis* families were previously available (BioProjects PRJNA549161,
 PRJNA526297). Reduced representation genome sequencing from *X.
 calcaratus* and *X. epitropicalis* families** have been deposited in the
 Short Read Archive (BioProject PRJNA1124953, respectively). Whole genome
 sequences for *X. tropicalis*, *X. calcaratus,* and *X. mellotropicalis*
 are also available (BioProject PRJNA577946, PRJNA1124553). Specimens and
 genetic samples that were collected from Nigeria are archived at the
 Museum of Comparative Zoology. The Liberia specimen and genetic sample
 (ROM19161) is archived at the Royal Ontario Museum.