Data from: Persistence of an unusual triple sex chromosome system through allopolyploidization in African clawed frogs (Xenopus, subgenus Silurana)
Data files
Dec 13, 2025 version files 40.64 GB
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2025_artificial_allotetraploid.pl
7.56 KB
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2025_Liberia_ABBA_BABA_windowz.pl
6.85 KB
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2025_Liberia_ABBA_BABA.pl
5.16 KB
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2025_Liberia_autapomorphy_windowz.pl
4.61 KB
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2025_Liberia_autapomorphy.pl
3.10 KB
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allsites_Chr1_1-217471166.g.vcf.gz_genotyped.vcf.gz
5.75 GB
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allsites_Chr10_1-52432566.g.vcf.gz_genotyped.vcf.gz
1.26 GB
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allsites_Chr2_1-181034961.g.vcf.gz_genotyped.vcf.gz
4.33 GB
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allsites_Chr3_1-153873357.g.vcf.gz_genotyped.vcf.gz
3.98 GB
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allsites_Chr4_1-153961319.g.vcf.gz_genotyped.vcf.gz
3.93 GB
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allsites_Chr5_1-164033575.g.vcf.gz_genotyped.vcf.gz
4.18 GB
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allsites_Chr6_1-154486312.g.vcf.gz_genotyped.vcf.gz
3.96 GB
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allsites_Chr7_1-133565930.g.vcf.gz_genotyped.vcf.gz
3.38 GB
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allsites_Chr8_1-147241510.g.vcf.gz_genotyped.vcf.gz
3.50 GB
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allsites_Chr9_1-91218944.g.vcf.gz_genotyped.vcf.gz
2.28 GB
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allsites_Scafs.g.vcf.gz_genotyped.vcf.gz
17.14 MB
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C659_all_chromosomes.vcf.gz
27.58 MB
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C660_all_chromosomes.vcf.gz
48.41 MB
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calc_all_combined.g.vcf.gz_genotyped.vcf.gz
673.24 MB
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Does_block_jackknife_ABB_BAB.pl
4.35 KB
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Does_block_jackknife_ABBA_BABA.pl
7.24 KB
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epi_all_combined.g.vcf.gz_genotyped.vcf.gz
507.80 MB
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Gets_matpat_positions_from_vcf_file.pl
2.50 KB
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Makes_a_mat_and_pat_from_angsdoutput.pl
2.82 KB
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mell_all_chromosomes.vcf.gz
70.25 MB
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README.md
8.96 KB
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WZY_sims.pl
5.38 KB
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XT_Lsubgenome_Chr1L_genotyped_filtered_removed.vcf.gz
430.98 MB
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XT_Lsubgenome_Chr2L_genotyped_filtered_removed.vcf.gz
341.45 MB
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XT_Lsubgenome_Chr3L_genotyped_filtered_removed.vcf.gz
314.73 MB
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XT_Lsubgenome_Chr4L_genotyped_filtered_removed.vcf.gz
304.75 MB
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XT_Lsubgenome_Chr5L_genotyped_filtered_removed.vcf.gz
295.70 MB
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XT_Lsubgenome_Chr6L_genotyped_filtered_removed.vcf.gz
277.94 MB
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XT_Lsubgenome_Chr7L_genotyped_filtered_removed.vcf.gz
231.03 MB
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XT_Lsubgenome_Chr8L_genotyped_filtered_removed.vcf.gz
278.70 MB
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XT_Lsubgenome_Chr9_10L_genotyped_filtered_removed.vcf.gz
269.40 MB
Abstract
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
Dataset DOI: 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.