DOI: 10.5061/dryad.b5mkkwhc8
title: Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages

description: Sex determination systems are highly conserved among most vertebrates with
 genetic sex determination, but can be variable and evolve rapidly in some.
 Here, we study sex determination in a clade with exceptionally high sex
 chromosome turnover rates. We identify the sex determining chromosomes in
 three interspecific crosses of haplochromine cichlid fishes from Lakes
 Victoria and Malawi. We find evidence for different sex determiners in
 each cross. In the Malawi cross and one Victoria cross the same chromosome
 is sex-linked but while females are the heterogametic sex in the Malawi
 species, males are the heterogametic sex in the Victoria species. This
 chromosome has not previously been reported to be sex determining in
 cichlids, increasing the number of different chromosomes shown to be sex
 determining in cichlids to 12. All Lake Victoria species of our crosses
 are less than 15,000 years divergent, and we identified different sex
 determiners among them. Our study provides further evidence for the
 diversity and evolutionary flexibility of sex determination in cichlids,
 factors which might contribute to their rapid adaptive radiations.
description: Description of Data and Files:
 <strong>Genotype tables
 (unfiltered):</strong><br> Victoria1.vcf.gz<br>
 Victoria2.vcf.gz<br> Malawi.vcf.gz
 <strong>Genotype tables (quality filtered bi-allelic
 snps):</strong><br> Malawi_filtered.vcf.gz<br>
 Victoria1_filtered.vcf.gz<br> Victoria2_filtered.gz
 <strong>Genotype tables (quality filtered and
 phased):</strong><br> Victoria1.phased.vcf.gz<br>
 Victoria2.phased.vcf.gz<br> Malawi.phased.vcf.gz
 <strong>Linkage maps:</strong><br>
 Victoria1_linkagemap.txt<br> Victoria2_linkagemap.txt<br>
 Malawi_linkagemap.txt <strong>Phenotype &
 genotype tables for QTL mapping (in R/qtl input
 format):</strong><br> Victoria1_GenoPhenoTable.csv<br>
 Victoria2_GenoPhenoTable.csv<br> Malawi_GenoPhenoTable.csv<br>
 (also include some other phenotypes) <strong>Code
 for filtering / file preparation:</strong><br>
 bashScripts_vcfFiltering.txt<br> Malawi_vcf_to_JoinMap.R
 <strong>Code for analyses:</strong><br>
 QTLmapping.R<br> bashScripts_analyses.txt<br>
 singleMarkerRegressions.R<br> crossComparisons.R
 <strong>Info/results/input files from/used in analysis
 scripts:</strong><br> chrInfo.txt<br>
 Victoria1_LODscores_newmap.csv<br>
 Victoria1_singlemarkerregressionresults_famA.csv<br>
 Victoria1_singlemarkerregressionresults_famB.csv<br>
 Victoria1.stats<br> Victoria1A.permuted.hetDiff.csv<br>
 Victoria1B.permuted.hetDiff.csv<br>
 Victoria2_LODscores_Sep2020.csv<br>
 Victoria2_singlemarkerregressionresults_fam1.csv<br>
 Victoria2_singlemarkerregressionresults_fam2.csv<br>
 Victoria2_singlemarkerregressionresults.csv<br>
 Victoria2.permuted.hetDiff.csv<br> Victoria2.stats<br>
 Malawi_LODscores_Sep2020.csv<br>
 Malawi_singlemarkerregressionresults.csv<br>
 Malawi.females<br> Malawi.males<br>
 Malawi.permuted.hetDiff.csv<br> Malawi.stats<br>
 sexChromInds.zip (lists of individuals grouped by their sex
 chromosomes)