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 of Data and Files:

Genotype tables (unfiltered):
Victoria1.vcf.gz
Victoria2.vcf.gz
Malawi.vcf.gz

Genotype tables (quality filtered bi-allelic snps):
Malawi_filtered.vcf.gz
Victoria1_filtered.vcf.gz
Victoria2_filtered.gz

Genotype tables (quality filtered and phased):
Victoria1.phased.vcf.gz
Victoria2.phased.vcf.gz
Malawi.phased.vcf.gz

Linkage maps:
Victoria1_linkagemap.txt
Victoria2_linkagemap.txt
Malawi_linkagemap.txt

Phenotype & genotype tables for QTL mapping (in R/qtl input format):
Victoria1_GenoPhenoTable.csv
Victoria2_GenoPhenoTable.csv
Malawi_GenoPhenoTable.csv
(also include some other phenotypes)

Code for filtering / file preparation:
bashScripts_vcfFiltering.txt
Malawi_vcf_to_JoinMap.R

Code for analyses:
QTLmapping.R
bashScripts_analyses.txt
singleMarkerRegressions.R
crossComparisons.R

Info/results/input files from/used in analysis scripts:
chrInfo.txt
Victoria1_LODscores_newmap.csv
Victoria1_singlemarkerregressionresults_famA.csv
Victoria1_singlemarkerregressionresults_famB.csv
Victoria1.stats
Victoria1A.permuted.hetDiff.csv
Victoria1B.permuted.hetDiff.csv
Victoria2_LODscores_Sep2020.csv
Victoria2_singlemarkerregressionresults_fam1.csv
Victoria2_singlemarkerregressionresults_fam2.csv
Victoria2_singlemarkerregressionresults.csv
Victoria2.permuted.hetDiff.csv
Victoria2.stats
Malawi_LODscores_Sep2020.csv
Malawi_singlemarkerregressionresults.csv
Malawi.females
Malawi.males
Malawi.permuted.hetDiff.csv
Malawi.stats
sexChromInds.zip (lists of individuals grouped by their sex chromosomes)