DOI: 10.5061/dryad.5tb2rbp1n
title: Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids

description: One hallmark of the East African cichlid radiations is the rapid evolution
 of reproductive isolation that is robust to full sympatry of many closely
 related species. Theory predicts that species persistence and speciation
 in sympatry with gene flow are facilitated if loci of large effect or
 physical linkage (or pleiotropy) underlie traits involved in reproductive
 isolation. Here we investigate the genetic architecture of a key trait
 involved in behavioural isolation, male nuptial coloration, by crossing
 two sister species pairs of Lake Victoria cichlids of the genus Pundamilia
 and mapping nuptial coloration in the F2 hybrids. One is a young sympatric
 species pair, representative of an axis of colour motif differentiation,
 red-dorsum vs blue, that is highly recurrent in closely related sympatric
 species. The other is a species pair representative of colour motifs,
 red-chest vs blue, that are common in allopatric but uncommon in sympatric
 closely related species. We find significant QTLs with moderate to large
 effects (some overlapping) for red and yellow in the sympatric red-dorsum
 x blue cross, whereas we find no significant QTLs in the non-sympatric
 red-chest x blue cross. These findings are consistent with theory
 predicting that large effect loci or linkage/pleiotropy underlying mating
 trait differentiation could facilitate speciation and species persistence
 with gene flow in sympatry.
description: <strong>General Notes:</strong><br> PNPxPPP
 refers to the <em>Pundamilia</em> sp.
 "nyererei-like" x <em>Pundamilia</em> sp.
 "pundamilia-like" (red-dorsum x blue) cross<br> PPMxPRHZ
 refers to the <em>Pundamilia pundamilia</em> x
 <em>Pundamilia</em> sp. "red-head" (red-chest x blue
 cross)
 <strong>GenoPheno_PNPxPPP_final.csv</strong><br> <strong>GenoPheno_PPMxPRHZ_NewMap.csv</strong><br> R/qtl input format files for the two crosses, consisting of phenotypes (columns A-P),<br> and genotypes (columns T ff) for all F2 individuals (IDs in column S).<br> 1 = presence, 0 = absence, - = NA<br> Exception: column (R) where 1 = male, 0 = female <strong>PNPxPPP_final_map_1excl_LGadj.txt<br> PPMxPRHZ_NewMap_LGadj.txt</strong><br> Linkage maps for the two crosses.<br> Linkage group numbers have been adjusted to match chromosome numbers in the <em>Pundamilia nyererei</em> reference genome. <strong>PNPxPPP_final_Fam3_f1_r1_f2_r2_f3_homfixbalF1het.vcf<br> PPMxPRHZ_r1_f1_r2_f2_r3_f3_homfixbalF1het.vcf</strong><br> Quality filtered genotype files for the two crosses,<br> subset to fixed loci between the two respective parental species. <strong>PNPxPPP_sample_list.xlsx<br> PPMxPRHZ_sample_list.xlsx</strong><br> Overview of which of all genotyped individuals in the two crosses were used in which part<br> (linkage map construction and/or colour QTL mapping),<br> and also contains the sample- and filenames associated with the raw sequence (fastq) files on the NCBI short read archive<br> (see BioProjects PRJNA612290 (PNPxPPP) and PRJNA439430 (PPMxPRHZ)). <strong>Additional information on sequencing data on the SRA (see BioProject numbers just above):</strong><br> The PNPxPPP reads are trimmed to 85bp,<br> no quality filters applied yet.<br> The PPMxPRHZ  reads were trimmed to 92bp,<br> and already filtered for a minimum quality of 10 at all bases and of 30 in at least 95% of the read<br> by Feulner et al. 2018, G3 https://www.g3journal.org/content/8/7/2411.<br> (In our publication we then trimmed all reads of both crosses to 85bp.)