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.

General Notes:
PNPxPPP refers to the Pundamilia sp. "nyererei-like" x Pundamilia sp. "pundamilia-like" (red-dorsum x blue) cross
PPMxPRHZ refers to the Pundamilia pundamilia x Pundamilia sp. "red-head" (red-chest x blue cross)

GenoPheno_PNPxPPP_final.csv
GenoPheno_PPMxPRHZ_NewMap.csv
R/qtl input format files for the two crosses, consisting of phenotypes (columns A-P),
and genotypes (columns T ff) for all F2 individuals (IDs in column S).
1 = presence, 0 = absence, - = NA
Exception: column (R) where 1 = male, 0 = female

PNPxPPP_final_map_1excl_LGadj.txt
PPMxPRHZ_NewMap_LGadj.txt
Linkage maps for the two crosses.
Linkage group numbers have been adjusted to match chromosome numbers in the Pundamilia nyererei reference genome.

PNPxPPP_final_Fam3_f1_r1_f2_r2_f3_homfixbalF1het.vcf
PPMxPRHZ_r1_f1_r2_f2_r3_f3_homfixbalF1het.vcf
Quality filtered genotype files for the two crosses,
subset to fixed loci between the two respective parental species.

PNPxPPP_sample_list.xlsx
PPMxPRHZ_sample_list.xlsx
Overview of which of all genotyped individuals in the two crosses were used in which part
(linkage map construction and/or colour QTL mapping),
and also contains the sample- and filenames associated with the raw sequence (fastq) files on the NCBI short read archive
(see BioProjects PRJNA612290 (PNPxPPP) and PRJNA439430 (PPMxPRHZ)).

Additional information on sequencing data on the SRA (see BioProject numbers just above):
The PNPxPPP reads are trimmed to 85bp,
no quality filters applied yet.
The PPMxPRHZ  reads were trimmed to 92bp,
and already filtered for a minimum quality of 10 at all bases and of 30 in at least 95% of the read
by Feulner et al. 2018, G3 https://www.g3journal.org/content/8/7/2411.
(In our publication we then trimmed all reads of both crosses to 85bp.)