Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids
Feller, Anna F; Haesler, Marcel P; Peichel, Catherine L; Seehausen, Ole (2020), Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids, Dryad, Dataset, https://doi.org/10.5061/dryad.5tb2rbp1n
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)
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
Linkage maps for the two crosses.
Linkage group numbers have been adjusted to match chromosome numbers in the Pundamilia nyererei reference genome.
Quality filtered genotype files for the two crosses,
subset to fixed loci between the two respective parental species.
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.)
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung