DOI: 10.5061/dryad.560r4
title: Data from: RAD-Seq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene

description: Studies on the classic shell colour and banding polymorphism of the land
 snail Cepaea played a crucial role in establishing the importance of
 natural selection in maintaining morphological variation. Cepaea is also a
 pre-eminent model for ecological genetics because the outward colour and
 banding phenotype is entirely genetically determined, primarily by a
 ‘supergene’ of at least five loci. Unfortunately, progress in
 understanding the evolution and maintenance of the Cepaea polymorphism
 stalled, partly because of a lack of genetic markers. With a view to
 re-establish Cepaea as a prominent model of molecular ecology, we made six
 laboratory crosses of Cepaea nemoralis, five of which segregated for shell
 ground colour (C) and the presence or absence of bands (B). First, scoring
 of colour and banding in 323 individuals found no recombination between
 the C and B loci of the supergene. Second, using restriction
 site–associated DNA sequencing (RAD-Seq) of two parents and 22 offspring,
 we identified 44 anonymous markers putatively linked to the colour (C) and
 banding (B) loci. The genotype of eleven of the most promising RAD-Seq
 markers was independently validated in the same 22 offspring, then up to a
 further 146 offspring were genotyped. The closest RAD-Seq markers scored
 are within ~0.6 centimorgan (cM) of the C-B supergene linkage group, with
 the combined loci together forming a 35.8 cM linkage map of markers that
 flank both sides of the Cepaea C-B supergene.
description: Linkage map marker
 sequence assembliesRAD-tag sequences and
 paired-end contig assemblies for 11 RAD loci, which were used to develop a
 linkage map of genetic markers flanking the shell colour (C) and banding
 presence (B) loci of the Cepaea nemoralis supergene. The sequences were
 generated by Illumina sequencing of three RAD-Seq libraries comprising
 both parents and a total 24 F1 offspring from a single cross (C100 x C101)
 that segregated for shell colour (C) and presence or absence of banding
 (B). De novo assembly of RAD loci was performed using RADtools 1.2.4
 (http://www.RAD-Seq.info). A combination of Unix and Excel commands were
 then used to identify candidate RAD loci that cosegregate with colour and
 banding. Paired-end reads were assembled into contigs using
 VelvetOptimiser version 2.1.7, separately for each of the three RAD
 libraries. For the RAD markers shown, the corresponding contigs were
 concatenated and then manually aligned into longer, high-quality contigs.
 Each sequence is labelled: RAD marker ID – allelic phase with the
 supergene loci – sequence type – length – coverage. Contigs that could not
 be aligned are labelled as such.Cepaea nemoralis RAD markers
 RAD-tag and paired-end sequence
 assemblies.fasLinkage mapping
 genotypes datasetGenotypes used to
 produce a linkage map of 11 RAD-Seq derived markers flanking the shell
 colour (C) and banding presence (B) loci of the Cepaea nemoralis
 supergene. Data for two crosses are shown: C100 x C101 was a cross between
 a double homozygous recessive yellow-banded mother and a heterozygous
 father, resulting in either yellow-unbanded or pink-banded F1 offspring (n
 = 102). C118 x C119 was a cross between a double homozygous recessive
 yellow-banded parent and a pink-banded parent heterozygous for colour, but
 not banding. Full details of the crosses and the genotype assays are
 provided in the paper. Marker genotypes are provided in CRIMAP
 formatting.Cepaea linkage map genotypes
 dataset.xlsxShell colour and banding
 phenotype data from 6 Cepaea nemoralis crossesPhenotype data for the
 shell ground colour (C)and banding presence (B) supergene loci, scored in
 398 individuals from 6 crosses of Cepaea nemoralis. As C. nemoralis is a
 simultaneous hermaphrodite, offspring from both parents were used, except
 for crosses C100 x C101 and C108 x C109, where a non-virgin snail (C100
 and C108 respectively) was removed after mating. Full details of the
 crosses, rearing of the snails and analysis of the data are provided in
 the paper.Cepaea crosses colour and
 banding phenotype data.xlsx