Data from: Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

VCF file for experimental and natural populationsThis is the VCF file for the experimental and natural population comparisons. To test for differentiation genome wide among sympatric populations, we contrasted our apple7 and haw7 groups; for a response to selection in our experiment, we compared haw7 and haw30. Haw or apple represents the host plant from which the flies were collected; the number - 7 or 30 - represents the pre-winter warm period experienced by larvae/pupae prior to overwintering to match that found in nature on haw or apple plants. See txt file to match individual MID labels in the VCF file with the experimental group they were part of.snps.ScottSelection.05-400-20.filteredHwe0.05.wOutApple30.cleaned.vcfR_pomonella_denovo_assemblyThis file is the de novo assembly of Illumina sequence reads (20 million reads; 3% of total data) generated by Seqman NGen 4.0.0 (DNASTAR) using parameter values described in Gompert et al. 2012. See methods for more details.LatestRadFakeGenome.cut.fa.txtR. pomonella Linkage MapLinkage map giving the linear order of SNPs on each of the five chromosomes/linkage groups. Column labels: chromosome (1 to 5), Sn = SNP number ID (1-N by chromosome), locus = location of SNP in our de novo assembly by contig, then by location along contig, separated by an underscore, Position = distance along each linkage group/chromosome in centiMorgans.MapLinearOrderAllChrom.txt

用于实验种群与自然种群对比的变体调用格式（Variant Call Format，VCF）文件：本文件为实验种群与自然种群对比所用的VCF文件。为检验同域种群间的全基因组分化程度，本研究对比了apple7与haw7两组样本；为检测本实验中种群对选择压力的响应，本研究对比了haw7与haw30两组样本。其中"Haw"与"apple"分别代表采集实蝇所用的山楂与苹果寄主植物；后缀数字7或30则代表幼虫/蛹在越冬前经历的越冬前暖期时长，以匹配山楂或苹果寄主上的自然环境暖期参数。请查阅配套文本文件，以将VCF文件中的个体分子识别标签（Molecular Identifier，MID）与其所属实验组进行匹配。

文件名snps.ScottSelection.05-400-20.filteredHwe0.05.wOutApple30.cleaned.vcfR_pomonella_denovo_assembly对应的文件：该文件为基于Illumina测序读段（共2000万条读段，占总数据量的3%）构建的从头组装结果，由Seqman NGen 4.0.0（DNASTAR公司）依据Gompert等人2012年发表的参数设置生成。更多细节请参阅研究方法部分。

配套文本文件：LatestRadFakeGenome.cut.fa.txt

苹实蝇（Rhagoletis pomonella）连锁图谱：该图谱展示了5条染色体/连锁群上单核苷酸多态性（Single Nucleotide Polymorphism，SNP）的线性排列顺序。列标签说明如下：chromosome（染色体，编号1至5）、Sn=SNP编号ID（按染色体依次编号为1至N）、locus=SNP在本次从头组装结果中的位置，由重叠群（contig）标识及该重叠群上的坐标组成，二者以下划线分隔、Position=每条连锁群/染色体上的遗传距离，单位为厘摩根（centiMorgans，cM）。

该连锁图谱文件名为MapLinearOrderAllChrom.txt。