Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

Data from Louis M., Galimberti M, Archer F., Berrow S., Brownlow A., Fallon R., O'Brien J., Robertson K., Rosel P. E., Simon-Bouhet B., Wegmann D., Fontaine M. C. *, Foote A. D.*, Gaggiotti O. E.*. 2021. Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. (*these authors contributed equally). See materials and methods and supplementary material for details on data generation. This data archive includes 4 main files : The VCF file (called genotypes) 1_TtmappednewTtvar_biallelic.vcf.gz: Variant calling format (VCF) file including the biallelic single nucleotide variants (SNVs or SNPs) used in Louis et al. The sample names are in the vcf file header. See the materials and methods and supplementary material of the manuscript for details on data generation. Genotype likelihood Linkage-disequilibrium pruned input file 2_Tursiops_unlinkedSNPs.beagle.gz: Note that the sample order (Ind0 to Ind55) is given in the file Tursiops_samples_no7Tt182.bamlist. Sample 7Tt182 is not included in the beagle file due to its low coverage but clusters with the other NWAp. See materials and methods and supplementary material for details on data generation. haplo file (pseudo-haploid random call) 3_Tursiops_ALL.haplo: Individual order is given in Tursiops_samples_ALL.bamlist. Note that 7Tt182 is included there but was not included in the analyses, which are based on a subset of individuals (one coastal individual and all allopatric pelagic individuals except from 7Tt192).See materials and methods and supplementary material for details on data generation. GhostAncestry-master compressed folder (4_GhostAncestry-master.tar.gz) contains the codes written by Benoit Simon-Bouhet to generate the input files for the ghost ancestry analyses - also available at https://github.com/besibo/GhostAncestry ## The folder 1_One Scaffold contains the code to test the script on one scaffold only ## The folder 2_All scaffolds contains the code to run the script on all scaffolds # R code is FileMaker.R, note that you will need the script Custom_functions.R as well # Example input files are in _infiles # Example output files are in _outfiles - the input files for the ghost ancestry analyses from Skov et al. 2018. See materials and methods and supplementary material for details on data generation.

该数据集源自 Louis M.、Galimberti M、Archer F.、Berrow S.、Brownlow A.、Fallon R.、O'Brien J.、Robertson K.、Rosel P. E.、Simon-Bouhet B.、Wegmann D.、Fontaine M. C.* 等作者于 2021 年发表的研究成果。该研究揭示了祖先遗传变异对瓶鼻海豚生态型反复形成的影响。详细数据生成过程可参见材料与方法以及补充材料。数据存档包含以下四个主要文件：

1. VCF 文件（命名为基因型）1_TtmappednewTtvar_biallelic.vcf.gz：包含 Louis 等人研究中使用的双等位基因单核苷酸多态性（SNVs 或 SNPs）的变异数据，VCF 文件格式。样本名称位于文件头部。有关数据生成细节，请参阅论文中的材料与方法及补充材料。

2. 基因型似然连锁不平衡修剪输入文件 2_Tursiops_unlinkedSNPs.beagle.gz：请注意，样本顺序（Ind0 至 Ind55）由文件 Tursiops_samples_no7Tt182.bamlist 提供。样本 7Tt182 因覆盖度低而未包含在 beagle 文件中，但与其它 NWAp 样本聚类。数据生成细节请参阅材料与方法及补充材料。

3. 伪单倍型文件 3_Tursiops_ALL.haplo：个体顺序由 Tursiops_samples_ALL.bamlist 提供。请注意，7Tt182 虽然包含在该列表中，但未包含在分析中，分析基于个体子集（一个沿海个体以及所有非同域远洋个体，但 7Tt192 除外）。数据生成细节请参阅材料与方法及补充材料。

4. GhostAncestry-master 压缩文件夹（4_GhostAncestry-master.tar.gz）包含由 Benoit Simon-Bouhet 编写的生成 ghost ancestry 分析输入文件的代码，代码亦可在 https://github.com/besibo/GhostAncestry 上找到。

5. 1_One Scaffold 文件夹包含仅测试一个支架的代码。

6. 2_All scaffolds 文件夹包含在所有支架上运行脚本的代码。

R 语言代码位于 FileMaker.R，请注意，您还需要 Custom_functions.R 脚本。示例输入文件位于 _infiles，示例输出文件位于 _outfiles。这些输入文件是 Skov 等人于 2018 年发表的 ghost ancestry 分析的输入文件。数据生成细节请参阅材料与方法及补充材料。