Data from: Genomic analysis reveals limited hybridization among three giraffe species in Kenya

The data deposited here was generated by and reported in Coimbra et al. (2023). SNP calling and linkage pruning snp_calling_per_species.tar.gz: includes a genotype likelihoods (GL) file estimated with ANGSD for each giraffe species. sampled_ld.tar.gz: contains a random sample of estimated pairwise r2 values for each species used to fit linkage disequilibrium (LD) decay curves. ld_pruned_snps.tar.gz: contains an LD-pruned ANGSD GL file per species. snp_calling_combined.tar.gz: includes a single LD-pruned ANGSD GL file comprising all sampled individuals of the three giraffe species analyzed in this study. Relatedness relatedness.tar.gz: contains the input and output files used with NGSremix to estimate relatedness among giraffe in the dataset. snp_calling_combined_unrelated.tar.gz: includes a single LD-pruned ANGSD GL file comprising all unrelated individuals of the three giraffe species analyzed in this study. Population structure and admixture pcangsd.tar.gz: contains the covariance matrix generated by PCAngsd. ngsadmix.tar.gz: includes run likelihood lists for each K value ranging from 1 to 11, as well as the admixture proportions (stored in '.qopt' files) inferred from the run with the highest log-likelihood for each K in NGSadmix. evaladmix.tar.gz: contains the pairwise correlation of residuals between individuals estimated with evalAdmix for the NGSadmix runs with the highest log-likelihood run for each K. SNP-based phylogenomic inference snp_phylogeny.tar.gz: contains the input PHYLIP file and the IQ-TREE output tree and log files. Phylogeny of mitochondrial genomes mtdna_phylogeny.tar.gz: includes the 13 mitochondrial protein-coding gene alignments, the partitions file, and the IQ-TREE output tree and log files. Inference of migration events admixture_graphs.tar.gz: contains the TreeMix / OrientAGraph input file ('treemix.frq.strat.gz'), the output files for all TreeMix and OrientAGraph runs, and the OptM summary table of TreeMix runs ('optm.tsv'). Test for introgression dsuite_introgression.tar.gz: includes the input VCF, the admixture graph topology reconstructed by OrientAGraph, and the Dsuite output files for the estimation of Patterson's D, f4-ratio, and f-branch statistics. Contemporary migration rates ba3-snps.tar.gz: contains the input and output files for the BA3-SNPs-autotune and BA3-SNPs runs. Demographic reconstruction demographic_inference.tar.gz: includes the SFS files generated with ANGSD and realSFS and the StairwayPlot2 blueprint and output files. Other: metadata.csv: a companion file containing sample information used in conjunction with R scripts to plot the figures in the paper.本存档数据集由Coimbra等人（2023）生成并报道。 SNP分型与连锁修剪（SNP calling and linkage pruning） snp_calling_per_species.tar.gz：包含针对每一种长颈鹿物种的、由ANGSD估算得到的基因型似然值（genotype likelihoods, GL）文件。 sampled_ld.tar.gz：包含用于拟合连锁不平衡（linkage disequilibrium, LD）衰减曲线的各物种的随机抽样成对r²值数据集。 ld_pruned_snps.tar.gz：包含针对各物种的、经连锁不平衡修剪后的ANGSD基因型似然值文件。 snp_calling_combined.tar.gz：包含单个经连锁不平衡修剪的ANGSD基因型似然值文件，涵盖本研究中分析的三种长颈鹿物种的全部采样个体。 亲缘关系分析（Relatedness） relatedness.tar.gz：包含用于NGSremix估算数据集内长颈鹿个体间亲缘关系的输入与输出文件。 snp_calling_combined_unrelated.tar.gz：包含单个经连锁不平衡修剪的ANGSD基因型似然值文件，涵盖本研究中分析的三种长颈鹿物种的全部无关个体。 种群结构与遗传混合（Population structure and admixture） pcangsd.tar.gz：包含由PCAngsd生成的协方差矩阵。 ngsadmix.tar.gz：包含K值范围为1至11的各次运行的似然值列表，以及针对每个K值在最高对数似然值运行中得到的遗传混合比例（存储于'.qopt'文件中），该结果由NGSadmix推断得到。 evaladmix.tar.gz：包含针对每个K值下最高对数似然值的NGSadmix运行结果，由evalAdmix估算得到的个体间残差两两相关性数据。 基于SNP的系统基因组学推断（SNP-based phylogenomic inference） snp_phylogeny.tar.gz：包含输入的PHYLIP格式文件以及IQ-TREE输出的系统发育树与日志文件。 线粒体基因组系统发育（Phylogeny of mitochondrial genomes） mtdna_phylogeny.tar.gz：包含13个线粒体蛋白编码基因的比对序列、分区文件以及IQ-TREE输出的系统发育树与日志文件。 迁移事件推断（Inference of migration events） admixture_graphs.tar.gz：包含TreeMix / OrientAGraph的输入文件（'treemix.frq.strat.gz'）、所有TreeMix与OrientAGraph运行的输出文件，以及TreeMix运行的OptM汇总表（'optm.tsv'）。 基因渗入检测（Test for introgression） dsuite_introgression.tar.gz：包含输入的VCF格式文件、由OrientAGraph重构的遗传混合拓扑结构，以及用于估算Patterson's D、f4-ratio与f-branch统计量的Dsuite输出文件。 当代迁移率估算（Contemporary migration rates） ba3-snps.tar.gz：包含BA3-SNPs-autotune与BA3-SNPs运行的输入与输出文件。 种群历史重建（Demographic reconstruction） demographic_inference.tar.gz：包含由ANGSD与realSFS生成的站点频率谱（site frequency spectrum, SFS）文件，以及StairwayPlot2的蓝图文件与输出文件。 其他（Other:） metadata.csv：配套样本信息文件，用于配合R脚本绘制论文中的相关图表。