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

<p>The data deposited here was generated by and reported in&nbsp;Coimbra&nbsp;<em>et al.</em> (2023).</p> <p><em>SNP calling and linkage pruning</em></p> <ul> <li><strong>snp_calling_per_species.tar.gz:</strong> includes a genotype likelihoods (GL) file&nbsp;estimated with&nbsp;ANGSD for each giraffe species.</li> <li><strong>sampled_ld.tar.gz:</strong> contains a random sample of estimated&nbsp;pairwise&nbsp;<em>r²</em> values for each species used to fit linkage disequilibrium (LD) decay curves.</li> <li><strong>ld_pruned_snps.tar.gz:</strong> contains an LD-pruned ANGSD GL file&nbsp;per species.</li> <li><strong>snp_calling_combined.tar.gz:</strong> includes a single LD-pruned&nbsp;ANGSD GL&nbsp;file comprising all sampled&nbsp;individuals of the three giraffe species analyzed in this&nbsp;study.</li> </ul> <p><em>Relatedness</em></p> <ul> <li><strong>relatedness.tar.gz:</strong> contains the input and output files used with NGSremix&nbsp;to estimate relatedness among giraffe in the dataset.</li> <li><strong>snp_calling_combined_unrelated.tar.gz:</strong> includes a single LD-pruned&nbsp;ANGSD GL&nbsp;file comprising all unrelated individuals of the three giraffe species analyzed in this&nbsp;study.</li> </ul> <p><em>Population structure and admixture</em></p> <ul> <li><strong>pcangsd.tar.gz:</strong> contains the covariance matrix generated by PCAngsd.</li> <li><strong>ngsadmix.tar.gz:</strong> includes run likelihood lists for each K value ranging from 1 to 11, as well as the admixture proportions (stored in &#39;.qopt&#39; files) inferred from the run with the highest log-likelihood for each K in NGSadmix.</li> <li><strong>evaladmix.tar.gz:</strong>&nbsp;contains the pairwise correlation of residuals between individuals estimated with evalAdmix for the&nbsp;NGSadmix runs with the&nbsp;highest log-likelihood run for each K.</li> </ul> <p><em>SNP-based phylogenomic inference</em></p> <ul> <li><strong>snp_phylogeny.tar.gz:</strong> contains the input PHYLIP file&nbsp;and the IQ-TREE output tree&nbsp;and&nbsp;log files.</li> </ul> <p><em>Phylogeny of mitochondrial genomes</em></p> <ul> <li><strong>mtdna_phylogeny.tar.gz:</strong> includes the 13 mitochondrial protein-coding gene alignments, the partitions file, and the IQ-TREE output tree&nbsp;and&nbsp;log files.</li> </ul> <p><em>Inference of migration events</em></p> <ul> <li><strong>admixture_graphs.tar.gz:</strong> contains the TreeMix / OrientAGraph input file (&#39;treemix.frq.strat.gz&#39;), the output files for all TreeMix and OrientAGraph runs, and the OptM summary table of TreeMix runs (&#39;optm.tsv&#39;).</li> </ul> <p><em>Test for introgression</em></p> <ul> <li><strong>dsuite_introgression.tar.gz:</strong> includes the input VCF, the admixture graph topology reconstructed by OrientAGraph,&nbsp;and the Dsuite output files for the estimation of Patterson&#39;s D, f4-ratio, and f-branch statistics.</li> </ul> <p><em>Contemporary migration rates</em></p> <ul> <li><strong>ba3-snps.tar.gz:</strong> contains the input and output files for the BA3-SNPs-autotune and BA3-SNPs runs.</li> </ul> <p><em>Demographic reconstruction</em></p> <ul> <li><strong>demographic_inference.tar.gz:</strong> includes the SFS&nbsp;files generated with ANGSD and realSFS and the StairwayPlot2 blueprint and output files.</li> </ul> <p>Other:</p> <ul> <li><strong>metadata.csv:</strong>&nbsp;a companion file containing sample information used in conjunction with&nbsp;R scripts&nbsp;to plot the figures in the paper.</li> </ul>