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.