Fig. 1

Population structure of Nubian, reticulated, and Masai giraffe s. str. a Geographical distribution of Nubian, reticulated, and Masai giraffe s. str. (colored shadings) in East Africa and sampling locations (colored shapes and numbers). Hatched areas show the estimated range of Nubian and reticulated giraffe populations. b PCA of 484,876 unlinked SNPs from 116 individuals representing Nubian, reticulated, and Masai giraffe s. str. PC1 separates Nubian and reticulated from Masai giraffe s. str., and PC2 separates Nubian from reticulated giraffe. The PCA space is further explored in Additional file 2: Fig. S2. c Ancestry proportions estimated from the same SNP dataset for K = 3 and K = 9. The estimates shown represent the runs with the highest log-likelihood out of 100 runs for their respective K. Colors indicate an individual’s cluster membership. The numbers in between plots represent sampling locations according to a. Interspecies admixture is found mostly between Nubian and reticulated giraffe at K = 3 and is restricted to two individuals from Loisaba Conservancy at K = 9. Admixture analyses for K = 2–11 are shown in Additional file 2: Fig. S3. d The mean likelihood and standard error (SE) across 100 runs per K. The mean likelihoods start plateauing at K = 3. e Assessment of admixture model fit based on the correlation of residuals for K = 3 and K = 9. The assessed models are the runs with the highest log-likelihood out of 100 runs for their respective K. Plotted values are the mean correlation within and between individuals from each sampling locality. Model fit assessments for K = 1–11 showing the pairwise correlation of residuals between all individuals are available in Additional file 2: Fig. S4. The order of sampling localities is the same as in c. Localities with only one sampled individual are shown in gray