Fig. 2

Nuclear and mitochondrial phylogenomic relationships among giraffe. Maximum likelihood phylogenies estimated from a 364,675 SNPs from 125 giraffe and b 13 mitochondrial protein-coding genes from 146 giraffe. The okapi was used as an outgroup (not shown). Colored tip labels indicate taxonomic assignment. Branch support was assessed with 1000 replicates of UFboot and SH-aLRT. Highly supported nodes (UFboot ≥ 95 and SH-aLRT ≥ 80) are marked with a black circle. In the nuclear tree, individuals formed clades corresponding to their respective species with high support. Mitochondrial introgression is observed from reticulated to Masai and from Masai to South African giraffe. Individual GF292 carries a Nubian giraffe mitochondrion and falls between the northern giraffe (i.e., West African, Kordofan, and Nubian) and the reticulated giraffe clades in the nuclear phylogeny, thus likely representing a natural hybrid