Data from: Multi-locus analyses reveal four giraffe species instead of one

Traditionally, one giraffe species and up to eleven subspecies have been recognized [ 1 ]; however, nine subspecies are commonly accepted [ 2 ]. Even after a century of research, the distinctness of each giraffe subspecies remains unclear, and the genetic variation across their distribution range has been incompletely explored. Recent genetic studies on mtDNA have shown reciprocal monophyly of the matrilines among seven of the nine assumed subspecies [ 3, 4 ]. Moreover, until now, genetic analyses have not been applied to biparentally inherited sequence data and did not include data from all nine giraffe subspecies. We sampled natural giraffe populations from across their range in Africa, and for the first time individuals from the nominate subspecies, the Nubian giraffe, Giraffa camelopardalis camelopardalis Linnaeus 1758 [ 5 ], were included in a genetic analysis. Coalescence-based multi-locus and population genetic analyses identify at least four separate and monophyletic clades, which should be recognized as four distinct giraffe species under the genetic isolation criterion. Analyses of 190 individuals from maternal and biparental markers support these findings and further suggest subsuming Rothschild’s giraffe into the Nubian giraffe, as well as Thornicroft’s giraffe into the Masai giraffe [ 6 ]. A giraffe survey genome produced valuable data from microsatellites, mobile genetic elements, and accurate divergence time estimates. Our findings provide the most inclusive analysis of giraffe relationships to date and show that their genetic complexity has been underestimated, highlighting the need for greater conservation efforts for the world’s tallest mammal.传统上，长颈鹿曾被划分为1个有效物种及至多11个亚种[1]；但目前学界普遍认可9个亚种的分类方案[2]。即便历经百余年研究，各长颈鹿亚种的分类界定仍不明确，其分布范围内的遗传变异也尚未得到充分探究。近期针对线粒体DNA（mitochondrial DNA, mtDNA）的遗传学研究显示，9个假定亚种中的7个的母系支系呈现相互单系性[3,4]。此外，截至目前相关遗传分析尚未采用双亲遗传的序列数据，且未覆盖全部9个长颈鹿亚种。本研究对非洲全境的长颈鹿自然种群开展采样，且首次将指名亚种——努比亚长颈鹿（Giraffa camelopardalis camelopardalis Linnaeus 1758）[5]的个体纳入遗传分析。基于溯祖理论的多位点群体遗传分析鉴定出至少4个独立的单系支系，依据遗传隔离标准，这些支系应被认定为4个独立的长颈鹿物种。对190个个体的母系及双亲遗传标记分析验证了上述结论，并进一步提出将罗氏长颈鹿并入努比亚长颈鹿、将索氏长颈鹿并入马赛长颈鹿的分类建议[6]。长颈鹿调查基因组研究获取了微卫星、可移动遗传元件的有效数据，并实现了精确的分化时间估算。本研究的分析是迄今为止覆盖范围最广的长颈鹿亲缘关系研究，结果表明长颈鹿的遗传复杂性此前被低估，凸显了加强对这一世界最高哺乳动物保护工作的必要性。