The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477–0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0–0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.

中文翻译：

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揭开非洲豹 (Panthera pardus pardus) 的母系进化史

非洲豹（Panthera pardus pardus）已经失去了很大一部分其历史分布范围，特别是在非洲西北部和南非。最近的研究探索了整个非洲大陆非洲豹的遗传多样性和种群结构。一个值得注意的遗传观察是存在两个不同的线粒体谱系：PAR-I 和 PAR-II。这两个谱系似乎分布广泛，其中 PAR-II 常见于南部非洲。到目前为止，还没有研究尝试确定这两个谱系的出现日期、评估单倍型分布或详细探索它们的进化历史。为了研究这些未被充分认识的问题，我们编制了迄今为止最大且最具地理代表性的豹子线粒体 NADH-5 基因数据集。我们将在南非普马兰加省的海拔样带收集的样本 (n = 33) 与之前发表的非洲豹序列 (n = 211) 结合起来，其中已知两个豹种群存在遗传接触。我们估计母系 PAR-I 和 PAR-II 谱系在大约 0.7051 (0.4477–0.9632) 万年前 (Ma) 出现分歧。通过空间和人口统计分析，我们表明，虽然 PAR-I 经历了中更新世种群扩张，产生了几种密切相关的单倍型，在其大部分范围内几乎没有地理结构，但 PAR-II 的大小保持不变，甚至可能在最后0.1 Ma。 PAR-II 中经历的更高的遗传漂变驱动了更大程度的结构，在中非、开普敦、夸祖鲁-纳塔尔省和南非高地草原上几乎没有单倍型共享和独特的单倍型。 PAR-II的系统发育地理学结构，随着其向南频率的增加以及仅出现在南非东南部，表明该谱系可能在更新世中期在南非被隔离。这一假说得到了古气候历史变化的支持，这些变化在 1.0-0.6 Ma 之间促进了林波波盆地周围的强烈干旱化，可能减少基因流并促进遗传漂变。有趣的是，我们确定之前的研究确定的东普马兰加和西普马兰加的两个核DNA群体分别对应于PAR-I和PAR-II，并且它们在南非的Lowveld地区进行了二次接触。我们的结果表明，非洲豹 mtDNA 细分为两个分支，其中一个几乎只发生在南非，并且我们确定了这一观察到的结构的潜在环境驱动因素。我们警告说，我们的结果是基于单个 mtDNA 位点，但它仍然提供了一个假设，可以用密集的核 DNA 数据样本（最好是整个基因组）进一步测试。如果我们的解释成立，这将为在非洲分布范围最南端观察到的豹子体型较小提供第一个遗传学解释。