Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA.
Mol Phylogenet Evol. 2010 Jul;56(1):64-76. doi: 10.1016/j.ympev.2010.01.036. Epub 2010 Feb 4.
The pantherine lineage of cats diverged from the remainder of modern Felidae less than 11 million years ago and consists of the five big cats of the genus Panthera, the lion, tiger, jaguar, leopard, and snow leopard, as well as the closely related clouded leopard. A significant problem exists with respect to the precise phylogeny of these highly threatened great cats. Despite multiple publications on the subject, no two molecular studies have reconstructed Panthera with the same topology. These evolutionary relationships remain unresolved partially due to the recent and rapid radiation of pantherines in the Pliocene, individual speciation events occurring within less than 1 million years, and probable introgression between lineages following their divergence. We provide an alternative, highly supported interpretation of the evolutionary history of the pantherine lineage using novel and published DNA sequence data from the autosomes, both sex chromosomes and the mitochondrial genome. New sequences were generated for 39 single-copy regions of the felid Y chromosome, as well as four mitochondrial and four autosomal gene segments, totaling 28.7 kb. Phylogenetic analysis of these new data, combined with all published data in GenBank, highlighted the prevalence of phylogenetic disparities stemming either from the amplification of a mitochondrial to nuclear translocation event (numt), or errors in species identification. Our 47.6 kb combined dataset was analyzed as a supermatrix and with respect to individual partitions using maximum likelihood and Bayesian phylogenetic inference, in conjunction with Bayesian Estimation of Species Trees (BEST) which accounts for heterogeneous gene histories. Our results yield a robust consensus topology supporting the monophyly of lion and leopard, with jaguar sister to these species, as well as a sister species relationship of tiger and snow leopard. These results highlight new avenues for the study of speciation genomics and understanding the historical events surrounding the origin of the members of this lineage.
猫科豹属的谱系与现代猫科动物的其余部分分化不到 1100 万年前，包括五种大型猫科动物，即狮、虎、美洲豹、豹和雪豹，以及密切相关的云豹。这些高度受威胁的大型猫科动物的精确系统发育存在一个重大问题。尽管已经有多篇关于这个主题的出版物，但没有两项分子研究能够重建豹属的相同拓扑结构。这些进化关系仍然没有得到解决，部分原因是豹属在上新世的快速辐射，个别物种形成事件发生在不到 100 万年的时间内，以及在它们分化后可能发生的谱系内基因渗入。我们使用来自常染色体、性染色体和线粒体基因组的新的和已发表的 DNA 序列数据，提供了豹属谱系进化历史的替代、高度支持的解释。为了生成新的序列，我们对猫科动物 Y 染色体的 39 个单拷贝区域进行了测序，以及四个线粒体和四个常染色体基因片段，总共 28.7 kb。对这些新数据的系统发育分析，以及 GenBank 中所有已发表的数据，突出了系统发育差异的普遍性，这些差异要么源于线粒体到核转移事件（numt）的扩增，要么源于物种鉴定的错误。我们的 47.6 kb 综合数据集被分析为一个超级矩阵，并针对单个分区使用最大似然和贝叶斯系统发育推断，以及贝叶斯物种树估计（BEST），该方法考虑了基因历史的异质性。我们的结果产生了一个稳健的共识拓扑结构，支持狮子和豹的单系性，以及美洲豹与这些物种的姐妹关系，以及老虎和雪豹的姐妹物种关系。这些结果突出了研究物种基因组学和理解该谱系成员起源周围历史事件的新途径。
