Departamento de Genética, Rio de Janeiro, Universidade Federal do Rio de Janeiro, CCS, Instituto de Biologia, Rio de Janeiro, Brazil.
Departamento de Zoologia, Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Maracanã, Rio de Janeiro, Brazil.
PLoS One. 2024 Sep 6;19(9):e0307380. doi: 10.1371/journal.pone.0307380. eCollection 2024.
Despite their importance as members of the Glires group, lagomorph diversification processes have seldom been studied using molecular data. Notably, only a few phylogenetic studies have included most of the examined lagomorph lineages. Previous studies that included a larger sample of taxa and markers used nonconservative tests to support the branches of their proposed phylogeny. The objective of this study was to test the monophyly of families and genera of lagomorphs and to evaluate the group diversification process. To that end, this work expanded the sampling of markers and taxa in addition to implementing the bootstrap, a more rigorous statistical test to measure branch support; hence, a more robust phylogeny was recovered. Our supermatrix included five mitochondrial genes and 14 nuclear genes for eighty-eight taxa, including three rodent outgroups. Our maximum likelihood tree showed that all tested genera and both families, Leporidae and Ochotonidae, were recovered as monophyletic. In the Ochotona genus, the subgenera Conothoa and Pika, but not Ochotona, were recovered as monophyletic. Six calibration points based on fossils were used to construct a time tree. A calibration test was performed (via jackknife) by removing one calibration at a time and estimating divergence times for each set. The diversification of the main groups of lagomorphs indicated that the origin of the order's crown group was dated from the beginning of the Palaeogene. Our diversification time estimates for Lagomorpha were compared with those for the largest mammalian order, i.e., rodent lineages in Muroidea. According to our time-resolved phylogenetic tree, the leporids underwent major radiation by evolving a completely new morphospace-larger bodies and an efficient locomotor system-that enabled them to cover wide foraging areas and outrun predators more easily than rodents and pikas.
尽管兔形目作为啮齿类动物群的重要成员，但利用分子数据研究兔形目多样化过程的情况很少。值得注意的是，只有少数系统发育研究包括了大多数被检查的兔形目谱系。以前的研究包括了更大的分类群和标记物样本，使用非保守测试来支持其提出的系统发育的分支。本研究的目的是检验兔形目科和属的单系性，并评估该群体的多样化过程。为此，这项工作除了实施bootstrap（一种更严格的统计测试来衡量分支支持的方法）来扩展标记物和分类群的采样外，还恢复了一个更强大的系统发育树。我们的超级矩阵包括 5 个线粒体基因和 14 个核基因，用于 88 个分类群，包括 3 个啮齿动物外群。我们的最大似然树表明，所有测试的属和两个科，兔科和鼠兔科，都是单系的。在鼠兔属中，亚属 Conothoa 和 Pika，但不是 Ochotona，被恢复为单系的。使用 6 个基于化石的校准点来构建一个时间树。通过一次删除一个校准点并对每个集合进行分歧时间估计来进行校准测试（通过 jackknife）。兔形目的主要群体的多样化表明，该目的冠群的起源可以追溯到始新世早期。我们对兔形目多样化时间的估计与最大的哺乳动物目，即 Muroidea 中的啮齿动物谱系的估计进行了比较。根据我们的时间分辨系统发育树，兔形目经历了主要的辐射，进化出了一个全新的形态空间——更大的体型和更有效的运动系统——使它们能够覆盖更广泛的觅食区域，并比啮齿动物和鼠兔更容易逃脱捕食者。
