The hares and rabbits belonging to the family Leporidae have a nearly worldwide distribution and approximately 72% of the genera have geographically restricted distributions. Despite several attempts using morphological, cytogenetic, and mitochondrial DNA evidence, a robust phylogeny for the Leporidae remains elusive. To provide phylogenetic resolution within this group, a molecular supermatrix was constructed for 27 taxa representing all 11 leporid genera. Five nuclear (SPTBN1, PRKCI, THY, TG, and MGF) and two mitochondrial (cytochrome b and 12S rRNA) gene fragments were analyzed singly and in combination using parsimony, maximum likelihood, and Bayesian inference. The analysis of each gene fragment separately as well as the combined mtDNA data almost invariably failed to provide strong statistical support for intergeneric relationships. In contrast, the combined nuclear DNA topology based on 3601 characters greatly increased phylogenetic resolution among leporid genera, as was evidenced by the number of topologies in the 95% confidence interval and the number of significantly supported nodes. The final molecular supermatrix contained 5483 genetic characters and analysis thereof consistently recovered the same topology across a range of six arbitrarily chosen model specifications. Twelve unique insertion-deletions were scored and all could be mapped to the tree to provide additional support without introducing any homoplasy. Dispersal-vicariance analyses suggest that the most parsimonious solution explaining the current geographic distribution of the group involves an Asian or North American origin for the Leporids followed by at least nine dispersals and five vicariance events. Of these dispersals, at least three intercontinental exchanges occurred between North America and Asia via the Bering Strait and an additional three independent dispersals into Africa could be identified. A relaxed Bayesian molecular clock applied to the seven loci used in this study indicated that most of the intercontinental exchanges occurred between 14 and 9 million years ago and this period is broadly coincidental with the onset of major Antarctic expansions causing land bridges to be exposed.

中文翻译：

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兔和野兔（兔科）的分子超矩阵允许识别中新世期间的五个洲际交换

属于兔科的野兔和兔子几乎在世界范围内都有分布，大约 72% 的属具有地域限制分布。尽管使用形态学、细胞遗传学和线粒体 DNA 证据进行了多次尝试，但 Leporidae 的强大系统发育仍然难以捉摸。为了在该组内提供系统发育分辨率，为代表所有 11 个 leporid 属的 27 个分类群构建了一个分子超矩阵。使用简约、最大似然和贝叶斯推理单独和组合分析了五个核（SPTBN1、PRKCI、THY、TG 和 MGF）和两个线粒体（细胞色素 b 和 12S rRNA）基因片段。对每个基因片段的单独分析以及合并的 mtDNA 数据几乎总是无法为属间关系提供强有力的统计支持。相比之下，基于 3601 个字符的组合核 DNA 拓扑大大提高了 leporid 属之间的系统发育分辨率，95% 置信区间中的拓扑数量和显着支持的节点数量证明了这一点。最终的分子超矩阵包含 5483 个遗传特征，其分析在六个任意选择的模型规格范围内一致地恢复了相同的拓扑结构。对 12 个独特的插入-缺失进行评分，所有这些都可以映射到树上以提供额外的支持，而不会引入任何同质性。分散-替代分析表明，解释该群体当前地理分布的最简洁的解决方案涉及 Leporids 的亚洲或北美起源，其次是至少 9 次分散和 5 次替代事件。在这些扩散中，至少有 3 次通过白令海峡在北美和亚洲之间发生了洲际交流，另外还可以确定另外 3 次独立扩散到非洲。应用于本研究中使用的七个位点的松弛贝叶斯分子钟表明，大部分洲际交换发生在 14 到 900 万年前之间，这一时期与导致陆桥暴露的主要南极扩张的开始大致一致。