Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by systematists is likely a product of the difficulties in assessing morphological informative traits and of the scarcity or unavailability of fresh tissue samples for DNA sequencing. The highly discrepant taxonomic arrangements are a consequence of the lack of phylogenies and the exclusive phenotypic-based classifications, which can be misleading in a group with conservative morphology. Here we used high-throughput sequencing and an unprecedented sampling of museum specimens to provide the first comprehensive phylogeny of tree squirrels, with a special emphasis on Neotropical taxa. We obtained complete or partial mitochondrial genomes from 232 historical and modern samples, representing 40 of the 43 currently recognized species of Sciurini. Our phylogenetic analyses—performed with datasets differing on levels of missing data and taxa under distinct analytical methods—strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least six lineages that represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of mammae indicated that alternative conditions of both characters must have evolved multiple times throughout the evolutionary history of tree squirrels. Complete mitogenomes were obtained from museum specimens as old as 120 years, reinforcing the potential of historical samples for phylogenetic inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help explain the incongruence between phylogenetic results and the classification schemes presented so far. Based on our phylogenetic results we suggest a tentative supraspecific taxonomic arrangement for Sciurini, employing 13 generic names used in previous taxonomic classifications.

中文翻译：

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树松鼠的博物馆组学：线粒体基因组的密集分类采样揭示了隐藏的多样性、表型趋同以及分类学改革的需要。

树松鼠（Sciuridae、Sciurini），特别是高度多样化的新热带谱系，是哺乳动物生命之树中多样化最快的分支之一，但也是一些最不为人所知的分支。系统学家对这一群体的忽视可能是由于难以评估形态信息性状以及缺乏或无法获得用于 DNA 测序的新鲜组织样本。高度差异的分类排列是由于缺乏系统发育和基于表型的排他性分类的结果，这在形态保守的群体中可能会产生误导。在这里，我们使用高通量测序和前所未有的博物馆标本采样，提供了第一个全面的树松鼠系统发育学，特别强调新热带类群。我们从 232 个历史和现代样本中获得了完整或部分线粒体基因组，代表了目前公认的 43 个 Sciurini 物种中的 40 个。我们的系统发育分析（在不同的分析方法下使用不同程度的缺失数据和类群的数据集进行）强烈支持 Sciurini 的单系性，并一致地恢复了该部落内的 12 个主要分支。我们发现有证据表明新热带树松鼠的多样性被低估，至少有六个代表类群的谱系被命名或重新验证。上前臼齿数量和乳房数量的祖先状态重建表明，在树松鼠的进化史上，这两个特征的替代条件必定已经进化了多次。从长达 120 年的博物馆标本中获得了完整的线粒体基因组，增强了历史样本对生命之树难以捉摸的谱系进行系统发育推断的潜力。迄今为止为树松鼠提出的分类学安排都没有完全符合我们的系统发育重建，只有少数目前公认的属恢复为单系。通过研究该类群分类学中广泛采用的两种形态特征的进化，我们发现它们的同质性可以帮助解释系统发育结果与迄今为止提出的分类方案之间的不一致。根据我们的系统发育结果，我们建议对 Sciurini 进行暂定的超种分类学安排，采用先前分类学分类中使用的 13 个属名。