Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul

Background: 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 phylogeneticists is likely a product of the scarcity or unavailability of fresh tissue samples for DNA sequencing. Lack of comprehensive phylogenies result in highly discrepant taxonomic arrangements that are based exclusively on morphological data—impressively, these are the only classification schemes available for the group. Here we used high-throughput sequencing and an unprecedented sampling effort of museum specimens to provide the first comprehensive phylogenetic analysis of tree squirrels, with a special emphasis on Neotropical taxa.
Results: We gathered mitochondrial genome data from 232 modern and historical samples, representing 40 out of the 43 currently recognized species of Sciurini. We found no correlation between specimen age and completeness of mitogenomes recovered for historical samples. Our phylogenetic analyses—performed with datasets differing on levels of missing data and taxa under distinctanalytical 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 seven lineages that might represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of pairs of mammae indicated that alternative conditions of both characters must have evolved multiple times along the evolutionary history of tree squirrels.
Conclusions: We were able to obtain complete mitogenomes for samples as old as 120 years, reinforcing the potential of historical samples for phylogenetic and evolutionary 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 to explain the incongruence between phylogenetic results and classification schemes presented so far, and we recommend a substantial taxonomic overhaul.

背景：树松鼠（Sciuridae, Sciurini），尤其是物种高度多样的新热带类群，是哺乳动物生命之树中分化速率最快的分支之一，同时也是研究程度最低的类群之一。系统发育学家对该类群的忽视，大概率源于用于DNA测序的新鲜组织样本稀缺或难以获取。由于缺乏全面的系统发育研究，仅基于形态数据建立的分类体系存在极大分歧——而此类形态分类方案仍是该类群目前仅有的分类框架。本研究借助高通量测序技术与前所未有的博物馆标本采样强度，首次完成了树松鼠类群的全面系统发育分析，研究重点特别聚焦于新热带类群。
结果：我们从232份现代及历史标本中获取了线粒体基因组数据，涵盖当前已正式确认的43种松鼠族（Sciurini）物种中的40种。我们未发现历史标本的保存时长与所获得的线粒体基因组组装完整性之间存在相关性。本研究采用了不同缺失数据水平与类群组成的数据集，并通过多种分析方法开展系统发育推断，结果强力支持松鼠族为单系群，且一致恢复出该族内的12个主要演化支。研究发现新热带树松鼠的物种多样性被严重低估，至少存在7个亟待命名或重新审定有效性的演化支。对上前臼齿数量与乳腺对数的祖先状态重建结果表明，这两个形态性状的不同状态在树松鼠的演化历史中均经历了多次独立起源与演化。
结论：我们成功从距今120年的历史标本中获得了完整的线粒体基因组，进一步证实了历史标本在生命之树中珍稀类群的系统发育与演化研究中的应用潜力。目前已提出的所有树松鼠分类体系均未与本研究的系统发育重建结果完全吻合，仅少数当前已确认的属被恢复为单系群。通过调查该类群分类学中广泛采用的两个形态性状的演化模式，我们揭示了二者的异源同形特征可解释此前系统发育结果与既有分类方案之间的不一致性，并建议对该类群开展大规模的分类学修订。