Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, 13418900, Brazil.
Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20013, USA.
BMC Evol Biol. 2020 Jun 26;20(1):77. doi: 10.1186/s12862-020-01639-y.
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.
树松鼠（松鼠科，松鼠族），尤其是高度多样化的新热带谱系，是生命之树中分化最快的哺乳动物分支之一，但也是知之甚少的分支之一。系统发育学家对这个群体的忽视可能是由于评估形态学信息特征的困难以及缺乏或无法获得用于 DNA 测序的新鲜组织样本。这种高度不一致的分类安排是由于缺乏系统发育和仅基于表型的分类，这在形态保守的群体中可能具有误导性。在这里，我们使用高通量测序和对博物馆标本的前所未有的采样，提供了树松鼠的第一个综合系统发育，特别强调了新热带分类群。
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，代表了目前已识别的 43 种松鼠族中的 40 种。我们的系统发育分析 - 基于不同缺失数据水平和不同分析方法下的分类群数据集进行 - 强烈支持松鼠族的单系性，并一致恢复了该部落内的 12 个主要分支。我们发现证据表明，新热带树松鼠的多样性被低估了，至少有六个谱系代表有待命名或重新验证的分类群。上臼齿数量和乳腺数量的祖先状态重建表明，在树松鼠的进化历史中，这两个特征的替代条件必须多次进化。
从 120 岁的博物馆标本中获得了完整的线粒体基因组，这加强了历史样本在难以捉摸的生命之树谱系的系统发育推断中的潜力。松鼠族从未提出过的分类安排完全符合我们的系统发育重建，只有少数目前公认的属被恢复为单系。通过研究广泛用于该类群分类的两个形态特征的进化，我们揭示了它们的同形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，我们建议对松鼠族提出一个暂定的超种分类安排，使用之前分类学分类中使用的 13 个属名。
