A surprising amount of hidden phylogenetic diversity exists in the small to medium size, drab colored squirrels of the genus Sundasciurus. This genus is endemic to Sundaland and the Philippines, where it is widespread. An earlier revision of this genus found that the high elevation ‘populations’ of the widespread, lowland slender squirrel (S. tenuis) were different species. Previous phylogenies based on mitochondrial cytochrome b sequences also suggested that the widespread, lowland Low’s squirrel (S. lowii) and the narrow endemic Fraternal squirrel (S. fraterculus) are not reciprocally monophyletic. Additionally, deep divergences have been identified between lineages within Low’s squirrel that date to the early Pliocene. Here we focus on evaluating the relationships and differences within and between populations of these two nominal species using whole mitochondrial genome sequences, nuclear intron sequences, and morphology. We reassess the taxonomy of this group, revalidate the species status of Robinson’s squirrel (Sundasciurus robinsoni Bonhote, 1903) support the species level recognition of the Natuna squirrel (Sundasciurus natunensis Thomas, 1895) and identify three other lineages that require further study. We estimate times of divergence and integrate geologic history to find that most of the divergences are pre-Pleistocene, and thus predate the Pleistocene flooding of Sundaland. Biogeographic, and ecological factors may have played a more important role than climatic factors in generating these patterns. While divergence in allopatry seems to be the main process driving speciation in lowland Sundaland squirrels (Sundasciurus), ecomorphological and behavioral adaptations in this clade suggest an important role of niche divergence.

中文翻译：

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依赖森林的巽他兰树松鼠的地理隔离和生态适应驱动的古代分歧

Sundasciurus 属的中小型、单调颜色的松鼠中存在数量惊人的隐藏系统发育多样性。该属是巽他兰和菲律宾的特有种，在那里广泛分布。该属的较早版本发现分布广泛的低地细长松鼠（S. tenuis）的高海拔“种群”是不同的物种。先前基于线粒体细胞色素 b 序列的系统发育还表明，广泛存在的低地低地松鼠 (S. lowii) 和狭窄的地方性松鼠 (S. fraterculus) 不是相互单系的。此外，在可以追溯到上新世早期的 Low 松鼠的谱系之间已经确定了深刻的分歧。在这里，我们专注于使用整个线粒体基因组序列、核内含子序列和形态来评估这两个名义物种的种群内部和种群之间的关系和差异。我们重新评估了该组的分类，重新验证了罗宾逊松鼠 (Sundasciurus robinsoni Bonhote, 1903) 的物种状态，支持了纳土纳松鼠 (Sundasciurus natunensis Thomas, 1895) 的物种水平识别，并确定了其他三个需要进一步研究的谱系。我们估计了分歧的时间并整合了地质历史，发现大多数分歧是更新世之前的，因此早于巽他大陆的更新世洪水。在产生这些模式方面，生物地理和生态因素可能比气候因素发挥了更重要的作用。