Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil; Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA.
Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA.
Mol Phylogenet Evol. 2022 Oct;175:107576. doi: 10.1016/j.ympev.2022.107576. Epub 2022 Jul 6.
Ultraconserved Elements (UCEs) have been useful to resolve challenging phylogenies of non-model clades, unpuzzling long-conflicted relationships in key branches of the Tree of Life at both deep and shallow levels. UCEs are often reliably recovered from historical samples, unlocking a vast number of preserved natural history specimens for analysis. However, the extent to which sample age and preservation method impact UCE recovery as well as downstream inferences remains unclear. Furthermore, there is an ongoing debate on how to curate, filter, and properly analyze UCE data when locus recovery is uneven across sample age and quality. In the present study we address these questions with an empirical dataset composed of over 3800 UCE loci from 219 historical and modern samples of Sciuridae, a globally distributed and ecologically important family of rodents. We provide a genome-scale phylogeny of two squirrel subfamilies (Sciurillinae and Sciurinae: Sciurini) and investigate their placement within Sciuridae. For historical specimens, recovery of UCE loci and mean length per locus were inversely related to sample age; deeper sequencing improved the number of UCE loci recovered but not locus length. Most of our phylogenetic inferences-performed on six datasets with alternative data-filtering strategies, and using three distinct optimality criteria-resulted in distinct topologies. Datasets containing more loci (40% and 50% taxa representativeness matrices) yielded more concordant topologies and higher support values than strictly filtered datasets (60% matrices) particularly with IQ-Tree and SVDquartets, while filtering based on information content provided better topological resolution for inferences with the coalescent gene-tree based approach in ASTRAL-III. We resolved deep relationships in Sciuridae (including among the five currently recognized subfamilies) and relationships among the deepest branches of Sciurini, but conflicting relationships remain at both genus- and species-levels for the rapid Neotropical tree squirrel radiation. Our results suggest that phylogenomic consensus can be difficult and heavily influenced by the age of available samples and the filtering steps used to optimize dataset properties.
超保守元件 (UCEs) 在解决非模型类群的具有挑战性的系统发育以及解开生命之树的深、浅分支中关键分支的长期冲突关系方面非常有用。UCEs 通常可以从历史样本中可靠地回收，从而为分析提供大量保存的自然历史标本。然而，样本年龄和保存方法对 UCE 回收以及下游推论的影响程度尚不清楚。此外，当因样本年龄和质量不同而导致基因座回收率不均匀时，如何管理、筛选和正确分析 UCE 数据仍存在争议。在本研究中，我们使用由 219 个历史和现代松鼠科样本的 3800 多个 UCE 基因座组成的经验数据集来解决这些问题，松鼠科是分布广泛且具有重要生态意义的啮齿动物科。我们提供了两个松鼠亚科（Sciurillinae 和 Sciurinae: Sciurini）的基因组规模系统发育，并研究了它们在松鼠科中的位置。对于历史标本，UCE 基因座的回收率和每个基因座的平均长度与样本年龄呈反比；更深的测序提高了 UCE 基因座的回收率，但没有改善基因座长度。我们的大多数系统发育推断——使用六种具有替代数据过滤策略的数据集，并使用三种不同的最优性标准——产生了不同的拓扑结构。包含更多基因座的数据集（40%和 50%分类群代表性矩阵）产生了更一致的拓扑结构和更高的支持值，而严格过滤的数据集（60%矩阵）则不然，特别是使用 IQ-Tree 和 SVDquartets 时，而基于信息量的过滤则为 ASTRAL-III 中的基于合并基因树的方法提供了更好的拓扑分辨率推断。我们解决了松鼠科的深系关系（包括目前公认的五个亚科之间的关系）以及 Sciurini 最深分支之间的关系，但在快速的新热带树松鼠辐射中，种属水平的关系仍然存在冲突。我们的结果表明，基因组共识可能很困难，并且会受到可用样本年龄和用于优化数据集特性的过滤步骤的严重影响。
