Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
复制标题
DOI：
10.1016/j.ympev.2022.107559
复制
发表时间：
2022-07-16
影响因子：
4.1
通讯作者：
Faircloth，Brant C.
中科院分区：
文献类型：
--
作者：
Salter，Jessie F.;Hosner，Peter A.;Faircloth，Brant C.
由于基因组学的重点是在物种和种群/亚种水平上进行全面的分类单元采样，因此从历史标本中整合基因组数据变得越来越普遍。虽然历史样本可以填补我们对不同群体进化历史的理解中的关键空白，但它们也引入了额外的基因组不确定性来源，使得很难从样本质量问题引起的人为因素中辨别出新的进化关系。这些问题突出了需要改进的策略，从真正的生物信号解开人为模式的历史标本变得更加普遍的基因组数据集。在这里，我们测试了历史上的鹌鹑驱动的基因组学的限制，以解决亚种级的关系内的一个高度多型的家庭，新世界鹌鹑（Odontophoridae），使用数千个ultraconserved元素（UCE）。我们发现，在物种水平和以上的关系得到了很好的解决，并高度支持所有的分析，除了两个最多型属，其中包括许多历史标本的不一致的关系。我们研究了不一致的原因，发现从分类群的子集推断出的不一致解决了分歧，这表明分析亚分支可以帮助消除包括历史样本的数据集中不一致的人为原因。在亚种水平上，我们发现了两个最多型的属，包括在这个家庭，北方Bobwhites（Colinus virginianus）的最多型的地理结构，表明UCE内的可变位点能够解决低于物种水平的系统发育结构。我们的研究结果突出了完整的分类学采样的重要性，解决多型物种之间的关系，往往通过列入历史标本，我们提出了一个综合性的战略，了解和解决的不确定性，历史样本有时引入系统发育分析。
As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.