Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT.
Mol Biol Evol. 2021 Mar 9;38(3):1090-1100. doi: 10.1093/molbev/msaa277.
Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. Incongruence originates from uncertainty in underlying evolutionary processes (e.g., incomplete lineage sorting) and from difficulties in determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences and demonstrate practical ways to confidently resolve them. Here, we present results of a phylogenomic study based on the analysis 197 taxa and 2,526 ultraconserved element (UCE) loci. We investigate evolutionary relationships of Eucerinae, a diverse subfamily of apid bees (relatives of honey bees and bumble bees) with >1,200 species. We sampled representatives of all tribes within the group and >80% of genera, including two mysterious South American genera, Chilimalopsis and Teratognatha. Initial analysis of the UCE data revealed two conflicting hypotheses for relationships among tribes. To resolve the incongruence, we tested concatenation and species tree approaches and used a variety of additional strategies including locus filtering, partitioned gene-trees searches, and gene-based topological tests. We show that within-locus partitioning improves gene tree and subsequent species-tree estimation, and that this approach, confidently resolves the incongruence observed in our data set. After exploring our proposed analytical strategy on eucerine bees, we validated its efficacy to resolve hard phylogenetic problems by implementing it on a published UCE data set of Adephaga (Insecta: Coleoptera). Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.
系统发育结果的不一致在基于基因组规模数据集的分析中已变得很常见。不一致性源于基础进化过程中的不确定性（例如不完全谱系分选），以及确定每种情况最佳分析方法的困难。为了克服这些困难，需要更多的研究来识别不一致性，并展示有信心解决它们的实际方法。在这里，我们根据对 197 个分类群和 2526 个超保守元件 (UCE) 位点的分析，展示了系统基因组学研究的结果。我们研究了多样化的 Apidae（与蜜蜂和熊蜂有关的亲戚）亚科 Eucerinae 的进化关系，该亚科有超过 1200 个物种。我们对该组内的所有部落以及 80%以上的属，包括两个神秘的南美属 Chilimalopsis 和 Teratognatha 进行了采样。对 UCE 数据的初步分析揭示了部落之间关系的两个相互冲突的假设。为了解决不一致性，我们测试了串联和种系树方法，并使用了各种其他策略，包括基因过滤、分区基因树搜索和基于基因的拓扑测试。我们表明，基因内分区可改善基因树和随后的种系树估计，并且这种方法可以自信地解决我们数据集观察到的不一致性。在对 Eucerinae 蜜蜂进行了分析后，我们验证了其在解决硬系统发育问题方面的有效性，方法是在昆虫纲鞘翅目（Coleoptera）的已发表 UCE 数据集上实施该方法。我们的结果为 Eucerinae 提供了一个稳健的系统发育假说，并展示了一种在其他系统基因组学数据集上解决不一致性的实用策略。
