Evangelista Dominic A, Gilchrist Michael A, Legendre Frédéric, O'Meara Brian
Department of Ecology and Evolutionary Biology, The University of Tennessee, Dabney Hall, 1416 Circle Dr, Knoxville, TN, 37996, USA.
Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE-PSL, UA, 57 Rue Cuvier, CP50, Paris, FR, 75005, USA.
BMC Ecol Evol. 2025 Jul 21;25(1):72. doi: 10.1186/s12862-025-02409-4.
Patterns of discordance between gene trees and the species trees they reside in are crucial to the coalescent vs. concatenation debate and may be key to resolving rapid radiations. However, errors in gene trees complicate the issue as topological errors can cause gene trees to appear erroneously discordant with the species tree. In this study, we evaluate the prevalence of discordance between gene trees and their species tree using an empirical dataset for a clade with a rapid radiation (Blaberidae). One key advance of our study is the use of complex, computationally intensive, selection-based codon models (FMutSel0 and SelAC) to identify the maximum likelihood gene tree. Our main hypothesis predicted that, if there are two competing topologies for a particular gene tree, then the one that is less discordant with the species tree will have less systematic error.
Our experimental framework failed to show evidence for this, but only when discordance was measured in reference to a concatenation topology. In follow-up tests we see that the best candidate gene set yielded a coalescent species tree that was less discordant with gene trees.
We conclude from these tests that, although the frequency of discordance is on the low end of what is predicted by a range of modelling strategies, it is still extremely common overall and must be accounted for in order to achieve a biologically realistic outcome. These results allow us to support other relationships among blaberid cockroaches that were previously in flux as they now demonstrate molecular and morphological congruence. We suggest a few key improvements to the Blaberidae phylogeny, including identification of an anomaly zone spanning 10 backbone nodes and 6 additional nodes.
基因树与其所存在的物种树之间的不一致模式对于溯祖法与串联法的争论至关重要，并且可能是解决快速辐射问题的关键。然而，基因树中的错误使问题变得复杂，因为拓扑错误会导致基因树看似与物种树错误地不一致。在本研究中，我们使用一个具有快速辐射的类群（蜚蠊科）的实证数据集来评估基因树与其物种树之间不一致的普遍性。我们研究的一个关键进展是使用复杂的、计算密集型的基于选择的密码子模型（FMutSel0和SelAC）来识别最大似然基因树。我们的主要假设预测，如果特定基因树存在两种相互竞争的拓扑结构，那么与物种树不一致程度较小的那个将具有较小的系统误差。
我们的实验框架未能证明这一点，但仅当根据串联拓扑结构来衡量不一致时才是如此。在后续测试中，我们发现最佳候选基因集产生的溯祖物种树与基因树的不一致程度较小。
我们从这些测试中得出结论，尽管不一致的频率处于一系列建模策略预测范围的低端，但总体上仍然极为常见，为了获得生物学上现实的结果，必须考虑到这一点。这些结果使我们能够支持蜚蠊科蟑螂之间以前不确定的其他关系，因为它们现在显示出分子和形态上的一致性。我们建议对蜚蠊科系统发育进行一些关键改进，包括识别一个跨越10个主干节点和6个额外节点的异常区域。
