Data from: When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny

Simulation studies suggest that coalescent-based species-tree methods are generally more accurate than concatenated analyses. However, these species-tree methods remain impractical for many large datasets. Thus, a critical but unresolved issue is when and why concatenated and coalescent species-tree estimates will differ. We predict such differences for branches in concatenated trees that are short, weakly supported, and have conflicting gene trees. We test these predictions in Scincidae, the largest lizard family, with data from 10 nuclear genes for 17 ingroup taxa and 44 genes for 12 taxa. We support our initial predictions, and suggest that simply considering uncertainty in concatenated trees may sometimes encompass the differences between these methods. We also found that relaxed-clock concatenated trees can be surprisingly similar to the species-tree estimate. Remarkably, the coalescent species-tree estimates had slightly lower support values when based on many more genes (44 vs. 10) and a small (∼30%) reduction in taxon sampling. Thus, taxon sampling may be more important than gene sampling when applying species-tree methods to deep phylogenetic questions. Finally, our coalescent species-tree estimates tentatively support division of Scincidae into three monophyletic subfamilies, a result otherwise found only in concatenated analyses with extensive species sampling.

模拟研究表明，基于溯祖的物种树（coalescent-based species-tree）方法总体上比串联分析（concatenated analyses）更为精准。然而，这类物种树方法在诸多大型数据集上仍难以实用化。因此，一个关键且尚未解决的问题是：串联分析与溯祖物种树估计结果何时会产生分歧，以及为何会产生此类分歧。我们预测，串联树中长度较短、支持度较弱且存在冲突基因树的分支，会出现这类分析结果分歧。我们以蜥蜴类群中最大的科——石龙子科（Scincidae）为研究对象，采用两套数据集开展预测检验：一套包含17个内群类群的10个核基因数据，另一套包含12个类群的44个核基因数据。研究结果验证了我们的初始预测，并提出：仅考虑串联树的不确定性，有时便可涵盖这两类分析方法之间的结果分歧。我们还发现，松弛分子钟（relaxed-clock）串联树与物种树估计结果的相似程度远超预期。值得注意的是，当基于更多基因（44个相较于10个）且类群采样量小幅减少（约30%）时，溯祖物种树估计的支持度反而略低。因此，在针对深度系统发育问题应用物种树方法时，类群采样或许比基因采样更为关键。最后，我们的溯祖物种树估计结果初步支持将石龙子科划分为三个单系亚科，这一结果此前仅在采用大量类群采样的串联分析中被观测到。