Data from: Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

Two common approaches for estimating phylogenies in species-rich groups are to: (i) sample many loci for few species (e.g. phylogenomic approach), or (ii) sample many species for fewer loci (e.g. supermatrix approach). In theory, these approaches can be combined to simultaneously resolve both higher-level relationships (with many genes) and species-level relationships (with many taxa). However, fundamental questions remain unanswered about this combined approach. First, will higher-level relationships more closely resemble those estimated from many genes or those from many taxa? Second, will branch support increase for higher-level relationships (relative to the estimate from many taxa)? Here, we address these questions in squamate reptiles. We combined two recently published datasets, one based on 44 genes for 161 species, and one based on 12 genes for 4161 species. The likelihood-based tree from the combined matrix (52 genes, 4162 species) shared more higher-level clades with the 44-gene tree (90% vs. 77% shared). Branch support for higher level-relationships was marginally higher than in the 12-gene tree, but lower than in the 44-gene tree. Relationships were apparently not obscured by the abundant missing data (92% overall). We provide a time-calibrated phylogeny based on extensive sampling of genes and taxa as a resource for comparative studies.

在物种丰富类群中估算系统发育树（phylogeny）通常采用两种常见策略：其一为对少量物种采样大量基因座（locus，复数loci），即系统发育组学方法（phylogenomic approach）；其二为对大量物种采样少量基因座，即超级矩阵法（supermatrix approach）。理论上，可将这两种策略结合，同时借助大量基因解析高级阶元亲缘关系，借助大量类群（taxon，复数taxa）解析物种级亲缘关系。然而，这种联合策略仍存在若干尚未解决的核心问题：其一，联合策略得到的高级阶元亲缘关系，是否更接近基于大量基因估算的结果，还是基于大量类群的估算结果？其二，相较于仅基于大量类群的估算结果，联合策略下高级阶元亲缘关系的支系支持度是否会提升？本研究以有鳞目爬行动物（squamate reptile）为研究对象，对上述问题展开探讨。我们整合了两份新近发表的数据集：一份基于161个物种的44个基因，另一份基于4161个物种的12个基因。基于联合矩阵（包含52个基因、4162个物种）构建的似然法系统发育树，与仅基于44个基因的树共享的高级阶元演化支（clade）比例更高（分别为90%与77%）。高级阶元亲缘关系的支系支持度略高于仅基于12个基因的树，但低于仅基于44个基因的树。整体缺失率达92%的大量缺失数据并未明显干扰亲缘关系的解析。本研究提供了一套基于广泛基因与类群采样的时间校准系统发育树，可为比较生物学研究提供参考资源。