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.当前针对物种丰富类群的系统发育（phylogeny）树估算，主要存在两类主流方案：(i) 为少量物种选取大量基因座（locus，复数loci），即系统发育组学方法（phylogenomic approach）；(ii) 为大量物种选取少量基因座，即超级矩阵法（supermatrix approach）。理论上，可将这两类方案结合，同时解析高阶分类群关系（依托大量基因）与物种种级关系（依托大量分类群（taxon，复数taxa））。但该联合方案仍存在若干核心问题尚未得到解答：其一，联合方案得到的高阶分类群关系，与仅基于大量基因或仅基于大量分类群的估算结果相比，更趋近于哪一种？其二，相较于仅基于大量分类群的估算结果，联合方案能否提升高阶分类群关系的分支支持度（branch support）？ 本研究以有鳞目爬行动物（squamate reptiles）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：一份涵盖161个物种的44个基因，另一份涵盖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个基因的系统发育树共享的高阶演化支（clade）比例更高（分别为90%与77%）。高阶分类群关系的分支支持度略高于仅基于12个基因的结果，但低于仅基于44个基因的结果。即便整体缺失率高达92%，系统发育关系也未受到明显干扰。本研究构建了一套基于大规模基因与分类群取样的时间校准系统发育树（time-calibrated phylogeny），可为比较生物学研究提供基础数据资源。