Journal
MOLECULAR PHYLOGENETICS AND EVOLUTION
Volume 94, Issue -, Pages 537-547Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2015.10.009
Keywords
Missing data; Phylogenomic; Phylogeny; Squamata; Supermatrix
Funding
- National Natural Science Foundation of China [NSFC-31372181]
- Chinese Academy of Sciences [Y1C3051100]
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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. (C) 2015 Elsevier Inc. All rights reserved.
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