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

Shea M. Lambert, Tod W. Reeder & John J. Wiens
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...
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