Confronting sources of systematic error to resolve historically contentious relationships: a case study using gadiform fishes (Teleostei, Paracanthopterygii, Gadiformes)

Adela Roa-Varon, Rebecca Dikow, Giorgio Carnevale, Luke Tornabene, Carole Baldwin, Chenhong Li & Eric Hilton
Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large datasets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or...
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