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bioRxiv · 10.1101/049643

Inferring node dates from tip dates in fossil Canidae: the importance of tree priors

Nicholas Joseph Matzke·April Wright
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Abstract

Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using Beast 2.1.3 and MrBayes 3.2.5. We find that for key nodes (Canis, ~3.2 Ma, Caninae ~11.7 Ma) a non-mechanistic model using a uniform tree prior produces estimates that are unrealistically old (27.5, 38.9 Ma). Mechanistic models (incorporating lineage birth, death, and sampling rates) estimate ages that are closely in line with prior research. We provide a discussion of these two families of models (mechanistic vs. non-mechanistic) and their applicability to fossil datasets.

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Nicholas Joseph Matzke, April Wright. 2016-04-21. Inferring node dates from tip dates in fossil Canidae: the importance of tree priors. https://doi.org/10.1101/049643

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