Ground truthing tip-dating methods using fossil Canidae reveals major differences in performance

Tip-dating methods are becoming popular alternatives to traditional "node-dating." However, they have not been extensively tested. We "ground-truth" the most popular methods against a dated tree of fossil Canidae derived from monographs by Wang and Tedford. Using a revised canid morphology dataset we compare MrBayes 3.2.5 to Beast 2.1.3 combined with BEASTmasteR (phylo.wikidot.com/beastmaster), an R package that automates the conversion of dates, priors, and NEXUS character matrices into the complex Beast2 XML format. We find that unconstrained MrBayes analysis under the uniform node age prior fails to retrieve reasonable results, exhibiting extremely high uncertainty in dates. On the other hand, Beast2 inference matches the ground-truth well, under both birth-death serially sampled (BDSS, disallowing direct ancestors) and sampled ancestor (SABD) tree models, as does MrBayes using BDSS. MrBayes using SABD seems to have difficulty converging in some analyses. These results, on a high quality fossil dataset, indicate that while tip-dating is very promising, methodological issues in tip-dating can have drastic effects, and require close attention, especially on more typical datasets where the distinction between "method problems" and "data problems" will be more difficult to detect.

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