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

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 v. 2.1.3 and MrBayes v. 3.2.5. We find that for key nodes (Canis, approx. 3.2 Ma, Caninae approx. 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 versus non-mechanistic) and their applicability to fossil datasets.canidae_traceLogs_ALL_v2Trace plots of key variables for all 60 analyses.canidae_treeLogs_ALL_v2Plots of the MCC trees for all 60 analyses.expert_vs_estimated_node_agesLinear regressions showing the correlation between the expert tree and estimated node ages, for nodes shared between the expert tree and estimated trees. Caveats for these regressions are discussed in Supplemental Text.Canidae_expertThe "expert" tree, derived from digitization of the phylogenies of Canidae published in the monographs of Wang and Tedford, using TreeRogue.Table_S2_TipDate_runs_v3Summary of all 60 variant analyses (contains Supplemental Table S2, and some associated notes and file locations).Matzke_Wright_SuppData1A zipfile of all inputs, outputs, and scripts for all analyses. (pt 1/3)Matzke_Wright_SuppData2A zipfile of all inputs, outputs, and scripts for all analyses. (pt 2/3)Matzke_Wright_SuppData3A zipfile of all inputs, outputs, and scripts for all analyses. (pt 3/3