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

View ORCID ProfileNicholas J. Matzke, April Wright
doi: https://doi.org/10.1101/049643
Nicholas J. Matzke
1Discovery Early Career Researcher Award (DECRA) Fellow, Moritz Lab, Division of Ecology, Evolution, and Genetics, The Australian National University, Canberra, ACT 2601.
2Work also performed at: National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, TN 37996-3410.
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  • For correspondence: nick.matzke@anu.edu.au
April Wright
3Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011-4009.
4Department of Ecology, Evolution and Behavior. University of Kansas, Lawrence, KS 66045.
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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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Posted August 02, 2016.
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Inferring node dates from tip dates in fossil Canidae: the importance of tree priors
Nicholas J. Matzke, April Wright
bioRxiv 049643; doi: https://doi.org/10.1101/049643
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Inferring node dates from tip dates in fossil Canidae: the importance of tree priors
Nicholas J. Matzke, April Wright
bioRxiv 049643; doi: https://doi.org/10.1101/049643

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