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dc.contributor.author Matzke, Nicholas J.
dc.contributor.author Wright, April
dc.coverage.spatial North America
dc.coverage.temporal Cenozoic
dc.date.accessioned 2016-08-03T13:26:44Z
dc.date.available 2016-08-03T13:26:44Z
dc.date.issued 2016-08-10
dc.identifier doi:10.5061/dryad.vn52f
dc.identifier.citation Matzke NJ, Wright A (2016) Inferring node dates from tip dates in fossil Canidae: the importance of tree priors. Biology Letters 12(8): 20160328.
dc.identifier.issn 1744-9561
dc.identifier.uri http://hdl.handle.net/10255/dryad.121447
dc.description 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.
dc.relation.haspart doi:10.5061/dryad.vn52f/1
dc.relation.haspart doi:10.5061/dryad.vn52f/2
dc.relation.haspart doi:10.5061/dryad.vn52f/3
dc.relation.haspart doi:10.5061/dryad.vn52f/4
dc.relation.haspart doi:10.5061/dryad.vn52f/5
dc.relation.haspart doi:10.5061/dryad.vn52f/6
dc.relation.haspart doi:10.5061/dryad.vn52f/7
dc.relation.haspart doi:10.5061/dryad.vn52f/8
dc.relation.isreferencedby doi:10.1098/rsbl.2016.0328
dc.relation.isreferencedby PMID:27512133
dc.subject Tip-dating
dc.subject total evidence dating
dc.subject MrBayes
dc.subject BEASTmasteR
dc.subject uniform tree prior
dc.title Data from: Inferring node dates from tip dates in fossil Canidae: the importance of tree priors
dc.type Article
dwc.ScientificName Canidae
dwc.ScientificName Caninae
dwc.ScientificName Canis
dwc.ScientificName Borophaginae
dwc.ScientificName Hesperocyoninae
dc.contributor.correspondingAuthor Matzke, Nicholas J.
prism.publicationName Biology Letters
dryad.dansTransferDate 2018-05-10T10:30:42.201+0000
dryad.dansEditIRI https://easy.dans.knaw.nl/sword2/container/d4df5180-4a14-48d9-afe6-1939bee4f12a
dryad.dansArchiveDate 2018-05-10T12:01:17.190+0000
dryad.dashTransferDate 2019-07-04T00:00:03.490+0000
dryad.dashStoredDate 2019-07-12T08:28:19.726+0000

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Title canidae_traceLogs_ALL_v2
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Description Trace plots of key variables for all 60 analyses.
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Title canidae_treeLogs_ALL_v2
Downloaded 67 times
Description Plots of the MCC trees for all 60 analyses.
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Title expert_vs_estimated_node_ages
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Description Linear 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.
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Title Canidae_expert
Downloaded 42 times
Description The "expert" tree, derived from digitization of the phylogenies of Canidae published in the monographs of Wang and Tedford, using TreeRogue.
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Title Table_S2_TipDate_runs_v3
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Description Summary of all 60 variant analyses (contains Supplemental Table S2, and some associated notes and file locations).
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Title Matzke_Wright_SuppData1
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Description A zipfile of all inputs, outputs, and scripts for all analyses. (pt 1/3)
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Title Matzke_Wright_SuppData2
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Description A zipfile of all inputs, outputs, and scripts for all analyses. (pt 2/3)
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Title Matzke_Wright_SuppData3
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Description A zipfile of all inputs, outputs, and scripts for all analyses. (pt 3/3)
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