University of Groningen

The Fossil Calibration DatabaseKsepka, Daniel T.; Parham, James F.; Allman, James F.; Benton, Michael J.; Carrano,Matthew T.; Cranston, Karen A.; Donoghue, Philip C. J.; Head, Jason J.; Hermsen, ElizabethJ.; Irmis, Randall B.Published in:Systematic biology

DOI:10.1093/sysbio/syv025

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Citation for published version (APA):Ksepka, D. T., Parham, J. F., Allman, J. F., Benton, M. J., Carrano, M. T., Cranston, K. A., ... Warnock, R.C. M. (2015). The Fossil Calibration Database: A new resource for divergence dating. Systematic biology,64(5), 853-859. https://doi.org/10.1093/sysbio/syv025

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Syst. Biol. 64(5):853–859, 2015© The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.For Permissions, please email: journals.permissions@oup.comDOI:10.1093/sysbio/syv025Advance Access publication April 27, 2015

The Fossil Calibration Database—A New Resource for Divergence Dating

DANIEL T. KSEPKA1,∗, JAMES F. PARHAM2, JAMES F. ALLMAN3, MICHAEL J. BENTON4, MATTHEW T. CARRANO5,KAREN A. CRANSTON6, PHILIP C. J. DONOGHUE4, JASON J. HEAD7, ELIZABETH J. HERMSEN8, RANDALL B. IRMIS9,

WALTER G. JOYCE10, MANPREET KOHLI11, KRISTIN D. LAMM12, DAN LEEHR6,13, JOSÉS L. PATANÉ14, P. DAVID POLLY15,MATTHEW J. PHILLIPS16, N. ADAM SMITH17, NATHAN D. SMITH18, MARCEL VAN TUINEN19, JESSICA L. WARE11,

AND RACHEL C. M. WARNOCK5

1Bruce Museum, 1 Museum Drive, Greenwich, CT 06830, USA; 2John D. Cooper Archaeological and Paleontological Center, Department of GeologicalSciences, California State University, Fullerton, CA 92834, USA; 3Interrobang Digital Media,1034 Pebblebrook Drive, Wake Forest, NC 27587, USA;

4School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK; 5Department of Paleobiology, P.O. Box 37012, MRC 121, Smithsonian Institution,Washington DC 20013-7012, USA; 6National Evolutionary Synthesis Center, 2024 West Main Street Suite A200, Durham, NC 27705, USA; 7Departmentof Earth and Atmospheric Sciences, University of Nebraska-Lincoln, 228 Bessey Hall, Lincoln, NE 68588, USA; 8Department of Environmental and PlantBiology, Ohio University, Athens, OH 45701, USA; 9Natural History Museum of Utah and Department of Geology & Geophysics, University of Utah, 301

Wakara Way, Salt Lake City, UT 84108, USA; 10Department of Geosciences, University of Fribourg, Chemin du Musée 6, 1700 Fribourg, Switzerland;11Department of Biology, Rutgers University, 195 University Ave, Newark, NJ, 07102, USA; 12Bioinformatics Research Center, North Carolina State

University, Raleigh, NC 27965, USA; 13Duke Center for Genomic and Computational Biology, Duke University, 101 Science Drive, Durham, NC 27708,USA; 14Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000, Brazil; 15Department of Geological Sciences, Indiana

University, 1001 E. 10th Street, Bloomington, IN 47401, USA; 16School of Earth, Environmental and Biological Sciences, Queensland University ofTechnology, Brisbane 4000, Australia; 17Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA; 18Department of Biology,

Howard University, 415 College Street NW, Washington, DC, 20059, USA; 19Centre of Evolutionary and Ecological Studies, Marine Evolution andConservation Group, Univerity of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands;

∗Correspondence to be sent to: Bruce Museum, 1 Museum Drive, Greenwich, CT 06830, USA;E-mail: dksepka@brucemuseum.org.

Daniel T. Ksepka and James F. Parham contributed equally to this article.

Received 26 September 2014; reviews returned 2 December 2014; accepted 22 April 2015Associate Editor: Laura Kubatko

Abstract.—Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence datinganalyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important—often leastappreciated—step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological,and geological evidence and can be difficult for nonspecialists to formulate. The dynamic nature of the fossil record (e.g., newdiscoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continuallylest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this databaseare based on individual fossil specimens and follow best practices for phylogenetic justification and geochronologicalconstraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, willserve as a key pipeline for peer-reviewed calibrations to enter the database. [Calibration; divergence dating; fossil.]

Fossils provide a direct source of temporal datafor evolutionary events. In concert with molecularsequence data, fossil-based calibrations provide theessential information for scaling phylogenetic trees togeological time. The proper translation of fossil datainto calibrations is the single most important factorfor establishing constraints for divergence dating (e.g.,Brochu 2004; Parham and Irmis 2008; Joyce et al. 2013;Magallón et al. 2013; Warnock et al. 2015) which, in turn,is the most important factor influencing the accuracy ofresults (e.g., van Tuinen and Hadly 2004; Inoue et al. 2010;Sauquet et al. 2012; Warnock et al. 2012). Poor estimationof divergence dates as a result of inaccurate fossilcalibrations has been demonstrated for both empirical(e.g., Joyce et al. 2013) and theoretical (e.g., dos Reis andYang 2013) data sets. Similarly, the distribution of fossilcalibrations across the phylogeny of interest (Brochu2004), as well as the assignment of prior distributionsto individual calibrations (e.g., Ho and Phillips 2009;Inoue et al. 2010; Clarke et al. 2011; Warnock et al.

2012), can have large effects on estimates of divergencedates.

Given the importance of fossil calibrations, there is apressing need to increase their number and phylogeneticspread. Because calibrations can have a large impact onresults throughout the tree (Ho and Phillips 2009; Clarkeet al. 2011), quality control remains critical even whenlarge numbers of calibrations are used. Furthermore,fossil calibrations are needed for poorly covered areas ofthe Tree of Life, where secondary calibrations continueto be used at a high rate despite widely acknowledgedflaws in this approach (Hipsley and Müller 2014). Giventhese trends and concerns, it is necessary to increase thequality and quantity of fossil calibrations.

Unfortunately, methods for estimating thephylogenetic positions and geological ages of fossilspecimens used for node-calibration are often treatedless rigorously in divergence dating studies than stepssuch as sequence alignment, model selection, andsearching for optimal trees. This weakness is due in

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FIGURE 1. Example of the Fossil Calibration Database interface. The browse function allows users to enter any NCBI taxon name and tobrowse toward the root via the “Lineage” bread-crumb trail or toward a tip by selecting any of the “Calibrations within clade” results. Searchingvia taxon, age, and/or author is also possible.

part to the breadth of interdisciplinary knowledgerequired to assess potential fossil calibrations, especiallythe difficulty in interpreting the relevant systematic,stratigraphic, and geochronological literature. Moreover,phylogenetic hypotheses and age estimates of fossilscan, and often do, change over time. Widely usedcalibrations have been discarded due to new discoveriesor revisions to ages and taxonomy (e.g., Parham et al.2012; Benton et al. 2015). These concerns are notobviated by the introduction of tip-based calibrationmethods (so-called ‘Total Evidence Dating’; e.g.,Pyron et al. 2011; Ronquist et al. 2012), which mustalso accommodate rigorous fossil dating. While tip-based approaches represent an exciting new class ofmethods for including fossil data, methodologicalconcerns remain over the accuracy of “morphologicalclocks” (e.g., Arcila et al. 2015) and node-basedcalibrations are frequently used even within thecontext of tip-dating studies (e.g., Beck and Lee 2014).Furthermore, limitations of currently available softwarepreclude tractable dating using data sets that combinegenomic-scale molecular data and morphologicaldata in a probabilistic framework (Giribet 2015).Thus, node-calibration approaches are likely to retainimportance, especially as phylogenomic data setsbecome increasingly common.

A DATABASE APPROACH TO FOSSIL CALIBRATIONS

BackgroundWe introduce the Fossil Calibration Database,

(Figures 1–2) an open-access electronic resource forvetted, peer-reviewed fossil calibrations developed bya NESCent Working Group (Ksepka et al. 2011) andhosted in collaboration with the journal PalaeontologiaElectronica. Calibrations must undergo peer reviewand meet the Best Practices (Table 1) articulated byParham et al. (2012) to be accessioned into the database,offering a greater level of scientific rigor and clarity tousers than might be obtained by harvesting putativedates from the general paleontological literature. Insupplying calibrations to facilitate new analyses, theFossil Calibration Database is distinct from TimeTree(Hedges et al. 2006), which serves as a database ofpublished molecular divergence estimates.

A database approach is advantageous because thefossil record is not static. New fossil specimens areconstantly being discovered, and the phylogeneticpositions of known fossil taxa are frequentlyreinterpreted in light of new methods of study orphylogenetic revisions. Stratigraphic revisions regularlyshift the best age estimates for individual fossils atboth the local (e.g., new stratigraphic correlations or

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FIGURE 2. Example of the Fossil Calibration Database search result. Specimen data and the justifications for the recommended age andphylogenetic placements are provided, along with references, a tree image, and a link to the Fossil Calibration Series paper providing the fulldata.

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TABLE 1. Best practices for justifying fossil calibrations (Parhamet al. 2012), which must be met by calibrations accessioned into theFossil Calibration Database

Best practices

1. Museum numbers of specimen(s) that demonstrateall the relevant characters and provenance datashould be listed. Referrals of additional specimens tothe focal taxon should be justified.

2. An apomorphy-based diagnosis of the specimen(s)or an explicit, up-to-date, phylogenetic analysis thatincludes the specimen(s) should be referenced.

3. Explicit statements on the reconciliation ofmorphological and molecular data sets should begiven.

4. The locality and stratigraphic level (to the best ofcurrent knowledge) from which the calibratingfossil(s) was/were collected should be specified.

5. Reference to a published radioisotopic age and/ornumeric timescale and details of numeric ageselection should be given.

radiometric dates) and global scales (e.g., updatesto major boundaries in the Geological Time Scale).The Fossil Calibration Database can accommodatesuch fluctuations by adding new calibrations as theyare formulated, alerting users to alternate proposedcalibrations for nodes, and flagging calibrations thathave been superseded by newly discovered fossils.

A recent revision of fossil calibrations for majornodes in the animal phylogeny serves to illustrate thedynamic nature of fossil data. Benton (1990) compiled asuite of key fossil calibrations within Metazoa, whichhas been updated and revised several times (Bentonand Donoghue 2007; Donoghue and Benton 2007;Benton et al. 2009). This compilation was most recentlyexpanded and vetted against Best Practices as part of theFossil Calibrations Database project (Benton et al. 2015).As may be expected, new discoveries are an importantdriver of updates: A different fossil now calibrates morethan half of the 48 nodes that are examined in boththe new and previous contributions (Table 2). It isillustrative to note that although new fossil discoveriesare an important driver of revised dates, the majorityof updates are due to phylogenetic and stratigraphicrevisions.

Utilizing the DatabaseFossil Calibration Database users can browse

calibrations based on the extended NCBI taxonomy, orsearch by clade name, most recent common ancestorof the tip taxa of interest (MRCA of taxon A andtaxon B), and/or age or geological time period.For each calibration result, the fossil specimen,hard minimum, soft maximum (if available), andrecommended citation(s) are provided. Direct links topdfs of papers in Palaeontologia Electronica are provided

for those calibrations whose justification has beenpublished in the Fossil Calibration Series (FCS) (seebelow). A tree graphic is provided alongside everycalibration to ensure phylogenetic placement is properlyconveyed and avoid confusion due to variation inthe application of NCBI taxon names (e.g., applyingnames to stem-based vs. crown-based clades). For allcalibrations of named clades and/or based on fossilsof named taxa, links are provided to relevant pagesof the Paleobiology Database (paleodb.org), AnimalDiversity Web (animaldiversity.org), and Wikipedia(en.wikipedia.org). Links to NCBI taxonomy pages fortaxa within the clade of interest are also provided.The Fossil Calibration Database and Open Tree of Lifeboth allow API access to their data, allowing for dataintegration. Fossil information will be useful for addingbranch lengths to Open Tree of Life, or as an annotationlayer on the Tree. The use of taxon names from the NCBItaxonomy in both resources will help facilitate futureinteraction.

The Fossil Calibration Database also includes anoption to provide data and justification for maximumdates. Maximum dates are, of course, far moreargumentative than minimum dates, which is whymost methods use "soft" maxima. Nonetheless, mostcurrently favored methods for divergence dating requireat least one maximum date (whether in the form of apoint calibration, hard maximum, or soft maximum)to operate. We do not require maximum boundsin calibration papers and the database, althoughwhere possible we encourage contributors to provideinformation relevant to users for choosing soft maximumbounds.

Although the primary function of the FossilCalibration Database is to provide an easily accessibleand updatable source for calibrations, the databaseis designed to encourage proper citation of thepaleontological research that forms the basis for fossilcalibrations. We recognize citing the database itselfis useful in highlighting its utility, but we stronglyencourage authors to also cite the primary literature forindividual calibrations. To date, many divergence datingstudies have cited a previous divergence dating studyor a general review paper (which may lack primarydata as a reference for calibrations), or provide nocitations for calibrations at all. Directing database usersto the appropriate literature for individual calibrationsshould ensure that an explicit and reproducible chainof evidence exists for use of these fossil calibrations.This approach will also increase the citation ratesof papers laying out the justification for calibrations,thereby encouraging paleontologists to pursue theresearch required to translate fossil data into usable fossilcalibrations.

Contributing to the Fossil Calibration DatabaseAn important source of contribution to the Fossil

Calibration Database will be the Fossil Calibration Series,

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TABLE 2. Evolution of minimum clade age constraints

Crown clade Benton Benton and Donoghue Donoghue and Benton Benton et al. Benton et al.1990 2007 2007 2009 2015

Metazoa 634.9 550.25a

Eumetazoa 531.5 550.25a

Cnidaria 520.5 529b

Bilateria 531.5 531.5 531.5 550.25a

Protostomia 531.5 550.25a

Deuterostomia 518.5 518.5 515.5b

Chordata 518.5 514b

Olfactores 518.5 514b

Vertebrata 460.6 457.5c

Gnathostomata 421.75 420.7d

Osteichthyes 416.1 416b 416 420.7d

Clupeocephala 149.85 149.85 149.85 150.94a

Ovalentaria– 96.9 96.9 96.9 69.71d

TetraodontiformesGasterosteiformes– 96.9 96.9 96.9 69.71d

TetraodontiformesTetraodontidae 32.25 32.25 32.25 32.02b

Tetrapoda 363 330.4a 330.4 330.4 337a

Amniota 305 312.3a 312.3 312.3 318b

Diapsida 255 259.7b 259.7 255.9b 255.9Archosauria 240 235e 235 239b 247.1e

Neornithes 79 6e 66 66 66Neognathae 70 66e 66 66 66Mammalia 105 162.5e,d 162.5 162.9b 164.9b

Marsupialia 61.5 61.5 61.5 47.6d

Theria 94 124.6e 124.3b 124b 156.3e

Placentalia 59 62.5e 61.6a,b

Afrotheria 48.4 48.4 48.4 56e

Atlantogenata 55.6 56e

Bovidae 18.3 18b 18 16a

Whippomorpha-Ruminantia 52.4 52.4Cetartiodactyla 48.3 48b 52.4e 52.4Carnivora 42.8 43b 39.68a 37.3b

Laurasiatheria 65.2 62.5a 61.6a

Lipotyphla 61.5 61.5 61.6a

Boreoeutheria 95.3 71.2d 61.5a 61.6b

Muridae 10 11b 10.4b 10.4Rodentia 55.8 55.6 56b

Lagomorpha 48.6 47.6b

Glires 59 61.5e 61.7b 61.5a 56b

Archontoglires 61.5 61.7b 61.5a 61.6a,b

Archonta 67 65.2a 61.5a 61.6a,b

Primates 55.5 55.6a 56b

Strepsirhini 33.7 33.9b

Anthropoidea 33.7 33.9b

Catarrhini 23 23.5b 23.5 24.44a

Hominidae 11.2 11.6b

Homininae 6.5 6.5 5.7b 6.5b

Homo sapiens 0.2 0.2

Note: Ages are in millions of years before present.The clade age constraints required are principally by:aChange to a different but existing fossil.bRevision of timescale.cChange required to meet increased stringency of best practices.dRevision of phylogeny.eDiscovery of a new fossil.

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a series of peer-reviewed articles in the open-accessjournal Palaeontologia Electronica. Articles published inthe FCS will detail the phylogenetic and stratigraphicjustifications for fossil calibrations, and these papers willbe directly linked to individual calibrations in the FossilCalibration Database. The FCS provides an importantset of calibrations for the Fossil Calibration Database,with an initial set of 120 calibrations covered in theinaugural set of papers and many additional calibrationsto follow in the second wave of FCS publications. Thesecalibrations span a broad swath of the Tree of Life, andalthough vertebrates are best represented in the initialdata set we are actively recruiting contributors workingon sparsely represented clades. The FCS will be themain source of contributions to the data base, becauseit is peer reviewed. However, calibrations from othersources will also be considered by the Fossil CalibrationAdvisory Board, a rotating board of taxonomic andmethodological experts, for entry into the database ifthey adhere to the Best Practices articulated by Parhamet al. (2012).

This Fossil Calibration Advisory Board is alsoresponsible for annotating the database to indicateupdates and disagreements. Users can criticize existingcalibrations using the "Comment on this Calibration"button. This allows the user to send a message tothe FCD administrators, which can be used to alertthem to incorrect or obsolete data. Beyond serving as aplatform for new calibrations, the FCS welcomes papersdiscussing all aspects of calibration implementation,debates over contentious calibrations, and empiricalcalibration-based analyses.

AvailabilityThe database is hosted by Palaeontologia Electronica

and freely accessible at http://fossilcalibrations.org.Data are available through the graphical interface andsearch results can be downloaded as JavaScript ObjectNotation (JSON) or comma-separated values (csv).Data are also made available through an ApplicationProgramming Interface (API) that replicates the searchcapability of the graphical interface. The API adopts aRESTful architecture and documentation is available athttp://docs.fcdb.apiary.io. All data are released with aCC0 waiver. The software is an open source and availableat http://github.com/nescent/fossilcalibrations with aBSD 2-clause license. Ongoing hosting and support isprovided by Palaeontologia Electronica.

FUNDING

This project was supported by the NationalEvolutionary Synthesis Center (NSF EF-0905606)as part of the Working Group grant “Synthesizingand Databasing Fossil Calibrations: Divergence Datingand Beyond” (to DTK and JFP), and funding from theJohn D. and Catherine T. MacArthur Foundation for the

Biodiversity Synthesis Group of the Encyclopedia of Lifeand a BioSynC Synthesis Meeting (to JFP.). PalaeontologiaElectronica is funded by the Palaeontological Association,the Paleontological Society, the Society of VertebratePaleontology, and the Western Interior PaleontologicalSociety.

ACKNOWLEDGMENTS

We thank Barbara Dobrin, María A. Gandolfo-Nixon,and Christopher Torres for discussion; Mark Sutton andVladimir Gapeyev for technical expertise; and CandaceBrown Wiggins, Stephanie Ribson, Jeff Sturkey, andDanielle Wiggins for logistical support. We also wishto thank Editor Frank Anderson, Associate Editor DavidPosada, April Wright, and an anonymous reviewer forcomments and suggestions that improved the quality ofthe article.

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