PDF-Version - South Dakota School of Mines and Technology

David W. Bapst Last Updated: 01/16/2015
Email: david.bapst@sdsmt.edu or dwbapst@gmail.com
501 E. St. Joseph
Rapid City, SD 57701
Website: http://webpages.sdsmt.edu/~dbapst/
R Package ‘paleotree’: http://cran.r-project.org/web/packages/paleotree/index.html
Professional Appointments
Adjunct Assistant Professor, South Dakota School of Mines and Technology (2013-Present)
Department of Geology and Geological Engineering
Postdoctoral Scholar, University of California Davis (2014-Present)
Department of Earth and Planetary Sciences, Advisor: Dr. Sandy Carlson
Education
University of Chicago. Geophysical Sciences. PhD, March 2013
Dissertation: ‘Phylogenetic Trees in the Fossil Record: Resolution, Temporal Scaling, and
Uncertainty’, Advisor: Michael Foote.
State University of New York at Buffalo. Geology. Bachelor of Science, 2007
Publications
Bapst, D. W. 2014. Preparing Paleontological Datasets for Phylogenetic Comparative Methods.
Pp. 515-544. In L. Z. Garamszegi, ed. Modern Phylogenetic Comparative Methods and
Their Application in Evolutionary Biology. Springer Berlin Heidelberg. doi:10.1007/978-3-
662-43550-2_22 (Invited) (Link to Free PDF, courtesy of publisher)
Bapst, D. W. 2014. Assessing the effect of time-scaling methods on phylogeny-based analyses
in the fossil record. Paleobiology. 40(3):331-351. doi:10.1666/13033
Bapst, D. W. 2013. A stochastic rate-calibrated method for time-scaling phylogenies of fossil
taxa. Methods in Ecology and Evolution. 4(8):724-733. doi:10.1111/2041-210X.12081
(Invited)
Bapst, D. W. 2013. When Can Clades Be Potentially Resolved with Morphology? PLoS ONE
8(4):e62312. doi:10.1371/journal.pone.0062312
Bapst, D. W. 2012. paleotree: an R package for paleontological and phylogenetic analyses of
evolution. Methods in Ecology and Evolution 3: 803-807. doi:10.1111/j.2041-
210X.2012.00223.x
Bapst, D. W., P. C. Bollock, M. J. Melchin, H. D. Sheets, and C. E. Mitchell. 2012. Graptoloid
diversity and disparity became decoupled during the Ordovician mass extinction.
Proceedings of the National Academy of Science 109(9):3428-3433.
doi:10.1073/pnas.1113870109 (Press Release Link or use: http://bit.ly/AD2T0S)
Publications in prep.
Bapst, D. W., E. A. King and M. W. Pennell. In prep. Probability models for branch lengths of
paleontological phylogenies.
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Bapst, D. W. and C. E. Mitchell. In prep. An inclusive generic phylogeny reveals constraint and
convergence in the Graptoloidea.
Lloyd, G. T., D. W. Bapst, K. E. Davis, and M. Friedman. In prep. A probabilistically time-scaled
1,000-taxon phylogenetic hypothesis for Mesozoic dinosaurs and the origins of flight
and crown birds.
Matzke, N., A. Wright, D. Bapst and G. Lloyd. In prep. Fossils-Only Tip-Dating of
Deinonychosaurian Theropods: a Comparison of Methods and Models.
Schreiber, H. A., D. W. Bapst and S. J. Carlson. In prep. Combined analysis of extant
Rhynchonellida using morphological and molecular data.
Funding Received
Hinds Grant for Dissertation Research in Evolutionary Biology
University of Chicago Doolittle-Harrison Fund
A. Tagliacozzo Memorial Fund from American Institute of Professional Geologists
Invited Talks
Bapst, D.W. Time-Scaling Trees in the Fossil Record. Society of Vertebrate Paleontology 72 nd
Annual Meeting. Invited for Symposium on 'Phylogenetic and Comparative
Paleobiology -- New Approaches to the Study of Vertebrate Macroevolution' for
October 19 th , 2012.
Bapst, D.W. Submersible Cathedrals: What Were Graptoloids Doing? SDSM&T
Geology/Geological Engineering/Paleontology Seminar Series. South Dakota School of
Mines and Technology. September 28 th , 2012.
Conference Abstracts
Lloyd, G. T., D. W. Bapst, K. E. Davis and M Friedman. 2014. Automated generation of large
phylogenies and a probabilistically time-scaled 1,000-taxon phylogenetic hypothesis for
Mesozoic dinosaurs: dating the origins of flight and crown-birds. Palaeontological
Association Annual Meeting 2014.
Lloyd, G. T., D. W. Bapst, K. E. Davis and M Friedman. 2014. A probabilistically time-scaled
1,000-taxon phylogenetic hypothesis for Mesozoic dinosaurs and the origins of flight
and crown-birds. Society of Vertebrate Paleontology 74 th Annual Meeting.
Matzke, N., A. Wright and D. Bapst. Incorporation of Absolute and Relative Fossil Dating
Information In Bayesian Tip-Dating Analyses Using the R Package BeastmasteR:
Examples From Assassin Spiders, Salmonids, and Hominids. Society of Vertebrate
Paleontology 74 th Annual Meeting.
Wright, A., G. Lloyd, N. Matzke and D. Bapst. Fossils-Only Tip-Dating of Deinonychosaurian
Theropods: a Comparison of Methods and Models. Society of Vertebrate Paleontology
74 th Annual Meeting.
Carlson, S., H. Schreiber, and D. Bapst. 2014. Evolution of the lophophore and its mineralized
supports. 4th International Palaeontological Congress; IPC4 Abstracts, page 130.
Carlson, S., H. Schreiber, and D. Bapst. 2014. The 5% solution: is it sufficient? Joint annual
meeting of the Society for the Study of Evolution, the Society of Systematic Biologists,
and the American Society of Naturalists; Evolution 2014 Abstracts, page 131.
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Bapst, D. W. and C. E. Mitchell. 2014. An Inclusive Generic Phylogeny Reveals Constraint and
Convergence in the Graptoloidea. NAPC 2014. Gainesville, FL.
Bapst, D. W. 2013. The Impact of Time-Scaling Methods on Phylogenetic Comparative Methods
in the Fossil Record. Evolution 2013. Snowbird, UT.
Bapst, D. W., M. Pennell and E. King. 2012. Fitting Diversification Models to Paleo-Phylogenies.
Evolution 2012, Ottawa.
Bapst, D. W. 2011. Comparing methods for time-scaling trees of extinct taxa in GSA Abstracts
with Programs. 45:161. (Link to Abstract)
Bapst, D. W. 2011. Patterns of Diversification on a Large Species-level Supertree of the Extinct
Planktic Graptolites. Evolution 2011. Abstract #058002. (Link to Abstract)
Bapst, D. W. 2010. Trends, Stasis, or Diffusion: Functional and Phylogenetic Evolution of
Graptoloid Thecae in GSA Abstracts with Programs. 42:534. (Link to Abstract)
Bapst, D. W. 2010. Using sinking experiments to understand graptoloid function in International
Palaeontological Congress 3, London, UK. (Link to Abstract)
Mitchell, C. E., and D. W. Bapst. 2009. Graptolite Astogeny: Controlling Urban Sprawl in The
Plankton in North American Paleontological Conference, Cincinnati, OH.
(Link to Abstract)
Bapst, D. W., and M. Melchin. 2009. The Development of Morphological Gradients within Early
Silurian Graptoloid Colonies in North American Paleontological Conference, Cincinnati,
OH. (Link to Abstract)
Bapst, D. W., M. Melchin, H. D. Sheets, and C. E. Mitchell. 2008. Morphological Patterns in Late
Ordovician and Early Silurian Graptolites in GSA Abstracts with Programs. 40:391.
(Link to Abstract)
Bapst, D. W., C. E. Mitchell, and H. D. Sheets. 2007. Recovery and radiation following the end-
Ordovician mass extinction: testing for expansion and convergence in graptolite
morphological guilds in GSA Abstracts with Programs. 39:38. (Link to Abstract)
Educational Activities
Guest Lecturer for courses Search for Our Past, Oceanography and Paleontological
Systematics at South Dakota School of Mines and Technology and guest lecturer on
phylogenetic approaches to macroevolution for the University of Chicago course
Paleobiology Modeling and Analysis (February 2012) (Link to Lecture Notes)
Student workshop on phylogenetics in R at University of Chicago (Link to R Scripts)
Graduate teaching assistant at the University of Chicago for the following courses: Biological
Evolution, Dynamic Environment and Emergence of Humankind, Dynamic Environment and
Settlement Systems, Ice Age Earth, Chemistry and the Atmosphere, Global Warming,
Environmental History of the Earth, Natural Hazards, Biological Diversity, Field Course in
Modern and Ancient Carbonate Experiences (2007-2013)
Helped design and teach earth and life science lab exercises as outreach to minority middleschool
students at Perspectives Chicago charter school (2009-2011)
Interacted with primary school students by email as a respondent for ‘Ask-A-Paleontologist’
Participated in volunteer educational outreach to increase minority representation in the
geosciences with the NSF-sponsored Buffalo Geosciences Program (2005-2007)
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Professional and Synergistic Activities
Co-organized symposium with Nicholas Matzke, April Wright and Graeme Lloyd on Putting
Fossils in Trees: New Methods for Combining Morphology, Time, and Molecules to
Estimate Phylogenetic Position and Divergence Times of Living and Fossil Taxa at the
Society of Vertebrate Paleontology 74 th Annual Meeting, 2014.
Invited participant for NESCent catalysis group in April 2013 on Integrating Approaches to
Macroevolution: Combining Fossils and Phylogenies, which focused on fostering discussion
and interaction between evolutionary biologists and paleobiologists.
Co-organized session with Emily King on Phylogenetic Approaches to Paleobiology:
Diversity, Rates, and Trends at Geological Society of America National Meeting 2011,
providing increased interaction between paleontological and biological researchers. (Link)
Field Experiences: Field Coursework in Colorado, Utah, Wyoming, the San Juan Islands,
Nevada, Arizona and San Salvador Island (Bahamas). Assisted with collecting paleontological
samples in New York (Pleistocene, 2003-2009), Kansas (Miocene, 2004) and Pennsylvania
(Ordovician, 2006).
Reviewer for the following journals: Evolution, Methods in Ecology and Evolution,
Palaeontology, PLoS One, Systematic Palaeontology.
UChicago Paleobiology Journal Club Organizer 2011-2012
Research assistant at SUNY Buffalo tasked with developing a database of graptolite
systematics and analyzing morphological disparity through the late Ordovician (2005-2007)
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