Faculty & Research
P. David Polly
- Contact Information
- Contact P. David Polly by pdpolly [at] indiana [dot] edu
- By telephone: 812-855-7994
- Geology Building, 513
- Research Areas
Ph.D., 1993, Department of Integrative Biology, University of California–Berkeley
B.A, 1987, Plan II Honors Program, University of Texas–Austin
I work in the field of vertebrate paleontology, specifically with fossil mammals from the Cenozoic Era (65 million years ago to the present). Paleontology is an interdisciplinary science, rooted firmly in evolution biology, anatomy, ecology, and geology. Through paleontology, these disciplines have many connections, and I have intentionally structured my research to demonstrate how the rich historical context of geology – my primary discipline – can be used to improve understanding life on Earth, past and present.
Quantitative Functional Paleontology
This research is concerned with developing new approaches for measuring the complex morphological structures of fossils and the many processes that govern their evolution and geographic distribution through geological time. Some of the most important properties of fossils -- their shape, their function, their relationship to sediments and stratigraphy, their geographic distributions through time, their variety, and their evolutionary trajectories – are difficult to capture with ordinary measurements. One of my contributions has been to help develop the evolutionary side of geometric morphometric methods. This work has included modeling evolutionary processes on multivariate phenotypic traits in GMM space, measuring the empirical patterns in teeth or limb bones from living populations and modeling their evolution over millions of generations to test how well competing hypotheses about the mode of evolution explain the observed fossil record. With my former post-doc Anjali Goswami, I have extended this approach to simulate the evolutionary consequences of patterns of correlation between structures (such as those observed between the functionally integrated bones of the skull in living species) so that their relevance to evolution can be tested against the varieties of shape that are documented in the fossil record. Norman MacLeod and I developed the “Eigensurface” method for measuring complete three-dimensional structures and modeling their evolution.
Response of Vertebrates to Changing Climates and Environments
My research also addresses the response of vertebrates to changing climates and environments. The geography of vertebrate species is influenced by climate and vegetation. The sorting process is important for understanding the evolutionary processes that are driven by climatic and environmental change, as well as for understanding past climates and environments from fossil vertebrates. Using mammalian species we have estimated paleotemperature and precipitation patterns during the last 2.6 million years of Earth’s history. With former post-doc Jason Head and other collaborators, we used the scaling between ambient temperature and body size in poikilothermic (“cold-blooded”) vertebrates to estimate the mean annual temperatures of the tropics in the Paleocene (65-55 million years ago) using Titanoboa, the giant Paleocene snake.
Software and Data
I have made available add-in packages for Mathematica to perform geometric morphometrics, evolutionary modeling, species distribution modeling, modularity analysis, and phylogenetic tree manipulation, which are available here. Geographic grids, paleoclimate data, and phylogenetic matrices are available here.
- Uhen, M.D., A.D. Barnosky, B. Bills, J. Blois, M.T. Carrano, M.A. Carrasco, G.M. Erickson, J.T. Eronen, M. Fortelius, R.W. Graham, E.C. Grimm, M.A. O'Leary, A. Mast, W.H. Piel, P.D. Polly, and L.K. Säilä. 2013. From card catalogs to computers: databases in vertebrate paleontology. Journal of Vertebrate Paleontology, 33: 13-28. [article]
- Smith, M.R. and P.D. Polly. 2013. A reevaluation of the Harrodsburg Crevice Fauna (Late Pleistocene of Indiana, USA) and the climatic implication of its mammals. Journal of Vertebrate Paleontology, 33: 410-420. [article]
- P. D. Polly, A. M. Lawing, A.-C. Fabre, and A. Goswami. 2013. Phylogenetic Principal Components Analysis and Geometric Morphometrics. Hystrix, 24: 1-9. [article]
- Gómez-Robles, A. and P.D. Polly. 2012. Morphological integration in the hominin dentition: evolutionary, developmental, and functional factors. Evolution, 66: 1024-1043. [article]
- Polly, P.D. 2012. Measuring the evolution of body size in mammals. PNAS, 109: 4027-4028. [article]
- Goswami, A., P.D. Polly, O.B. Mock, and M.R. Sánchez Villagra. 2012. Shape, variance, and integration during craniogenesis: constrasting marsupial and placental mamamls. Journal of Evolutionary Biology, 25: 862-872. [article]
- Lawing, A.M., J.J. Head, and P.D. Polly. 2012. The ecology of morphology: the ecometrics of locomotion and macroenvironment in North American snakes. Pp. 117-146 in J. Louys (ed), Paleontology in Ecology and Conservation. Springer-Verlag, Berlin and Heidelberg [article]
- Johnson, L.J., J.A. Cotton, C.P. Lichtenstein, G.S. Elgar, R.A. Nichols, P.D. Polly, and S.C. Le Comber. 2011. Stops making sense: translational trade-offs and stop codon reassignment. BMC Evolutionary Biology, 11: 227. [article]
- Polly, P.D., J.T. Eronen, M. Fred, G.P. Dietl, V. Mosbrugger, C. Scheidegger, D.C. Frank, J. Damuth, N.C. Stenseth & M. Fortelius. 2011. History matters: ecometrics and integrative climate change biology. Proceedings of the Royal Society B, 278: 1121-1130. [article]
- Lawing, A. M. and P.D. Polly. 2011. Pleistocene climate, phylogeny, and climate envelope models: an integrative approach to better understand species' response to climate change. PLoS ONE, 16: e28554 [article]
- Polly, P.D. and J.T. Eronen. 2011. Mammal associations in the Pleistocene of Britain: implications of ecological niche modelling and a method for reconstrucing palaeoclimate. Pp. 279-304 in N. Ashton, S. G. Lewis, and C. Stringer (eds.), The Ancient Human Occupation of Britain. Elsevier. [article]
- Goswami, A. and P.D. Polly. 2010 . Methods for studying morphological integration, modularity and covariance evolution. Pp. 213-243 in J. Alroy and G. Hunt (eds.), Quantitative Methods in Paleobiology. Paleontological Society Short Course, October 30th, 2010. The Paleontological Society Papers, Volume 16. [article]
- Polly, P.D. 2010. Tiptoeing through the trophics: geographic variation in carnivoran locomotor ecomorphology in relation to environment. In A. Goswami and A. Friscia (eds.), Carnivoran Evolution: New Views on Phylogeny, Form, and Function. [article]
- Lawing, A.M. and P.D. Polly. 2010. Geometric morphometrics: recent applications to the study of evolution and development. Journal of Zoology, 280: 1-7. [article]
- Goswami, A. and P.D. Polly. 2010. The influence of character correlations on phylogenetic analyses: a case study of the carnivoran craniu. Pp. 141-164 in A. Goswami and A. Friscia (eds.), Carnivoran Evolution: New Views on Phylogeny, Form, and Function. Cambridge University Press. [article]
- Head, J.J., J.I. Bloch, A.K. Hastings, J.R. Bourque, E. Cadena, F. Herrera, P.D. Polly, and C.A. Jaramillo. 2009. Giant boine snake from a Paleocene Neotropical rainforest indicates hotter past equatorial temperatures. Nature, 457: 715-718. [article]
- Polly, P.D. 2008. Developmental dynamics and G-matrices: Can morphometric spaces be used to model evolution and development? Evolutionary Biology, 35: 83-96. [article]
- Polly, P. D. 2008. Adaptive Zones and the Pinniped Ankle: A 3D Quantitative Analysis of Carnivoran Tarsal Evolution. Pp. 165-194 in (E. Sargis and M. Dagosto, Eds.) Mammalian Evolutionary Morphology: A Tribute to Frederick S. Szalay. Springer: Dordrecht, The Netherlands. [article]
- Polly, P.D. 2007. Development with a Bite. News & Views. Nature, 449: 413-415. [article]
- Gündüz, İ, M Jaarola, C. Tez, C. Yeniyurt, P.D. Polly, and J. B. Searle. 2007. Multigenic and morphometric differentiation of ground squirrels (Spermophilus, Scuiridae, Rodentia) in Anatolia, with a description of a new species. Molecular Phylogenetics and Evolution 43: 916-935. [article]
- Polly, P. D., G. D. Wesley-Hunt, R. E. Heinrich, G. Davis, and P. Houde. 2006. Earliest known carnivoran auditory bulla and support for a recent origin of crown-group Carnivora (Eutheria, Mammalia). Palaeontology, 49: 1019-1027.
- Caumul, R. and P. D. Polly. 2005. Comparative phylogenetic and environmental components of morphological variation: skull, mandible and molar shape in marmots (Marmota, Rodentia). Evolution, 59: 2460-2472.
- Polly, P. D. 2004. On the simulation of the evolution of morphological shape: multivariate shape under selection and drift. Palaeontologia Electronica, 7.2.7A: 28pp, 2.3MB. [article]