We combine computational approaches with empirical data to address problems in phenotypic evolution at large and small scales.  We answer questions about the phylogenetics of mammals; the role of development in channeling evolution; the limits of predictability of evolution from developmental and quantitative population genetic parameters; the analysis of three-dimensional, complex phenotypes; and comparative rates of geographic and evolutionary responses to environmental changes; and the role of Hox genes in the evolution of vertebrate body plans.

Our research aims to understand how species respond evolutionarily and ecologically to environmental change, one of the great challenges for the 21st century. The paleontological and geological records provide a comparative context to study how life responded to dramatic changes in climate, topography, and oceanic conditions through diversification, adaptation, and extinction. Using these deep-time records, we can measure the rates at which species respond, the factors that tip the balance between adaptation and extinction, and the conditions that lead to environmental collapse and mass extinction. However, the temporal, spatial, and taxonomic resolutions of the fossil record do not easily mesh with the scale at which we make observations on the living world. Our research makes these connections.

Our research bridges biological scales and domains using computational approaches to develop predictions at one scale that can be tested against empirical data collected at another scale. Van Valen in 1973 described evolution as “the control of development by ecology”. Long-term evolution is the outcome of the genetic and developmental processes that produce phenotypes, selection for phenotypes that maximize performance in local environments, and change in those environments that alters the adaptive landscape.  The steps in this hierarchy operate at very different temporal scales, each of which is a contributing factor to the diversification of clades on million-year timescales. 

Analysis of spatial environmental sorting of locomotor proportions within species and between clades. (download the paper) Polly et al. 2017, Evolutionary Ecology Research, 18: 61-95.
Analysis of spatial environmental sorting of locomotor proportions within species and between clades (from Polly et al. 2017).

Non-linear mapping of genetic parameter space onto phenotypic space filtered through developmental tissue-level interactions (from Polly, 2008 and Polly, 2017).

Our research is strongly quantitative and our most notable achievements have been new frameworks for analyzing complex morphology.  We have developed new morphometric methods that make use of the three-dimensional representations obtained from laser and CT scanning; new Monte Carlo methods for simulating the long-term patterns of phenotypic change in phylogenetic and environmental contexts; likelihood methods for analyzing vertebrate morphology; and Bayesian ecometric methods for measuring and comparing functional trait change in communities across space and through time. 

We have distributed many of these methods and others packages in a series of analytical packages for the Mathematica system. The two most widely used are Geometric Morphometrics for Mathematica and Phylogenetics for Mathematica, as well as Modularity for Mathematica for the analysis of morphological integration and modularity with former postdoc and long-term collaborator Anjali Goswami of the Natural History Museum in London.

Our research asks how the history of the Earth has influenced the history of life. How have the glacial-interglacial cycles of the last 2.6 million years affected speciation, extinction, and the reorganization of ecological communities? Did the 50 million years of climate cooling from the Eocene through Pliocene have a fundamentally different effect on evolution? 

To address these questions, we must know how speciation as we can detect it in the fossil record compares with speciation as we would understand it in living populations, how samples of fossils relate to each other and to living species, how to measure and compare rates of evolution in living populations and extinct species for which there are no living descendants, as well as how to compare the composition and structure of ecological communities in deep time and the modern world. 

We must also know something about how changes in climate might affect evolution in the traits observable in the fossil record.  What new functional specializations would mammals need to take advantage of new grassland habitats in the Miocene or new tundra habitats in the Quaternary? We must also know how genetic and developmental processes constrain and channel the evolution of new features.  Are some kinds of evolutionary innovations more likely than others?  These are the kinds of research we do.

Comparison of timing and duration fragmentation of the geographic range of the Common Eurasian shrew Sorex araneus during the last glacial phase based on fossil and geological records (top left and right) to the pattern of genetic differentiation in living populations of the same species (from Polly 2019).