Paul David Polly

Paul David Polly
Indiana University Bloomington | IUB · Department of Earth and Atmospheric Sciences

PhD, Paleontology (Integrative Biology), University of California-Berkeley

About

212
Publications
79,584
Reads
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5,888
Citations
Introduction
I am a vertebrate paleontologist with interests in phylogenetics, variation, mammals, evolution and development, and responses of taxa and faunas to environmental change.
Additional affiliations
July 2013 - June 2021
Indiana University Bloomington
Position
  • Professor
August 2006 - June 2013
Indiana University Bloomington
Position
  • Professor (Associate)
January 2001 - August 2006
Queen Mary, University of London
Position
  • Lecturer
Education
August 1988 - December 1993
University of California, Berkeley
Field of study
  • Paleontology (Integrative Biology)
August 1984 - December 1987
University of Texas at Austin
Field of study
  • Plan II Honors (subject: paleontology)

Publications

Publications (212)
Article
Full-text available
Climate change research is increasingly focusing on the dynamics among species, ecosystems and climates. Better data about the historical behaviours of these dynamics are urgently needed. Such data are already available from ecology, archaeology, palaeontology and geology, but their integration into climate change research is hampered by difference...
Article
Full-text available
The phenotype is a product of its phylogenetic history and its recent adaptation to local environments, but the relative importance of the two factors is controversial. We assessed the effects of diet, habitat, elevation, temperature, precipitation, body size, and mtDNA genetic divergence on shape variation in skulls, mandibles, and molars, structu...
Article
Full-text available
Comparative methods are used to reconstruct ancestral node values for continuously varying traits. The confidence intervals (CIs) around such estimates may be wider than the range of tip data from which they are calculated. Without historical data with which to compare estimates, it is not clear whether such broad CIs reflect evolutionary lability...
Article
Full-text available
Modern morphometrics, especially geometric morphometrics, is a powerful tool for modeling the evolution and development of the phenotype. Complicated morphological transformations can be simulated by using standard evolutionary genetic equations for processes such as selection and drift in the same morphospaces that are used for empirical morphomet...
Chapter
Full-text available
Ecometrics is the quantitative study of functional traits at the community level, and the environmental sorting of those traits at regional and continental scales. Functional traits are properties of organisms that have a direct physical or physiological relationship to an underlying quality of the environment, which in turn has indirect links to b...
Article
Factors that make species resilient to climate change can be difficult to study with empirical data because conditions cannot be experimentally controlled. We used trait‐based evolutionary ecological agent‐based modelling to understand how dispersal, selection, extirpation, and other factors contribute to resilience under three climate change scena...
Article
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This paper investigates a form of rank deficiency in phenotypic covariance matrices derived from geometric morphometric data, and its impact on measures of phenotypic integration. We first define a type of rank deficiency based on information theory, then demonstrate that this deficiency impairs the performance of phenotypic integration metrics in...
Article
Full-text available
Behavioral foraging differences are known to aid in food resource partitioning in pinniped communities, but it is not known whether skull biomechanical efficiency also contributes to dietary niche partitioning. We tested this hypothesis in a community of four sympatric species of pinnipeds that co-occur along the coast of Baja California: Californi...
Article
Full-text available
An accurate classification is the basis for research in biology. Morphometrics and morphospecies play an important role in modern taxonomy, with geometric morphometrics increasingly applied as a favourite analytical tool. Yet, really large samples are seldom available for modern species and even less common in palaeontology, where morphospecies are...
Conference Paper
Brain evolution involves changes in processing centres often marked by cerebral folds including sulci and gyri. In the temporal lobe, identification of major cerebral divisions relies on both external and internal sulci especially the superoposterior boundary for the temporoparietal-occipital complexes. Comprehensive quantification of noticeable su...
Article
Notiosorex is the only genus of shrews in North America with particular adaptations for arid habitats such as deserts. Five species currently are recognized in the genus, one of which, Notiosorex evotis, lives in deciduous rain forest from northern Sinaloa to the state of Jalisco in Mexico. Notiosorex evotis originally was described as a subspecies...
Conference Paper
Full-text available
Modern humans are acknowledged in having the largest absolute brain size among extant anthropoids with the past several decades focusing on differences in cerebral organisation, where modern humans have been argued to possess relatively larger temporal lobes for brain size compared to other extant anthropoids. Despite the implications for language...
Conference Paper
Full-text available
Brain evolution involves changes in processing centres that are often marked by folds on the surface of the cerebrum including sulci and gyri. Sulcal variation is considered high in modern humans, but quantification is lacking. We assessed the degree of sulcal variation of some major folds of the temporal cortex using a sample of T1-weighted in viv...
Article
Full-text available
Forests provide myriad ecosystem services, many of which are vital to local and regional economies. Consequently, there is a need to better understand how predicted changes in climate will impact forest dynamics and the implications of such changes for society as a whole. Here we focus on the impacts of climate change on Indiana forests, which are...
Article
The kinetic skull is a key innovation that allowed snakes to capture, manipulate, and swallow prey exclusively using their heads using the coordinated movement of 8 bones. Despite these unique feeding behaviors, patterns of evolutionary integration and modularity within the feeding bones of snakes in a phylogenetic framework have yet to be addresse...
Preprint
Full-text available
The kinetic skull is a key innovation that allowed snakes to capture, manipulate, and swallow prey exclusively using their heads using the coordinated movement of 8 bones. Despite these unique feeding behaviors, patterns of evolutionary integration and modularity within the feeding bones of snakes in a phylogenetic framework have yet to be addresse...
Article
Increased brain size is a characteristic of the Homo erectus hypodigm compared to early fossil hominins with changes in cerebral reorganization of evolutionary importance for the genus Homo. The close spatial proximity of the temporal lobes of the brain to the cranial base, specifically, the middle cranial fossa (MCF), provides inference of tempora...
Article
Cats possess some of the highest ankle gear ratios of any extant carnivorans, a feature that facilitates leaping and sprinting involved in ambush predation and scansorial lifestyles. In today's North American carnivoran communities, the high gear ratio of cats contributes to an overall high ecometric average for this trait and contributes strongly...
Article
Full-text available
Functional tradeoffs are often viewed as constraints on phenotypic evolution, but they can also facilitate evolution across the suboptimal valleys separating performance peaks. I explore this process by reviewing a previously published model of how disruptive selection from competing functional demands defines an intermediate performance optimum fo...
Article
Objectives We investigate the suitability of middle cranial fossa (MCF) size as a proxy for temporal lobe volume (TLV), examining the strength of the association between TLV and MCF metrics and assess the reliability predicting TLV in fossil anthropoids. The temporal lobe of the primate brain is a multimodal association cortex involved in long‐term...
Article
Full-text available
Between group PCA (bgPCA) has been developed to summarize group differences in high dimensional spaces like in geometric morphometrics and microarray data where the number of variables is often larger than sample size. However, it has been very recently shown that this technique inflates apparent differences as seen in scatterplots and, in extreme...
Article
Cerebral folding patterns include sulci and gyri visible on the external surface of the brain. Although paleoneurologists rely on sulcal imprints preserved on the endocranial surface for inferences in fossil species, the specific mechanisms behind sulcal formation remain unknown, but axonal-neuronal tensioning, genetic factors and biomechanical pre...
Article
Cerebral folding patterns include sulci and gyri visible on the external surface of the brain. Although paleoneurologists rely on sulcal imprints preserved on the endocranial surface for inferences in fossil species, the specific mechanisms behind sulcal formation remain unknown, but axonal-neuronal tensioning, genetic factors and biomechanical pre...
Conference Paper
Selection for functional efficiency typically pushes a morphological trait toward an adaptive optimum, but when a structure performs more than one function, the optimal solution may require a compromise in functional efficiency. This optimal solution is necessarily also a compromise with ontogenetic change and other processes that canalize morpholo...
Conference Paper
Cranial variation is known to be a mix of taxonomic, structural, and functional components, but our understanding of the evolutionary factors contributing to specific aspects of this diversity are not well known. To what extent is the amount of variation within great apes linked to the heterogeneity of the environments they inhabit? Most hominid sp...
Poster
The brain does not preserve in the fossil record and palaeoneurologists must rely on endocasts, moulds of the endocranium, to infer fossil brain morphology. Sulcal patterns on the external surface of the brain are often used in comparative neuroanatomy to infer differences in brain macroanatomy between species. For the application to fossil species...
Article
Full-text available
Phylogenetic comparative methods use tree topology, branch lengths, and models of phenotypic change to take into account non‐independence in statistical analysis. However, these methods normally assume that trees and models are known without error. Approaches relying on evolutionary regimes also assume specific distributions of character states acr...
Poster
Paleoneurologists have previously described changes in the relative proportions of cerebral regions during the evolution of Old World Monkeys (Cercopithecoidea). Compared to fossil catarrhines, extant cercopithecines have an absolute increase in total brain volume with relatively larger frontal lobes but reduced olfactory bulbs. There is no consens...
Poster
Paleoneurological investigations into Homo neanderthalensis have largely been confined to the cranial vault with the cranial base often highly fragmentary or incomplete, limiting interpretations of the temporal lobes. Tentative interpretations from fragmentary basicrania, extrapolation and comparison with extant Homo sapiens suggest H. neanderthale...
Poster
Paleoneurological investigations into Homo neanderthalensis have largely been confined to the cranial vault with the cranial base often highly fragmentary or incomplete, limiting interpretations of the temporal lobes. Tentative interpretations from fragmentary basicrania, extrapolation and comparison with extant Homo sapiens suggest H. neanderthale...
Article
Full-text available
The field of comparative morphology has entered a new phase with the rapid generation of high-resolution three-dimensional data. With freely available 3D data of thousands of species, methods for quantifying morphology that harness this rich phenotypic information are quickly emerging. Among these techniques, high-density geometric morphometric app...
Poster
The Asian paleoanthropological record contains few complete Homo erectus crania but many fragmentary basicrania which have limited paleoneurological investigations of change in Asian H. erectus temporal lobe morphology. Despite this, many different approaches have been used since the 1940s to the present to describe Asian H. erectus temporal lobe a...
Article
Shrews, Chromosomes and Speciation - edited by Jeremy B. Searle February 2019
Article
Shrews, Chromosomes and Speciation - edited by Jeremy B. Searle February 2019
Article
Cambridge Core - Cell Biology and Developmental Biology - Shrews, Chromosomes and Speciation - edited by Jeremy B. Searle
Chapter
Shrews, Chromosomes and Speciation - edited by Jeremy B. Searle February 2019
Chapter
Full-text available
Shrews, Chromosomes and Speciation - edited by Jeremy B. Searle February 2019
Chapter
Shrews, Chromosomes and Speciation - edited by Jeremy B. Searle February 2019
Article
2 H/ 1 H ratios in animal biomass reflect isotopic input from food and water. A 10-week controlled laboratory study raised 48 mice divided in two generations (8 mothers Mus musculus and their offspring). The mice were divided into four groups based on the combination of 2 H, 13 C, 15 N-enriched and non-enriched food and water. Glycine, the most com...
Conference Paper
Full-text available
In palaeoneurology, untangling the complexities of the cerebrocranial systems is evident in the reciprocal changes to the basicranium, specifically the middle cranial fossae (fossa), and the temporal lobes of the brain. In utilizing digital imaging sourced from ex-vivo cranial CT and in-vivo brain MRI, we investigated the association between fossa...
Article
Aim We use cluster analysis to delimit climatically and functionally distinct mammalian faunal clusters. These entities form regional species pools and are relevant to community assembly processes. Similar clusters can be differentiated in the fossil record, offering the potential for use as palaeoenvironmental proxies. Location North America with...
Article
Full-text available
Evolution is a fundamentally population level process in which variation, drift and selection produce both temporal and spatial patterns of change. Statistical model fitting is now commonly used to estimate which kind of evolutionary process best explains patterns of change through time using models like Brownian motion, stabilizing selection (Orns...
Article
Full-text available
Geometric morphometrics provide tools for analyzing the shapes of objects based on the coordinates of points placed on their surfaces. These tools can be used for a wide variety of analysis, ranging from statistical regression and MANOVA to ancestor reconstruction and evolutionary modeling. A central component of most geometric morphometric methods...
Article
Full-text available
In Table 1 of this article, the descriptions of landmarks 14, 15, and 36 are incorrect. Landmarks 14 and 36 should read “Posterior extremity of occipital condyle along margin of foramen magnum” and landmark 15 should read “Opisthion”. A correct version of Table 2 appears in the Author Correction associated with this article; the error has not been...
Article
Full-text available
A unique characteristic of mammals is a vertebral column with anatomically distinct regions, but when and how this trait evolved remains unknown. We reconstructed vertebral regions and their morphological disparity in the extinct forerunners of mammals, the nonmammalian synapsids, to elucidate the evolution of mammalian axial differentiation. Mappi...
Article
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The radiation and extinction of East African vertebrate fauna have been linked to key climatic changes that occurred around 2.8, 1.7, and 0.5 Ma. This study tests whether vegetation and diet changes were linked to these climatic fluctuations, focusing on the climatic event at 1.7 Ma, by analyzing the stable isotope composition of fossil herbivore t...
Article
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Conodont fossils are highly valuable for Paleozoic biostratigraphy and for interpreting evolutionary change, but identifying and describing conodont morphologies, and characterizing gradual shape variation remain challenging. We used geometric morphometric (GM) analysis to conduct the first landmark-based morphometric analysis of the biostratigraph...
Technical Report
Full-text available
This report from the Indiana Climate Change Impacts Assessment (IN CCIA) examines the direct and indirect impacts that climate change is expected to have on Indiana’s forests. The report specifically addresses forest regeneration, forest composition, tree growth and harvest, wildlife habitat and forest products. The findings presented here are base...
Article
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Insects show relatively little genital variation within species compared to extraordinary and often rapid diversification among species. It has been suggested that selection for reproductive isolation through differences in genital shape might explain this phenomenon. This hypothesis predicts that populations diverge faster in genital shape than in...
Chapter
Full-text available
Ecometrics is a trait-based approach to study ecosystem variability through time. An ecometric value is derived from describing the distribution of functional traits at the community level, which may arise by environmental filtering, extinction, or convergence. An ecometric relationship describes the correspondence between spatially explicit ecomet...
Conference Paper
The transition to flight from theropod dinosaurs to birds during the Jurassic and Cretaceous was one of the most significant innovations in locomotion in evolutionary history; it allowed birds to exploit new ecological niches and survive the Cretaceous-Paleogene extinction event - one of the worst mass extinctions in Earth’s history. Flight fundame...
Article
Full-text available
Geometric morphometrics is widely used to study underlying causal factors in phenotypic evolution and to reconstruct evolutionary history of phenotypes. However, non-linearities in the phenotypic landscape may exist such that analytical solutions derived from comparison of phenotypes in morphospace may have complex or contradictory relationships in...
Article
Full-text available
The developmental gene expression, morphogenesis, and population variation in mammalian molar teeth has become increasingly well understood, providing a model system for synthesizing evolution and developmental genetics. In this study, we estimated additive genetic covariances in molar shape (G) using parent-offspring regression in Cryptotis parva,...
Article
Full-text available
Background: Ecometric patterning is the sorting of mean values of functional traits in communities in space through time at continental scales. Ecometric patterns can emerge from intraspecific population-level processes (selection along an environmental gradient), species-level processes (geographic sorting of species based on functional trait diff...
Article
Full-text available
Background: Patterns of change in ecomorphological traits have traditionally been studied using data from the fossil record. Recent advances in molecular phylogenetics created new opportunities for inferring ancestral character states and estimating the modes and rates of trait evolution from phylogenetic hypotheses of extant organisms. However, wi...
Article
Full-text available
BACKGROUND: The pace and magnitude of human-caused global change has accelerated dramatically over the past 50 years, overwhelming the capacity of many ecosystems and species to maintain themselves as they have under the more stable conditions that prevailed for at least 11,000 years. The next few decades threaten even more rapid transformations be...
Article
Full-text available
The large brain and small postcanine teeth of modern humans are among our most distinctive features, and trends in their evolution are well studied within the hominin clade. Classic accounts hypothesize that larger brains and smaller teeth coevolved because behavioral changes associated with increased brain size allowed a subsequent dental reductio...
Article
Full-text available
Focusing on geometric morphometrics (GMM), we review methods for acquiring morphometric data from 3-D objects (including fossils), algorithms for producing shape variables and morphospaces, the mathematical properties of shape space, especially how they relate to mor-phogenetic and evolutionary factors, and issues posed by working with fossil objec...
Article
Full-text available
Quantitative genetics provides theory of the evolutionary processes that govern the evolution of phenotypic traits within and between populations. In principle, the same theory should govern the long-term evolution of traits in diverging species. However, non-population processes such as punctuated equilibrium, species selection, and evolutionary c...
Poster
Crocodylians possess simple, conical-shaped teeth that do not contain the unique variety of cusps and shapes that are found in mammalian teeth. Therefore, identifying a tooth to a specific position or region within the crocodylian dental arcade is normally based only on the shape of a tooth. Anterior teeth tend to be longer, more slender, and sharp...
Article
Fossils and other paleontological information can improve phylogenetic comparative method estimates of phenotypic evolution and generate hypotheses related to species diversification. Here, we use fossil information to calibrate ancestral reconstructions of suitable climate for Sceloporus lizards in North America. Integrating data from the fossil r...