Publications

2023

1. palaeoverse: A community-driven R package to support palaeobiological analysis

   Lewis A. Jones, William Gearty, Bethany J. Allen, Kilian Eichenseer, Christopher D. Dean, Sofía Galván, Miranta Kouvari, Pedro L. Godoy, Cecily S. C. Nicholl, Lucas Buffan, Erin M. Dillon, Joseph T. Flannery-Sutherland, and Alfio Alessandro Chiarenza

   Methods in Ecology and Evolution, 14(9), 2205-2215

   Abs HTML PDF Code

   The open-source programming language ‘R’ has become a standard tool in the palaeobiologist’s toolkit. Its popularity within the palaeobiological community continues to grow, with published articles increasingly citing the usage of R and R packages. However, there are currently a lack of agreed standards for data preparation and available frameworks to support the implementation of such standards. Consequently, data preparation workflows are often unclear and not reproducible, even when code is provided. Moreover, due to a lack of code accessibility and documentation, palaeobiologists are often forced to ‘reinvent the wheel’ to find solutions to issues already solved by other members of the community. Here, we introduce palaeoverse, a community-driven R package to aid data preparation and exploration for quantitative palaeobiological research. The package is freely available and has three core principles: (1) streamline data preparation and analyses; (2) enhance code readability; and (3) improve reproducibility of results. To develop these aims, we assessed the analytical needs of the broader palaeobiological community using an online survey, in addition to incorporating our own experiences. In this work, we first report the findings of the survey, which shaped the development of the package. Subsequently, we describe and demonstrate the functionality available in palaeoverse and provide usage examples. Finally, we discuss the resources we have made available for the community and our future plans for the broader Palaeoverse project. palaeoverse is a community-driven R package for palaeobiology, developed with the intention of bringing palaeobiologists together to establish agreed standards for high-quality quantitative research. The package provides a user-friendly platform for preparing data for analysis with well-documented open-source code to enhance transparency. The functionality available in palaeoverse improves code reproducibility and accessibility, which is beneficial for both the review process and future research.
2. rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes

   William Gearty and Lewis A. Jones

   Methods in Ecology and Evolution, 14(11), 2700-2708

   Abs HTML PDF Code

   Effective data visualisation is vital for data exploration, analysis and communication in research. In ecology and evolutionary biology, data are often associated with various taxonomic entities. Graphics of organisms associated with these taxa are valuable for framing results within a broader biological context. However, acquiring and using such resources can be challenging due to availability and licensing constraints. The PhyloPic database solves many of these issues by making organism silhouettes freely available. Tools that integrate this database with existing research workflows are needed to remove hurdles associated with data visualisation in the biological sciences. Here, we introduce rphylopic, an R package for fetching, transforming and visualising silhouettes of organisms from the PhyloPic database. In addition to making over 8000 organism silhouettes available within the R programming language, rphylopic empowers users to modify the appearance of these silhouettes for ultimate customisability when coding production–quality visualisations in both base R and ggplot2 workflows. In this work, we provide details about how the package can be installed, its implementation and potential use cases. For the latter, we showcase three examples across the ecology and evolutionary biology spectrum. Our hope is that rphylopic will make it easier for biologists to develop more accessible and engaging data visualisations by making external resources readily accessible, customisable and usable within R. In turn, by integrating into existing workflows, rphylopic helps to ensure that science is reproducible and accessible.

2022

1. Anthropogenic disruptions to longstanding patterns of trophic-size structure in vertebrates

   Rob Cooke*, William Gearty*, Abbie S. A. Chapman, Jillian Dunic, Graham J. Edgar, Jonathan S. Lefcheck, Gil Rilov, Craig R. McClain, Rick D. Stuart-Smith, S. Kathleen Lyons, and Amanda E. Bates

   Nature Ecology & Evolution, 6, 684–692

   Abs Press Release HTML PDF Code

   Diet and body mass are inextricably linked in vertebrates: while herbivores and carnivores have converged on much larger sizes, invertivores and omnivores are, on average, much smaller, leading to a roughly U-shaped relationship between body size and trophic guild. Although this U-shaped trophic-size structure is well documented in extant terrestrial mammals, whether this pattern manifests across diverse vertebrate clades and biomes is unknown. Moreover, emergence of the U-shape over geological time and future persistence are unknown. Here we compiled a comprehensive dataset of diet and body size spanning several vertebrate classes and show that the U-shaped pattern is taxonomically and biogeographically universal in modern vertebrate groups, except for marine mammals and seabirds. We further found that, for terrestrial mammals, this U-shape emerged by the Palaeocene and has thus persisted for at least 66 million years. Yet disruption of this fundamental trophic-size structure in mammals appears likely in the next century, based on projected extinctions. Actions to prevent declines in the largest animals will sustain the functioning of Earth’s wild ecosystems and biomass energy distributions that have persisted through deep time.
2. Reconstructed evolutionary patterns for crocodile-line archosaurs demonstrate impact of failure to log-transform body size data

   Roger B. J. Benson, Pedro Godoy, Mario Bronzati, Richard J. Butler, and William Gearty

   Communications Biology, 5(171)

   Abs HTML PDF Code

   Pseudosuchia includes crocodylians, plus all extinct species more closely related to them than to birds. They appeared around 250 million years ago and have a rich fossil history, with extinct diversity exceeding that of their living members. Recently, Stockdale & Benton presented analyses of a new dataset of body size estimates spanning the entire evolutionary history of Pseudosuchia. They quantified patterns of average body size, body size disparity through time and rates of evolution along phylogenetic lineages. Their results suggest that pseudosuchians exhibited considerable variation in rates of body size evolution, for which they provided various group-specific explanations and asserted the importance of climatic drivers. This differs from two recent studies that analysed a substantial portion of pseudosuchian body size evolution and proposed that adaptation to aquatic life, a biological innovation of some subgroups, was the main driver of body size evolution, with patterns of disparity also being influenced by size-dependent extinction risk. Here we show that the analytical results of Stockdale & Benton4 are strongly influenced by a methodological error in their body size index. Specifically, that they chose not to log-transform measurement data prior to analyses.

2021

1. Metabolic tradeoffs control biodiversity gradients through geological time

   Thomas H. Boag*, William Gearty*, and Richard G. Stockey*

   Current Biology, 31(13), 2906–2913

   Abs Press Release HTML PDF Code

   The latitudinal gradient of increasing marine biodiversity from the poles to the tropics is one of the most conspicuous biological patterns in modern oceans. Low-latitude regions of the global ocean are often hotspots of animal biodiversity, yet they are set to be most critically affected by anthropogenic climate change. As ocean temperatures rise and deoxygenation proceeds in the coming centuries, the volume of aerobically viable habitat is predicted to decrease in these zones. In contrast to the slightly asymmetrical modern latitudinal biodiversity gradient, compilations of fossil occurrences indicate peaks in biodiversity may have existed much further away from the equator in the past, with transitions between climate states hypothesized to explain this trend. We combine a new compilation of fossil mollusc occurrences, paleotemperature proxies, and biogeographic data to reveal a non-monotonic relationship between temperature and diversity in the paleontological record over the last 145 million years. We derive a metabolic model that integrates the kinetic effects of temperature on biodiversity with the recently described ‘Metabolic Index’ that calculates aerobic habitat availability based on the effect of temperature on hypoxia sensitivity. While factors such as coastal habitat area and homeothermy are important, we find strong congruence between our metabolic model and our fossil and paleotemperature meta-analysis. We therefore suggest that the effects of ocean temperature on the aerobic scope of marine ectotherms is a primary driver of migrating biodiversity peaks through geologic time and will likely play a role in the restructuring of biodiversity under projected future climate scenarios.
2. Ecological filtering and exaptation in the evolution of marine snakes

   William Gearty, Elsie Carrillo, and Jonathan L. Payne

   American Naturalist, 198(4), 506–521

   Abs HTML PDF Code

   Convergent evolution is often attributed to adaptation of form to function, but it can also result from ecological filtering, exaptation, or nonaptation. Testing among these possibilities is critical to understanding how and why morphological similarities emerge independently in multiple lineages. To address this challenge, we combined multiple preexisting phylogenetic methods to jointly estimate the habitats and morphologies of lineages within a phylogeny. We applied this approach to the invasions of snakes into the marine realm. We utilized a dataset for 1,243 extant snake species consisting of newly compiled biome occupancy information and preexisting data on reproductive strategy, body mass, and environmental temperature and elevation. We find evidence for marine clades arising from a variety of aquatic and terrestrial habitats. Furthermore, there is strong evidence of ecological filtering for non-marine ancestors that were already viviparous, had slightly larger-than-average body sizes, and that lived in environments with higher-than-average temperatures and lower-than-average elevations. In aggregate, similarities among independent lineages of marine snakes result from a combination of exaptation and strong ecological filtering. Strong barriers to entry of new habitats appear to be more important than common adaptations following invasions for producing similarities among independent lineages invading a shared, novel habitat.
3. Our past creates our present: a brief overview of racism and colonialism in Western paleontology

   Pedro M. Monarrez, Joshua B. Zimmt, Annaka M. Clement, William Gearty, John J. Jacisin, Kelsey M. Jenkins, Kristopher M. Kusnerik, Ashley W. Poust, Selina V. Robson, Judith A. Sclafani, Kelsey T. Stilson, Shamindri D. Tennakoon, and Carmi Milagros Thompson

   Paleobiology, 48(2), 173–185

   Abs HTML PDF

   As practitioners of a historical science, paleontologists and geoscientists are well versed in the idea that the ability to understand and to anticipate the future relies upon our collective knowledge of the past. Despite this understanding, the fundamental role that the history of paleontology and the geosciences plays in shaping the structure and culture of our disciplines is seldom recognized and therefore not acted upon sufficiently. Here, we present a brief review of the history of paleontology and geology in Western countries, with a particular focus on North America since the 1800s. Western paleontology and geology are intertwined with systematic practices of exclusion, oppression, and erasure that arose from their direct participation in the extraction of geological and biological resources at the expense of Black, Indigenous, and People of Color (BIPOC). Our collective failure to acknowledge this history hinders our ability to address these issues meaningfully and systemically in present-day educational, academic, and professional settings. By discussing these issues and suggesting some ways forward, we intend to promote a deeper reflection upon our collective history and a broader conversation surrounding racism, colonialism, and exclusion within our scientific communities. Ultimately, it is necessary to listen to members of the communities most impacted by these issues to create actionable steps forward while holding ourselves accountable for the past.

2020

1. Physiological constraints on body size distributions in crocodyliformes

   William Gearty and Jonathan L. Payne

   Evolution, 74(2), 245–255

   Abs Press Release HTML PDF Code

   At least 26 species of crocodylian populate the globe today, but this richness represents a minute fraction of the diversity and disparity of Crocodyliformes. Fossil forms are far more varied, spanning from erect, fully terrestrial species to flippered, fully marine species. To quantify the influence of a marine habitat on the directionality, rate, and variance of evolution of body size in Crocodyliformes and thereby identify underlying selective pressures, we compiled a database of body sizes for 264 fossil and modern species of crocodyliform covering terrestrial, semi-aquatic, and marine habitats.We find increases in body size coupled with increases in strength of selection and decreases in variance following invasions of marine habitats but not of semiaquatic habitats. A model combining constraints from thermoregulation and lung capacity provides a physiological explanation for the larger minimum and average sizes of marine species. It appears that constraints on maximum size are shared across Crocodyliformes, perhaps through factors such as the allometric scaling of feeding rate versus basal metabolism with body size. These findings suggest that broad-scale patterns of body size evolution and the shapes of body size distributions within higher taxa are often determined more by physiological constraints than by ecological interactions or environmental fluctuations.

2018

1. Energetic tradeoffs control the size distribution of aquatic mammals

   William Gearty, Craig R. McClain, and Jonathan L. Payne

   Proceedings of the National Academy of Sciences, 115(16), 4194–4199

   Abs Press Release HTML PDF Blog Code

   Four extant lineages of mammals have invaded and diversified in the water: Sirenia, Cetacea, Pinnipedia, and Lutrinae. Most of these aquatic clades are larger bodied, on average, than their closest land-dwelling relatives, but the extent to which potential ecological, biomechanical, and physiological controls contributed to this pattern remains untested quantitatively. Here, we use previously published data on the body masses of 3,859 living and 2,999 fossil mammal species to examine the evolutionary trajectories of body size in aquatic mammals through both comparative phylogenetic analysis and examination of the fossil record. Both methods indicate that the evolution of an aquatic lifestyle is driving three of the four extant aquatic mammal clades toward a size attractor at ∼500 kg. The existence of this body size attractor and the relatively rapid selection toward, and limited deviation from, this attractor rule out most hypothesized drivers of size increase. These three independent body size increases and a shared aquatic optimum size are consistent with control by differences in the scaling of energetic intake and cost functions with body size between the terrestrial and aquatic realms. Under this energetic model, thermoregulatory costs constrain minimum size, whereas limitations on feeding efficiency constrain maximum size. The optimum size occurs at an intermediate value where thermoregulatory costs are low but feeding efficiency remains high. Rather than being released from size pressures, water-dwelling mammals are driven and confined to larger body sizes by the strict energetic demands of the aquatic medium.

2016

1. Comparative anatomy of the bony labyrinth of extant and extinct porpoises (Cetacea: Phocoenidae)

   Rachel A. Racicot, William Gearty, Naoki Kohno, and John J. Flynn

   Biological Journal of the Linnean Society, 119(4), 831–846

   Abs HTML PDF

   The inner ear anatomy of cetaceans, now more readily accessible by means of nondestructive high‐resolution X‐ray computed tomographic (CT) scanning, provides a window into their acoustic abilities and ecological preferences. Inner ear labyrinths also may be a source for additional morphological characters for phylogenetic analyses. In this study, we explore digital endocasts of the inner ear labyrinths of representative species of extinct and extant porpoises (Mammalia: Cetacea: Phocoenidae), a clade of some of the smallest odontocete cetaceans, which produce some of the highest‐frequency clicks for biosonar and communication. Metrics used to infer hearing ranges based on cochlear morphology indicate that all taxa considered could hear high‐frequency sounds, thus the group had already acquired high‐frequency hearing capabilities by the Miocene (9–11 Mya) at the latest. Vestibular morphology indicates that extant species with pelagic preferences have similarly low semicircular canal deviations from 90°, values indicating more sensitivity to head rotations. Species with near‐shore preferences have higher canal deviation values, indicating less sensitivity to head rotations. Extending these analyses to the extinct species, we demonstrate a good match between those predicted to have coastal (such as Semirostrum cerutti) preferences and high canal deviation values. We establish new body length relationships based on correlations with inner ear labyrinth volume, which can be further explored among other aquatic mammals to infer body size of specimens consisting of fragmentary material.

2013

1. Melanin concentration gradients in modern and fossil feathers

   Daniel J. Field, Liliana D’Alba, Jakob Vinther, Samuel M Webb, William Gearty, and Matthew D. Shawkey

   PLoS One, 8(3)

   Abs HTML PDF

   In birds and feathered non-avian dinosaurs, within-feather pigmentation patterns range from discrete spots and stripes to more subtle patterns, but the latter remain largely unstudied. A  55 million year old fossil contour feather with a dark distal tip grading into a lighter base was recovered from the Fur Formation in Denmark. SEM and synchrotron-based trace metal mapping confirmed that this gradient was caused by differential concentration of melanin. To assess the potential ecological and phylogenetic prevalence of this pattern, we evaluated 321 modern samples from 18 orders within Aves. We observed that the pattern was found most frequently in distantly related groups that share aquatic ecologies (e.g. waterfowl Anseriformes, penguins Sphenisciformes), suggesting a potential adaptive function with ancient origins.