20 Works

Supplementary datasets, data analysis code, and R tutorials for: Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs

Daniel Moen, Elisa Cabrera-Guzmán, Itzue Caviedes-Solis, Edna González-Bernal & Allison Hanna
Comparative phylogenetic studies of adaptation are uncommon in biomechanics and physiology. Such studies require collecting data from many species, a challenge when data collection is experimentally intensive. Moreover, researchers struggle to employ the most biologically appropriate phylogenetic tools for identifying adaptive evolution. Here, we detail an established but greatly underutilized phylogenetic comparative framework—the Ornstein-Uhlenbeck process—that explicitly models long-term adaptation. We discuss challenges in implementing and interpreting the model, and we outline potential solutions. We demonstrate...

Data from: Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity

Jonathan L. Payne, Alison G. Boyer, James H. Brown, Seth Finnegan, Michal Kowaleski, , S. Kathleen Lyons, Craig R. McClain, Daniel W. McShea, Phillip M. Novack-Gottshall, Felisa A. Smith, Jennifer A. Stempien, Steve C. Wang, M. Kowalewski & R. A. Krause
NOTE: See also http://bodysize.nescent.org. ABSTRACT: The maximum size of organisms has increased enormously since the initial appearance of life >3.5 billion years ago (Gya), but the pattern and timing of this size increase is poorly known. Consequently, controls underlying the size spectrum of the global biota have been difficult to evaluate. Our period-level compilation of the largest known fossil organisms demonstrates that maximum size increased by 16 orders of magnitude since life first appeared in...

Group composition of individual personalities alters social network structure in experimental populations of forked fungus beetles

Phoebe Cook, Olivia Baker, Robin Costello, Vincent Formica & Edmund Brodie
Social network structure is a critical group character that mediates the flow of information, pathogens, and resources among individuals in a population, yet little is known about what shapes social structures. In this study, we experimentally tested whether social network structure depends on the personalities of group members. Replicate groups of forked fungus beetles (Bolitotherus cornutus) were engineered to include only members previously assessed as either more social or less social. We found that individuals...

Data from: Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi)

Graeme T Lloyd, Steve C Wang & Stephen L Brusatte
Quantifying rates of morphological evolution is important in many macroevolutionary studies, and critical when assessing possible adaptive radiations and episodes of punctuated equilibrium in the fossil record. However, studies of morphological rates of change have lagged behind those on taxonomic diversification, and most authors have focused on continuous characters and quantifying patterns of morphological rates over time. Here, we provide a phylogenetic approach, using discrete characters and three statistical tests to determine points on a...

Data from: Distribution and abundance of glucocorticoid and mineralocorticoid receptors throughout the brain of the great tit Parus major

Rebecca A. Senft, Simone L. Meddle & Alexander T. Baugh
The glucocorticoid stress response, regulated by the hypothalamic-pituitary-adrenal (HPA) axis, enables individuals to cope with stressors through transcriptional effects in cells expressing the appropriate receptors. The two receptors that bind glucocorticoids—the mineralocorticoid receptor (MR) and glucocorticoid receptor (GR)—are present in a variety of vertebrate tissues, but their expression in the brain is especially important. Neural receptor patterns have the potential to integrate multiple behavioral and physiological traits simultaneously, including self-regulation of glucocorticoid secretion through negative...

Data from: Biodiversity extinction thresholds are modulated by matrix type

Andrea Larissa Boesing, Elizabeth Nichols & Jean Paul Metzger
Biodiversity extinction thresholds are abrupt declines in biological diversity that occur with habitat loss, associated with a decline in habitat connectivity. Matrix quality should influence the location of thresholds along habitat loss gradients through its effects on connectivity; however these relationships have seldom been explored empirically. Using field data from 23 independent 1,254 ha landscapes in the Brazilian Atlantic Forest, we evaluated how tropical avian biodiversity responds to native forest loss within habitat patches embedded...

Data from: Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S attenuata) dolphins, from SNP data

Matthew S. Leslie & Phillip A. Morin
Little is known about global patterns of genetic connectivity in pelagic dolphins, including how circumtropical pelagic dolphins spread globally following the rapid and recent radiation of the subfamily delphininae. In this study, we tested phylogeographic hypotheses for two circumtropical species, the spinner dolphin (Stenella longirostris) and the pantropical spotted dolphin (Stenella attenuata), using >3,000 nuclear DNA single nucleotide polymorphisms (SNPs) in each species. Analyses for population structure indicated significant genetic differentiation between almost all subspecies...

Data from: Phenotypic assortment mediates the effect of social selection in a wild beetle population

Vincent A. Formica, Joel W. McGlothlin, Corlett Wolfe Wood, Malcolm E. Augat, R. Eileen Butterfield, Mollie E. Barnard &
Social interactions often have major fitness consequences, but little is known about how specific interacting phenotypes affect the strength of natural selection. Social influences on the evolutionary process can be assessed using a multilevel selection approach that partitions the effects of social partner phenotypes on fitness (referred to as social or group selection) from those of the traits of a focal individual (nonsocial or individual selection). To quantify the contribution of social selection to total...

Social network position experiences more variable selection than weaponry in wild subpopulations of forked fungus beetles

Vincent Formica, Hannah Donald, Hannah Marti, Zhazira Irgebay &
1. The phenotypic expression and fitness consequences of behaviors that are exhibited during social interactions are especially sensitive to their local social context. This context-dependence is expected to generate more variation in the sign and magnitude of selection on social behavior than that experienced by static characters like morphology. Relatively few studies, however, have examined selection on behavioral traits in multiple populations. 2. We estimated sexual selection in the wild to determine if the strength...

Group and individual social network metrics are robust to changes in resource distribution in experimental populations of forked fungus beetles

Robin Costello, Phoebe Cook, Vincent Formica &
Social interactions drive many important ecological and evolutionary processes. It is therefore essential to understand the intrinsic and extrinsic factors that underlie social patterns. A central tenet of the field of behavioral ecology is the expectation that the distribution of resources shapes patterns of social interactions. We combined experimental manipulations with social network analyses to ask how patterns of resource distribution influence complex social interactions. We experimentally manipulated the distribution of an essential food and...

Differences in neurotoxic outcomes of organophosphorus pesticides revealed via multi-dimensional screening in adult and regenerating planarians

Danielle Ireland
Organophosphorus pesticides (OPs) are a chemically diverse class of commonly used insecticides. Epidemiological studies suggest that low dose chronic prenatal and infant exposures can lead to life-long neurological damage and behavioral disorders. While inhibition of acetylcholinesterase (AChE) is the shared mechanism of acute OP neurotoxicity, OP-induced developmental neurotoxicity (DNT) can occur independently and/or in the absence of significant AChE inhibition, suggesting alternative targets. Moreover, different OPs can cause different adverse outcomes, suggesting that different OPs...

Data from: A shift in the long-term mode of foraminiferan size evolution caused by the end-Permian mass extinction

Jonathan L. Payne, Adam B. Jost, Steve C Wang & Jan M. Skotheim
Size is among the most important traits of any organism, yet the factors that control its evolution remain poorly understood. In this study, we investigate controls on the evolution of organismal size using a newly compiled database of nearly 25,000 foraminiferan species and subspecies spanning the past 400 million years. We find a transition in the pattern of foraminiferan size evolution from correlation with atmospheric pO2 during the Paleozoic (400-250 Mya) to long-term stasis during...

Data from: Adaptive credible intervals on stratigraphic ranges when recovery potential is unknown

Steve C. Wang, Philip J. Everson, Heather Jianan Zhou, Dasol Park & David J. Chudzicki
Numerous methods exist for estimating the true stratigraphic range of a fossil taxon based on the stratigraphic positions of its fossil occurrences. Many of these methods require the assumption of uniform fossil recovery potential—that fossils are equally likely to be found at any point within the taxon's true range. This assumption is unrealistic, because factors such as stratigraphic architecture, sampling effort, and the taxon's abundance and geographic range affect recovery potential. Other methods do not...

Data from: Gradual assembly of avian body plan culminated in rapid rates of evolution across dinosaur-bird transition

Stephen L. Brusatte, Graeme T. Lloyd, Steve C. Wang & Mark A. Norell
Brusatte et al. 2014 Current Biology Dryad File1Supplementary appendices: list of phylogenetic characters, phylogenetic character-taxon matrix, list of taxon ages, list of supplementary figure captions (relevant to Dryad File 2)BrusatteetalRevisionDryadFile1.docxBrusatte et al. 2014 Current Biology Dryad File2Supplementary figuresBrusatteetalRevisionDryadFile2.pdfBrusatte et al. 2014 Current Biology Dryad File3R code (Graeme T. Lloyd)BrusatteetalRevisionDryadFile3.zip

The genetic basis of coordinated plasticity across functional units in a Lake Malawi cichlid mapping population

Dina Navon, Paul Hatini, Lily Zogbaum & Craig Albertson
Adaptive radiations are often stereotypical, as populations repeatedly specialize along conserved environmental axes. Phenotypic plasticity may be similarly stereotypical, as individuals respond to environmental cues. These parallel patterns of variation, which are often consistent across traits, have led researchers to propose that plasticity can facilitate predictable patterns of evolution along environmental gradients. This “flexible stem” model of evolution raises questions about the genetic nature of plasticity, including: How complex is the genetic basis for plasticity?...

Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile–Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground

Emma L Carroll, Paulo Ott, Louise McMillan, Bárbara Galletti Vernazzani, Petra Neveceralova, Els Vermeulen, Oscar Gaggiotti, Artur Andriolo, C. Scott Baker, Connor Bamford, Peter Best, Elsa Cabrera, Susannah Calderan, Andrea Chirife, Rachel M. Fewster, Paulo A. C. Flores, Timothy Frasier, Thales R. O. Freitas, Karina Groch, Pavel Hulva, Amy Kennedy, Russell Leaper, Mathew S. Leslie, Michael Moore, Larissa Oliviera … & Jennifer A Jackson
As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds...

A global ecological signal of extinction risk in terrestrial vertebrates

Maya Munstermann, Noel Heim, Douglas McCauley, Jonathan Payne, Nathan Upham, Steve Wang & Matthew Knope
To determine the distribution and causes of extinction threat across functional groups of terrestrial vertebrates, we assembled a dataset on ecological traits for 18,016 species and tested, using phylogenetic comparative methods, which categories of habitat association, mode of locomotion, and feeding mode best predict extinction risk. We found that cave-dwelling amphibians, brachiating mammals (all of which are primates), aerial and scavenging birds, and pedal squamates are all disproportionately threatened with extinction. Across four vertebrate classes,...

Data from: Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi)

Graeme T Lloyd, Steve C Wang & Stephen L Brusatte
Quantifying rates of morphological evolution is important in many macroevolutionary studies, and critical when assessing possible adaptive radiations and episodes of punctuated equilibrium in the fossil record. However, studies of morphological rates of change have lagged behind those on taxonomic diversification, and most authors have focused on continuous characters and quantifying patterns of morphological rates over time. Here, we provide a phylogenetic approach, using discrete characters and three statistical tests to determine points on a...

Data from: Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity

Jonathan L. Payne, Alison G. Boyer, James H. Brown, Seth Finnegan, Michal Kowaleski, , S. Kathleen Lyons, Craig R. McClain, Daniel W. McShea, Phillip M. Novack-Gottshall, Felisa A. Smith, Jennifer A. Stempien, Steve C. Wang, D. W. McShea, M. Kowalewski, J. L. Payne, R. A. Krause, S. C. Wang, P. M. Novack-Gottshall, A. G. Boyer, J. H. Brown & F. A. Smith
NOTE: See also http://bodysize.nescent.org. ABSTRACT: The maximum size of organisms has increased enormously since the initial appearance of life >3.5 billion years ago (Gya), but the pattern and timing of this size increase is poorly known. Consequently, controls underlying the size spectrum of the global biota have been difficult to evaluate. Our period-level compilation of the largest known fossil organisms demonstrates that maximum size increased by 16 orders of magnitude since life first appeared in...

Data from: Phenotypic assortment mediates the effect of social selection in a wild beetle population

Vincent A. Formica, Joel W. McGlothlin, Corlett Wolfe Wood, Malcolm E. Augat, R. Eileen Butterfield, Mollie E. Barnard &
Social interactions often have major fitness consequences, but little is known about how specific interacting phenotypes affect the strength of natural selection. Social influences on the evolutionary process can be assessed using a multilevel selection approach that partitions the effects of social partner phenotypes on fitness (referred to as social or group selection) from those of the traits of a focal individual (nonsocial or individual selection). To quantify the contribution of social selection to total...

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