450 Works

Data from: Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT)

Charles L. Nunn & Natalie Cooper
For traits showing correlated evolution, one trait may evolve more slowly than the other, producing evolutionary lag. The species-pairs evolutionary lag test (SPELT) uses an independent contrasts based approach to detect evolutionary lag on a phylogeny. We investigated the statistical performance of SPELT in relation to degree of lag, sample size (species pairs), and strength of association between traits. We simulated trait evolution under two models: one in which trait X changes during speciation and...

Data from: Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures

Taj Morton, Jalean Petricka, David L. Corcoran, Song Li, Cara M. Winter, Alexa Carda, Philip N. Benfey, Uwe Ohler & Molly Megraw
Understanding plant gene promoter architecture has long been a challenge due to the lack of relevant large-scale data sets and analysis methods. Here, we present a publicly available, large-scale transcription start site (TSS) data set in plants using a high-resolution method for analysis of 5′ ends of mRNA transcripts. Our data set is produced using the paired-end analysis of transcription start sites (PEAT) protocol, providing millions of TSS locations from wild-type Columbia-0 Arabidopsis thaliana whole...

Data from: Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center

Sarah M. Zehr, Richard G. Roach, David Haring, Julie Taylor, Freda H. Cameron & Anne D. Yoder
Since its establishment in 1966, the Duke Lemur Center (DLC) has accumulated detailed records for nearly 4200 individuals from over 40 strepsirrhine primate taxa – the lemurs, lorises, and galagos. Here we present verified data for 3627 individuals of 27 taxa in the form of a life history table containing summarized species values for variables relating to ancestry, reproduction, longevity, and body mass, as well as the two raw data files containing direct and calculated...

Data from: Wood-inhabiting fungi with tight associations with other species have declined as a response to forest management

Nerea Abrego, David Dunson, Panu Halme, Isabel Salcedo & Otso Ovaskainen
Research on mutualistic and antagonistic networks, such as plant–pollinator and host–parasite networks, has shown that species interactions can influence and be influenced by the responses of species to environmental perturbations. Here we examine whether results obtained for directly observable networks generalize to more complex networks in which species interactions cannot be observed directly. As a case study, we consider data on the occurrences of 98 wood-inhabiting fungal species in managed and natural forests. We specifically...

Data from: The comparative hydrodynamics of rapid rotation by predatory appendages

Mathew J. McHenry, Philip S. L. Anderson, Sam Van Wassenbergh, David Matthews, Adam Summers & S. N. Patek
Countless aquatic animals rotate appendages through the water, yet fluid forces are typically modeled with translational motion. To elucidate the hydrodynamics of rotation, we analyzed the raptorial appendages of mantis shrimp (Stomatopoda) using a combination of flume experiments, mathematical modeling and phylogenetic comparative analyses. We found that computationally efficient blade-element models offered an accurate first-order approximation of drag, when compared with a more elaborate computational fluid-dynamic model. Taking advantage of this efficiency, we compared the...

Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta

Maggie R. Wagner & Thomas Mitchell-Olds
Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection (“adaptive plasticity”) or disfavored (“nonadaptive” plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1,500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho,...

Data from: Estimating infection prevalence: best practices and their theoretical underpinnings

Ian F. Miller, India Schneider-Crease, Charles L. Nunn & Michael P. Muehlenbein
Accurately estimating infection prevalence is fundamental to the study of population health, disease dynamics, and infection risk factors. Prevalence is estimated as the proportion of infected individuals (“individual-based estimation”), but is also estimated as the proportion of samples from which the disease-causing organisms are recovered (“anonymous estimation”). The latter method is often used when researchers lack information on individual host identity, which can occur during noninvasive sampling of wild populations or when the individual that...

Data from: Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

Dorothee Hodapp, Elizabeth T. Borer, W. Stanley Harpole, Eric M. Lind, Eric W. Seabloom, Peter B. Adler, Juan Alberti, Carlos A. Arnillas, Jonathan D. Bakker, Lori Biederman, Marc Cadotte, Elsa E. Cleland, Scott Collins, Philip A. Fay, Jennifer Firn, Nicole Hagenah, Yann Hautier, Oscar Iribarne, Johannes M.H. Knops, Rebecca L. McCulley, Andrew MacDougall, Joslin L. Moore, John W. Morgan, Brent Mortensen, Kimberly J. La Pierre … & Johannes M. H. Knops
Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta-diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major...

Data from: Costs and drivers of helminth parasite infection in wild female baboons

Mercy Y. Akinyi, David Jansen, Bobby Habig, Laurence Gesquiere, Susan C. Alberts & Elizabeth A. Archie
1. Helminth parasites can have wide ranging, detrimental effects on host reproduction and survival. These effects are best documented in humans and domestic animals, while only a few studies in wild mammals have identified both the forces that drive helminth infection risk and their costs to individual fitness. 2. Working in a well-studied population of wild baboons (Papio cynocephalus) in the Amboseli ecosystem in Kenya, we pursued two goals, to: (i) examine the costs of...

Genomic analyses of phenotypic differences between native and invasive populations of diffuse knapweed (Centaurea diffusa)

Kathryn Turner, Kate Ostevik, Christopher Grassa & Loren Rieseberg
Invasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically-important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a genome-wide association (GWAS) approach to identify the genetic basis of trait variation in the non-model, invasive, diffuse knapweed (Centaurea diffusa Lam. [Asteraceae]). To assist with this analysis, we...

Data from: Thermodynamic constraints on the utility of ecological stoichiometry for explaining global biogeochemical patterns

Ashley M. Helton, Marcelo Ardon & Emily S. Bernhardt
Carbon and nitrogen cycles are coupled through both stoichiometric requirements for microbial biomass and dissimilatory metabolic processes in which microbes catalyse reduction-oxidation reactions. Here, we integrate stoichiometric theory and thermodynamic principles to explain the commonly observed trade-off between high nitrate and high organic carbon concentrations, and the even stronger trade-off between high nitrate and high ammonium concentrations, across a wide range of aquatic ecosystems. Our results suggest these relationships are the emergent properties of both...

Data from: Priorities and motivations of marine coastal restoration research

Elisa Bayraktarov, Shantala Brisbane, Phoebe J Stewart-Sinclair, Audrey Van Herwaarden, Keila Stark, Valerie Hagger, Carter S Smith, Kerrie A Wilson, Catherine E Lovelock, Chris Gillies, Andrew D L Steven & Megan I Saunders
Active restoration is becoming an increasingly important conservation intervention to counteract the degradation of marine coastal ecosystems. Understanding what has motivated the scientific community to research the restoration of marine coastal ecosystems and how restoration research projects are funded is essential if we want to scale-up restoration interventions to meaningful extents.Here, we systematically review and synthesize data to understand the motivations for research on the restoration of coral reefs, seagrass, mangroves, saltmarsh, and oyster reefs....

Latitudinal gradients in population growth do not reflect demographic responses to climate

Megan Peterson, Graham Bailes, Lauren Hendricks, Laurel Pfeifer-Meister, Paul Reed, Scott Bridgham, Bart Johnson, Robert Shriver, Ellen Waddle, Hannah Wroton, Daniel Doak, Bitty Roy & William Morris
Spatial gradients in population growth, such as across latitudinal or elevational gradients, are often assumed to primarily be driven by variation in climate, and are frequently used to infer species’ responses to climate change. Here, we use a novel demographic, mixed model approach to dissect the contributions of climate variables vs. other latitudinal or local site effects on spatiotemporal variation in population performance in three perennial bunchgrasses. For all three species, we find that performance...

Data from: The effect of urban habitat use on parasitism in mammals: a meta-analysis

Courtney Werner & Charles Nunn
Rates of urbanization are increasing globally, with potential consequences for the dynamics of parasites and their wildlife hosts. A small subset of mammal species have the dietary and behavioural flexibility to survive in urban settings. The changes that characterize urban ecology – including landscape transformation, modified diets, and shifts in community composition – can either increase or decrease susceptibility and exposure to parasites. We used a meta-analytic approach to systematically assess differences in endoparasitism between...

Host-plant choices determined by reproductive interference between closely related butterflies

Naota Ohsaki, Masaaki Ohata, Yoshibumi Sato & Mark D. Rausher
A number of empirical studies have concluded that reproductive interference, RI, contributes to parapatric species distributions or sexual exclusion. However, the possibility that divergent host-plant use in phytophagous insects is due to sexual exclusion has seldom been considered. Here we present evidence that RI is responsible for different host-plant use by two Pierid butterfly species, Pieris napi and P. melete . When a novel host species was introduced about 50 years ago, two Pierid butterfly...

A molecular phylogenetic evaluation of the Ramalina siliquosa complex, with notes on species circumscription and relationships within Ramalina

Scott LaGreca
Lichens of the Ramalina siliquosa complex dominate seashore cliffs in Europe and Southeast Asia, but their taxonomy has been vigorously debated for over a century. On many cliffs, they exhibit a bewildering zonation of chemotypes that resembles the classic zonation of organisms that occupy the littoral zone below. Do the chemotypes represent separate species, or infraspecific variation? To better understand the systematics of this group, sequences from four genetic loci (ITS, IGS RPB1 and RPB2)...

Experimental data from: On Simultaneous Buckling, Contact and Load Carrying Capacity

Lawrence Virgin
This paper considers the case of a relatively large number of parallel columns that buckle simultaneously. The close proximity between columns results in the possibility of contact between adjacent columns as buckling proceeds, and this brings with it some interesting observations on load carrying capacity. Some experimental results verify the theoretical development based on the versatility of high-fidelity 3D-printing. The sensitive nature of initial geometric imperfections (slight lack of straightness) and load eccentricity strongly influence...

Biotic and anthropogenic forces rival climatic/abiotic factors in determining global plant population growth and fitness

William Morris
Multiple, simultaneous environmental changes, in climatic/abiotic factors, in interacting species, and in direct human influences, are impacting natural populations and thus biodiversity, ecosystem services, and evolutionary trajectories. Determining whether the magnitudes of the population impacts of abiotic, biotic, and anthropogenic drivers differ, accounting for their direct effects and effects mediated through other drivers, would allow us to better predict population fates and design mitigation strategies. We compiled 644 paired values of the population growth rate...

Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals

Kelsie E Hunnicutt, George P Tiley, Rachel C Williams, Peter A Larsen, Marina B Blanco, Rodin M Rasoloarison, Christopher Ryan Campbell, Kevin Zhu, David W Weisrock, Hiroaki Matsunami & Anne D Yoder
Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within...

Convergent evolution in lemur environmental niches

James Herrera
Aim: To test the hypothesis that adaptive convergent evolution of climate niches occurred in multiple independent lemur lineages. Location: Madagascar Taxon: Lemurs Methods: I collected climate and altitude data from WorldClim and summarized the niches of almost all living lemurs (83 species) into phylogenetically-controlled principal components. To test for convergent evolution, I searched for multiple, similar climate optima using multi-peak Ornstein-Uhlenbeck models (surface, l1-ou, bayou). I compared the observed level of climate convergence to that...

Data from: The distribution and numbers of cheetah (Acinonyx jubatus) in southern Africa

Florian J. Weise, Varsha Vijay, Andrew P. Jacobson, Rebecca F. Schoonover, Rosemary J. Groom, Jane Horgan, Derek Keeping, Rebecca Klein, Kelly Marnewick, Glyn Maude, Jorg Melzheimer, Gus Mills, Vincent Van Der Merwe, Esther Van Der Meer, Rudie J. Van Vuuren, Bettina Wacher, Stuart L. Pimm & Bettina Wachter
Assessing the numbers and distribution of threatened species is a central challenge in conservation, often made difficult because the species of concern are rare and elusive. For some predators, this may be compounded by their being sparsely distributed over large areas. Such is the case with the cheetah Acinonyx jubatus. The IUCN Red List process solicits comments, is democratic, transparent, widely-used, and has recently assessed the species. Here, we present additional methods to that process...

Data from: Punctuated changes in the morphology of an endemic diatom from Lake Titicaca

Trisha L. Spanbauer, Sherilyn C. Fritz & Paul A. Baker
High levels of biodiversity and endemism in ancient lakes have motivated research on evolutionary processes in these systems. Drill core records from Lake Titicaca (Bolivia, Peru), an ancient lake in the high-elevation Altiplano, record the history of climate, landscape dynamics, and diatom evolution. That record was used to examine the patterns and drivers of morphological evolution of an endemic species complex of diatoms in the lake, the Cyclostephanos andinus complex. In an attempt to delineate...

Data from: Foraging impacts of Asian megafauna on tropical rainforest structure and biodiversity

John Terborgh, Lisa C. Davenport, Lisa Ong & Ahimsa Campos-Arceiz
Megaherbivores are known to influence the structure, composition, and diversity of vegetation. In Central Africa, forest elephants act as ecological filters by breaking tree saplings and stripping them of foliage. Much less is known about impacts of megafauna on Southeast Asian rain forests. Here, we ask whether herbivory by Asian megafauna has impacts analogous to those of African forest elephants. To answer this, we studied forest (1) structure, (2) composition, (3) diversity, and (4) tree...

Data from: Transcriptomics in the wild: hibernation physiology in free‐ranging dwarf lemurs

Sheena L. Faherty, José Luis Villanueva‐Cañas, Marina B. Blanco, M. Mar Albà & Anne D. Yoder
Hibernation is an adaptive strategy some mammals use to survive highly seasonal or unpredictable environments. We present the first investigation on the transcriptomics of hibernation in a natural population of primate hibernators: Crossley's dwarf lemurs (Cheirogaleus crossleyi). Using capture–mark–recapture techniques to track the same animals over a period of 7 months in Madagascar, we used RNA‐seq to compare gene expression profiles in white adipose tissue (WAT) during three distinct physiological states. We focus on pathway...

Data from: Defaunation increases the spatial clustering of lowland Western Amazonian tree communities

Robert Bagchi, Varun Swamy, Jean-Paul Latorre Farfan, John Terborgh, César I. A. Vela, Nigel C. A. Pitman & Washington Galiano Sanchez
1.Declines of large vertebrates in tropical forests may reduce dispersal of tree species that rely on them, and the resulting undispersed seedlings might suffer increased distance- and density- dependent mortality. Consequently, extirpation of large vertebrates may alter the composition and spatial structure of plant communities and impair ecosystem functions like carbon storage. 2.We analysed spatial patterns of tree recruitment within six forest plots along a defaunation gradient in western Amazonia. We divided recruits into two...

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