137 Works

Data from: Imperfect pathogen detection from non-invasive skin swabs biases disease inference

Graziella V. DiRenzo, Evan H. Campbell Grant, Ana V. Longo, Christian Che-Castaldo, Kelly R. Zamudio & Karen R. Lips
1. Conservation managers rely on accurate estimates of disease parameters, such as pathogen prevalence and infection intensity, to assess disease status of a host population. However, these disease metrics may be biased if low-level infection intensities are missed by sampling methods or laboratory diagnostic tests. These false negatives underestimate pathogen prevalence and overestimate mean infection intensity of infected individuals. 2. Our objectives were two-fold. First, we quantified false negative error rates of Batrachochytrium dendrobatidis on...

Data from: Experimental tests of sex allocation theory with two species of simultaneously hermaphroditic acorn barnacles

J. Matthew Hoch
Sex allocation theory for simultaneous hermaphrodites predicts increases in relative allocation to male-specific function as competition for fertilizations increases. Theoretical models developed specifically for competing acorn barnacles predict that the proportional allocation to male function increases towards an asymptote of 50% as the number of competitors for fertilizations increases. Experimental manipulations were used to investigate how mate competition affected both relative and absolute allocation to the sex functions for two species of acorn barnacle: Semibalanus...

Data from: Genetic perturbation of key central metabolic genes extends life span in Drosophila and affects response to dietary restriction

Matthew E. Talbert, Brittany Barnett, Robert Hoff, Maria Amella, Caitlin Kuczynski, Erik Lavington, Spencer Koury, Evgeny Brud & Walter F. Eanes
There is a connection between nutrient inputs, energy-sensing pathways, lifespan variation and aging. Despite the role of metabolic enzymes in energy homeostasis and their metabolites as nutrient signals, little is known about how their gene expression impacts lifespan. In this report, we use P-element mutagenesis in Drosophila to study the effect on lifespan of reductions in expression of seven central metabolic enzymes, and contrast the effects on normal diet and dietary restriction. The major observation...

Data from: A function-valued trait approach to estimating the genetic basis of size at age and its potential role in fisheries induced evolution

Jin Gao & Stephan B. Munch
Natural selection is inherently a multivariate phenomenon. The selection pressure on size (natural and artificial) and the age at which selection occurs is likely to induce evolutionary changes in growth rates across the entire life history. However, the covariance structure that will determine the path of evolution for size-at-age has been studied in only a few fish species. We therefore estimated the genetic covariance function for size throughout ontogeny using Atlantic silversides (Menidia menidia) as...

Toward low-cloud-permitting cloud superparameterization with explicit boundary layer turbulence -- simulation data

Hossein Parishani, Michael Pritchard, Christopher Bretherton, Matthew Wyant & Marat Khairoutdinov
This data set contains the simulation outputs used in the study summarized below: Systematic biases in the representation of boundary layer (BL) clouds are a leading source of uncertainty in climate projections. A variation on superparameterization (SP) called ‘‘ultraparameterization’’ (UP) is developed, in which the grid spacing of the cloud-resolving models (CRMs) is fine enough (250x20 m) to explicitly capture the BL turbulence, associated clouds, and entrainment in a global climate model capable of multiyear...

Data from: Redescription and phylogenetic affinities of the caimanine Eocaiman cavernensis (Crocodylia, Alligatoroidea) from the Eocene of Argentina

Pedro L. Godoy, Giovanne Cidade, Felipe Montefeltro, Max Langer & Mark Norell
Caimaninae is one of the few crocodylian lineages that still has living representatives. Today, most of its six extant species are restricted to South and Central America. However, recent discoveries revealed a more complex evolutionary history, with a fossil record richer than previously thought and a possible North American origin. Among the oldest caimanines is Eocaiman cavernensis, from the Eocene of Patagonia, Argentina. It was described by George G. Simpson in the 1930s, representing the...

Hummingbird torpor in context: duration, more than temperature, is the key to nighttime energy savings

Anusha Shankar, Rebecca J. Schroeder, Susan M. Wethington, Catherine H. Graham & Donald R. Powers
Torpor is an important energy saving strategy in some small birds, but it has rarely been studied in natural field conditions. We compared torpor use across 43 wild-caught individuals of eight hummingbird species across sites with different natural temperature regimes. Most laboratory studies focus on the relationship between metabolic rate and temperature, but our aim was to evaluate what environmental factors most influence hummingbird nighttime energy management under natural conditions. We found that the probability...

Data from: Inbreeding shapes the evolution of marine invertebrates

Kevin Olsen, Will Ryan, Alice Winn, Ellen Kosman, Jose Moscoso, Stacy Krueger-Hadfield, Scott Burgess, David Carlon, Richard Grosberg, Susan Kalisz & Don Levitan
Inbreeding is a potent evolutionary force shaping the distribution of genetic variation within and among populations of plants and animals. Yet, our understanding of the forces shaping the expression and evolution of non-random mating in general, and inbreeding in particular, remains remarkably incomplete. Most research on plant mating systems focuses on self-fertilization and its consequences for automatic selection, inbreeding depression, purging, and reproductive assurance, whereas studies of animal mating systems have often assumed that inbreeding...

Spatiotemporal study of iron oxide nanoparticle monolayer formation at liquid/liquid interfaces by using in situ small-angle x‐ray scattering

Jiayang Hu, Evan W. C. Spotte-Smith, Brady Pan, Roy J. Garcia, Carlos Colosqui & Irving P. Herman
Spatial and temporal small angle x-ray scattering (SAXS) scans show that 8.6 and 11.8 nm iron oxide nanoparticles (NPs) in heptane drop-cast on top of a heptane layer atop a diethylene glycol (DEG) layer are trapped at the DEG/heptane interface to generally form a single ordered, hexagonal close packed monolayer (ML), and this occurs long before the heptane evaporates. Many NPs remain dispersed in the heptane after this NP assembly. Assembly occurs faster than expected...

Morphometric materials for analyzing Eulipotyphlans across the Paleocene-Eocene-Thermal Maximum

Natasha Vitek
Interpreting the impact of climate change on vertebrates in the fossil record can be complicated by the effects of potential biotic drivers on morphological patterns observed in taxa. One promising area where this impact can be assessed is a high-resolution terrestrial record from the Bighorn Basin, Wyoming, that corresponds to the Paleocene-Eocene Thermal Maximum (PETM), a geologically rapid (~170 ky) interval of sustained temperature and aridity shifts about 56 million years ago. The PETM has...

Telemetry validated nitrogen stable isotope clocks identify ocean-to-estuarine habitat shifts in mobile organisms

Oliver Shipley, Alisa Newton, Michael Frisk, Gregory Henkes, Jake LaBelle, Merry Camhi, Michael Hyatt, Hans Walters & Jill Olin
1. Throughout their life history, many animals transition among heterogenous environments to facilitate behaviors such as reproduction, foraging, and predator avoidance. The dynamic environmental and biological conditions experienced by mobile species are integrated in the chemical composition of their tissues, providing retrospective insight into movement. 2. Here, we present a unique nitrogen stable isotope clocks (‘isotopic clocks’), which integrate tissue turnover rates, consumer stable isotope ratios, and habitat-specific isotope baselines and can be used to...

Data from: A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

Robert Alexander Pyron & John J. Wiens
The extant amphibians are one of the most diverse radiations of terrestrial vertebrates (>6800 species). Despite much recent focus on their conservation, diversification, and systematics, no previous phylogeny for the group has contained more than 522 species. However, numerous studies with limited taxon sampling have generated large amounts of partially overlapping sequence data for many species. Here, we combine these data and produce a novel estimate of extant amphibian phylogeny, containing 2871 species (40% of...

Data from: Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia

Robert Alexander Pyron
Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological datasets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with...

Data from: Trpc2 Pseudogenization dynamics in bats reveal ancestral vomeronasal signaling, then pervasive loss

Laurel R. Yohe, Ramatu Abubakar, Christina Giordano, Elizabeth Dumont, Karen Sears, Stephen J. Rossiter, Liliana M. Davalos & Karen E. Sears
Comparative methods are often used to infer loss or gain of complex phenotypes, but few studies take advantage of genes tightly linked with complex traits to test for shifts in the strength of selection. In mammals vomerolfaction detects chemical cues mediating many social and reproductive behaviors and is highly conserved, but all bats exhibit degraded vomeronasal structures with the exception of two families (Phyllostomidae and Miniopteridae). These families either regained vomerolfaction after ancestral loss, or...

Data from: Museum specimen data reveal emergence of a plant disease may be linked to increases in the insect vector population

Adam R. Zeilinger, Giovanni Rapacciuolo, Daniel Turek, Peter T. Oboyski, Rodrigo P. P. Almeida & George K. Roderick
The emergence rate of new plant diseases is increasing due to novel introductions, climate change, and changes in vector populations, posing risks to agricultural sustainability. Assessing and managing future disease risks depends on understanding the causes of contemporary and historical emergence events. Since the mid-1990s, potato growers in the western United States, Mexico, and Central America have experienced severe yield loss from Zebra Chip disease and have responded by increasing insecticide use to suppress populations...

Data from: Limited evidence for third party affiliation during development in wild chimpanzees (Pan troglodytes schweinfurthii)

Jordan A. Miller, Margaret A. Stanton, Elizabeth V. Lonsdorf, Kaitlin R. Wellens, A. Catherine Markham & Carson M. Murray
Examining the ontogeny of conflict-mitigating behaviors in our closest living relatives is an important component of understanding the evolutionary origins of cooperation in our species. In this study, we used 26 years of data to investigate the emergence of third party affiliation (TPA), defined as affiliative contact given to recipients of aggression by uninvolved bystanders (regardless of initiation), in wild immature eastern chimpanzees (Pan troglodytes schweinfurthii) of Gombe National Park, Tanzania. We also characterized TPA...

Data from: Polygyny does not explain the superior competitive ability of dominant ant associates in the African ant-plant, Acacia (Vachellia) drepanolobium

John H. Boyle, Dino J. Martins, Julianne Pelaez, Paul M. Musili, Staline Kibet, S. Kimani Ndung'u, David Kenfack & Naomi E. Pierce
1. The Acacia drepanolobium (also known as Vachellia drepanolobium) ant-plant symbiosis is considered a classic case of species coexistence, in which four species of tree-defending ants compete for nesting space in a single host tree species. Coexistence in this system has been explained by trade-offs in the ability of the ant associates to compete with each other for occupied trees versus the ability to colonize unoccupied trees. 2. We seek to understand the proximal reasons...

Data from: Assessment of coyote-wolf-dog admixture using ancestry-informative diagnostic SNPs

Javier Monzón, Roland Kays & Daniel E. Dykhuizen
The evolutionary importance of hybridization as a source of new adaptive genetic variation is rapidly gaining recognition. Hybridization between coyotes and wolves may have introduced adaptive alleles into the coyote gene pool that facilitated an expansion in their geographic range and dietary niche. Furthermore, hybridization between coyotes and domestic dogs may facilitate adaptation to human-dominated environments. We genotyped 63 ancestry-informative single nucleotide polymorphisms in 427 canids in order to examine the prevalence, spatial distribution, and...

Data from: A meta-analysis of plant interaction networks reveals competitive hierarchies as well as facilitation and intransitivity

Nicole L. Kinlock
The extent to which competitive interactions and niche differentiation structure communities has been highly controversial. To quantify evidence for key features of plant community structure, I recharacterized published data from interaction experiments as networks of competitive and facilitative interactions. I measured the network structure of 31 woody and herbaceous communities, including the intensity, distribution, and diversity of interactions at the species-pair and community level to determine the generality of competition, winner-loser relationships, and unequal interaction...

Data from: Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

Anand Ranjan, Vu Q. Nguyen, Sheng Liu, Jan Wisniewski, Kim Jee Min, Xiaona Tang, Gaku Mizuguchi, Vivian Jou, Timothy J. Nickels, Brian P. English, Qinsi Zheng, Ed Luk, Timothee Lionnet, Luke D. Lavis, Carl Wu & Ejlal Elalaoui
The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit...

Data from: Explaining global variation in the latitudinal diversity gradient: meta-analysis confirms known patterns and uncovers new ones

Nicole L. Kinlock, Lisa Prowant, Emily M. Herstoff, Catherine M. Foley, Morodoluwa Akin-Fajiye, Mihir Umarani, Hae Yeong Ryu, Bilgecan Şen, Jessica Gurevitch & Nicole Bender
Aim: The pattern of increasing biological diversity from high latitudes to the equator [latitudinal diversity gradient (LDG)] has been recognized for > 200 years. Empirical studies have documented this pattern across many different organisms and locations. Our goal was to quantify the evidence for the global LDG and the associated spatial, taxonomic and environmental factors. We performed a meta-analysis on a large number of individual LDGs that have been published in the 14 years since...

Data from: Fossil grebes from the Truckee Formation (Miocene) of Nevada and a new phylogenetic analysis of Podicipediformes (Aves)

Daniel T. Ksepka, Amy M. Balanoff, Michael A. Bell & Michel D. Houseman
Podicipediformes is a cosmopolitan clade of foot-propelled diving birds that, despite inhabiting marine and lacustrine environments, have a poor fossil record. In this contribution, we describe three new grebe fossils from the diatomite beds of the Late Miocene Truckee Formation (10.2 ± 0.2 Ma) of Nevada (USA). Two postcranial skeletons and an associated set of wing elements indicate that at least two distinct grebe species occupied the large, shallow Lake Truckee during the Miocene. Phylogenetic...

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: Questioning assumptions of trophic behavior in a broadly ranging marine predator guild

Oliver N. Shipley, Jill A. Olin, Mike Power, Robert M. Cerrato, Michael G. Frisk, Robert. M. Cerrato & Michael Power
We evaluated whether existing assumptions regarding the trophic ecology of a poorly-studied predator guild, northwest (NW) Atlantic skates (family: Rajidae), were supported across broad geographic scales. Four hypotheses were tested using carbon (δ13C) and nitrogen (δ15N) stable isotope values as metrics of foraging behavior: 1) species exhibit ontogenetic shifts in habitat and thus display a shift in 13C with differential use of the continental shelf; 2) species exhibit ontogenetic prey shifts (i.e., from smaller to...

Data from: MotionMeerkat: integrating motion video detection and ecological monitoring

Ben G. Weinstein
1. Human observation is expensive and limits the breadth of data collection. For this reason, remotely placed video cameras are increasingly used to monitor animals. One drawback of field-based video recordings is extensive review time. Computer vision can mitigate this cost and enhance data collection by extracting biological information from images with minimal time investment. 2. MotionMeerkat is a new standalone program that identifies motion events from a video stream. After running a video, the...

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