138 Works

Data from: Strength of selection on Trpc2 gene predicts accessory olfactory bulb form in bat vomeronasal evolution

Laurel R. Yohe & Liliana M. Davalos
Vestigial characters are common across the tree of life, but the underlying evolutionary processes shaping phenotypic loss are poorly understood. The mammalian vomeronasal system, which detects social chemical cues important to fitness, is an impressive example of a sensory system lost multiple times. Three times more losses are inferred among bats than in other mammalian orders. We characterized the relationship between amino acid substitutions in a gene tightly linked to vomeronasal function (Trpc2) and the...

Data from: Predicting species’ vulnerability in a massively perturbed system: the fishes of Lake Turkana, Kenya

Natasha J. Gownaris, Ellen K. Pikitch, William O. Ojwang, Robert Michener & Les Kaufman
Background and Trophic Diversity Study: Lake Turkana is an understudied desert lake shared by Kenya and Ethiopia. This system is at the precipice of large-scale changes in ecological function due to climate change and economic development along its major inflowing river, the Omo River. To anticipate response by the fish community to these changes, we quantified trophic diversity for seven ecological disparate species (Alestes baremose, Hydrocynus forskalli, Labeo horie, Lates niloticus, Oreochromis niloticus, Synodontis schall,...

Data from: Increased susceptibility to fungal disease accompanies adaptation to drought in Brassica rapa

Niamh B. O'Hara, Joshua S. Rest & Steven J. Franks
Recent studies have demonstrated adaptive evolutionary responses to climate change, but little is known about how these responses may influence ecological interactions with other organisms, including natural enemies. We used a resurrection experiment in the greenhouse to examine the effect of evolutionary responses to drought on the susceptibility of Brassica rapa plants to a fungal pathogen, Alternaria brassicae. In agreement with previous studies in this population, we found an evolutionary shift to earlier flowering post-drought,...

Data from: Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens

Rafael J. Hernandez, Elze Hesse, Andrea J. Dowling, Nicola M. Coyle, Edward J. Feil, Will H. Gaze & Michiel Vos
Climate change, changing farming practices, social and demographic changes and rising levels of antibiotic resistance are likely to lead to future increases in opportunistic bacterial infections that are more difficult to treat. Uncovering the prevalence and identity of pathogenic bacteria in the environment is key to assessing transmission risks. We describe the first use of the Wax moth larva Galleria mellonella, a well-established model for the mammalian innate immune system, to selectively enrich and characterize...

Data from: Mek1 down regulates Rad51 activity during yeast meiosis by phosphorylation of Hed1

Tracy L. Callender, Raphaelle Laureau, Lihong Wan, Xiangyu Chen, Rima Sandhu, Saif Laljee, Sai Zhou, Ray T. Suhandynata, Evelyn Prugar, William A. Gaines, YoungHo Kwon, G. Valentin Börner, Alain Nicolas, Aaron M. Neiman & Nancy M. Hollingsworth
During meiosis, programmed double strand breaks (DSBs) are repaired preferentially between homologs to generate crossovers that promote proper chromosome segregation at Meiosis I. In many organisms, there are two strand exchange proteins, Rad51 and the meiosis-specific Dmc1, required for interhomolog (IH) bias. This bias requires the presence, but not the strand exchange activity of Rad51, while Dmc1 is responsible for the bulk of meiotic recombination. How these activities are regulated is less well established. In...

Data from: A comprehensive analysis of autocorrelation and bias in home range estimation

Michael J. Noonan, Marlee A. Tucker, Christen H. Fleming, Tom S. Akre, Susan C. Alberts, Abdullahi H. Ali, Jeanne Altmann, Pamela C. Antunes, Jerrold L. Belant, Dean Beyer, Niels Blaum, Katrin Böhning-Gaese, , Rogerio De Paula Cunha, Jasja Dekker, Jonathan Drescher-Lehman, Nina Farwig, Claudia Fichtel, Christina Fischer, Adam T. Ford, Jacob R. Goheen, René Janssen, Florian Jeltsch, Matthew Kauffman, Peter M. Kappeler … & Justin M. Calabrese
Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of...

Data from: Bats (Chiroptera: Noctilionoidea) challenge a recent origin of extant neotropical diversity

Danny Rojas, Omar M. Warsi & Liliana M. Dávalos
The mechanisms underlying the high extant biodiversity in the Neotropics have been controversial since the 19th century. Support for the influence of period-specific changes on diversification often rests on detecting more speciation events during a particular period. The timing of speciation events may reflect the influence of incomplete taxon sampling, protracted speciation, and null processes of lineage accumulation. Here we assess the influence of these factors on the timing of speciation with new multilocus data...

Data from: The evolution of locomotor rhythmicity in tetrapods

Callum F. Ross, Richard W. Blob, David R. Carrier, Monica A. Daley, Stephen M. Deban, Brigitte Demes, Janaya L. Gripper, Jose Iriarte-Diaz, Brandon Michael Kilbourne, Tobias Landberg, John D. Polk, Nadja Schilling & Bieke Vanhooydonck
Differences in rhythmicity (relative variance in cycle period) between mammal, fish, and lizard feeding systems have been hypothesized to be associated with differences in their sensorimotor control systems. We tested this hypothesis by examining whether the locomotion of tachymetabolic tetrapods (birds and mammals) is more rhythmic than that of bradymetabolic tetrapods (lizards, alligators, turtles, salamanders). Species averages of intra-individual coefficients of variation in cycle period were compared while controlling for gait and substrate. Variance in...

Data from: Selection and sex-biased dispersal in a coastal shark: the influence of philopatry on adaptive variation

David S. Portnoy, Jonathan B. Puritz, Christopher M. Hollenbeck, James Gelsleichter, Demian Chapman & John R. Gold
Sex-biased dispersal is expected to homogenize nuclear genetic variation relative to variation in genetic material inherited through the philopatric sex. When site fidelity occurs across a heterogeneous environment, local selective regimes may alter this pattern. We assessed spatial patterns of variation in nuclear-encoded, single nucleotide polymorphisms (SNPs) and sequences of the mitochondrial control region in bonnethead sharks (Sphyrna tiburo), a species thought to exhibit female philopatry, collected from summer habitats used for gestation. Geographic patterns...

Data from: Debugging diversity – a pan‐continental exploration of the potential of terrestrial blood‐feeding leeches as a vertebrate monitoring tool

Ida Bærholm Schnell, Kristine Bohmann, Sebastian E. Schultze, Stine R. Richter, Dáithí C. Murray, Mikkel-Holger S. Sinding, David Bass, John E. Cadle, Mason J. Campbell, Rainer Dulch, David P. Edwards, Thomas N. E. Gray, Teis Hansen, Anh N. Q. Hoa, Christina Lehmkuhl Noer, Sigrid Heise-Pavlov, Adam F. Sander Pedersen, Juliot C. Ramamonjisoa, Mark E. Siddall, Andrew Tilker, Carl Traeholt, Nicholas Wilkinson, Paul Woodcock, Douglas W. Yu, Mads Frost Bertelsen … & Ida Baerholm Schnell
The use of environmental DNA (eDNA) has become an applicable non-invasive tool with which to obtain information about biodiversity. A sub-discipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterise the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations....

Data from: Fires in protected areas reveal unforeseen costs of Colombian peace

Dolors Armenteras, Laura Schneider & Liliana María Dávalos
Armed conflict, and its end, can have powerful effects on natural resources, but the influence of war and peace on highly biodiverse tropical forests remains disputed. We found a sixfold increase in fires in protected areas across biodiversity hotspots following guerrilla demobilization in Colombia, and a 52% increase in the probability of per-pixel deforestation within parks for 2018. Peace requires urgent shifts to include real-time forest monitoring, expand programmes to pay for ecosystem services at...

Data from: Genetic differentiation but no reduction in genetic diversity at the northern range edge of two species with different dispersal modes

Abigail E. Cahill & Jeffrey S. Levinton
Theory predicts that genetic variation should be reduced at range margins, but empirical support is equivocal. Here, we used genotyping-by-sequencing technology to investigate genetic variation in central and marginal populations of two species in the marine gastropod genus Crepidula. These two species have different development and dispersal types, and might therefore show different spatial patterns of genetic variation. Both allelic richness and the proportion of private alleles were highest in the most central populations of...

Data from: Recent extinctions disturb path to equilibrium diversity in Caribbean bats

Luis Valente, Rampal Etienne & Liliana Dávalos
Islands are ideal systems to reconstruct changes in biodiversity and reveal the influence of humans on natural communities. While theory predicts biodiversity on islands tends towards equilibrium, the recent extinction of large proportions of island biotas complicates testing this model. The well-preserved subfossil record of Caribbean bats provides a rare opportunity to model diversity dynamics in an insular community. Here we reconstruct the diversity trajectory in noctilionoid bats of the Greater Antilles by applying a...

Data from: Evaluating the target‐tracking performance of scanning avian radars by augmenting data with simulated echoes

Samuel Urmy & Joseph Warren
1. Small scanning radars have been used for many years to track the movements of insects, birds, and bats. While the ability to track multiple flying animals simultaneously has numerous applications in basic ecology and applied conservation, translating radar tracks into accurate animal densities and fluxes requires estimates of detection and tracking probabilities. These can be challenging to determine, especially in environments with variable background clutter. 2. In order to assess radar tracking probabilities, we...

Raw data for: Biomechanical demands of percussive techniques in the context of early stone toolmaking

Robin Macchi, Guillaume Daver, Michel Brenet, Sandrine Prat, Laurent Hugueville, Sonia Harmand, Jason Lewis & Mathieu Domalain
Recent discoveries in archaeology and palaeoanthropology highlight that stone stool knapping could have emerged first within the genera Australopithecus or Kenyanthropus rather than Homo. To explore the implications of this hypothesis determining the physical demands and motor control needed for performing the percussive movements during the oldest stone toolmaking technology (i.e. Lomekwian) would help. We analysed the joint-angle patterns and muscle activity of a knapping expert using three stone tool replication techniques: unipolar flaking on...

Sound velocities and P-V-T data of phase A obtained at GSECARS beamline 13-ID-D

Nao Cai, Xintong Qi, Ting Chen, Siheng Wang, Tony Yu, Yanbing Wang, Toru Inoue, Duojun Wang & Baosheng Li
The sound velocities and lattice parameters for sample in the under review paper, "Enhanced visibility of subduction slabs by the formation of dense hydrous phase A", submitted to the journal 'Geophysical Research Letters', are published. The high pressure and high-temperature experiment was conducted in the 1000-ton Kawai type large volume apparatus (T-25) installed at the GSECARS beamline 13-ID-D of Advanced Photon Source, Argonne National Laboratory. The datasets were obtained at conditions up to 11 GPa...

Multi-city street-sidewalk imagery from pedestrian mobile cameras

Shubham Jain
We present TerraFirma, a multi-city dataset which captures street and sidewalk imagery from the pedestrians' perspective. Motivated by challenges in the realm of pedestrian safety, we present a diverse and extensive dataset that provides a foundation for the design and validation of pedestrian safety systems that rely on street-sidewalk imagery. The data was collected by 9 volunteers in 4 metropolitan cities across the world. Volunteers carried mobile cameras or smartphones in a texting position, such...

Data from: Late Cretaceous bird from Madagascar reveals unique development of beaks

Patrick O'Connor, Alan Turner, Joseph Groenke, Ryan Felice, Raymond Rogers, David Krause & Lydia Rahantarisoa
Mesozoic birds display considerable diversity in size, flight adaptations and feather organization, but exhibit relatively conserved patterns of beak shape and development. Although Neornithine (that is, crown group) birds also exhibit constraint on facial development, they have comparatively diverse beak morphologies associated with a range of feeding and behavioural ecologies, in contrast to Mesozoic birds. Here we describe a crow-sized stem bird, Falcatakely forsterae gen. et sp. nov., from the Late Cretaceous epoch of Madagascar...

Data from: Separation of realized ecological niche axes among sympatric tilefishes provides insight into potential drivers of co‐occurrence in the NW Atlantic

Jill A. Olin, Oliver Shipley, Robert Cerrato, Paul Nitschke, Cedric Magen & Michael Frisk
Golden and Blueline Tilefish (Lopholatilus chamaeleonticeps and Caulolatilus microps) are keystone taxa in northwest (NW) Atlantic continental shelf‐edge environments due to their biotic (trophic‐mediated) and abiotic (ecosystem engineering) functional roles combined with high‐value fisheries. Despite this importance, the ecological niche dynamics (i.e., those relating to trophic behavior and food‐web interactions) of these sympatric species are poorly understood, knowledge of which may be consequential for maintaining both ecosystem function and fishery sustainability. We used stable isotope...

Gibbon genome (Nleu3.0) custom gene annotation file

Mariam Okhovat, Kimberly A. Nevonen, Brett A. Davis, Pryce Michener, Samantha Ward, Mark Milhaven, Lana Harshman, Ajuni Sohota, Jason D. Fernandes, Sofie R. Salama, Rachel J. O'Neill, Nadav Ahituv, Krishna R. Veeramah & Lucia Carbone
Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA, which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of...

Data from: Characterization of the abiotic drivers of abundance of nearshore Arctic fishes

Noah Khalsa, Kyle Gatt, Trent Sutton & Amanda Kelley
Fish are critical ecologically and socioeconomically for subsistence economies in the Arctic, an ecosystem undergoing unprecedented environmental change. Our understanding of the responses of nearshore Arctic fishes to environmental change is inadequate because of limited research on the physicochemical drivers of abundance occurring at a fine scale. Here, high-frequency in-situ measurements of pH, temperature, salinity, and dissolved oxygen were paired with daily fish catches in nearshore Alaskan waters of the Beaufort Sea. This dataset includes...

Disentangling interactions among mercury, immunity, and infection in a Neotropical bat community

Daniel Becker, Kelly Speer, Jennifer Korstian, Dmitriy Volokhov, Hannah Droke, Alexis Brown, Catherene Baijnauth, Ticha Padgett-Stewart, Hugh Broders, Raina Plowright, Thomas Rainwater, Brock Fenton, Nancy Simmons & Matthew Chumchal
Contaminants such as mercury are pervasive and can have immunosuppressive effects on wildlife. Impaired immunity could be important for forecasting pathogen spillover risks, as many land-use changes that generate mercury contamination also bring wildlife into close contact with humans and domestic animals. However, the interactions among contaminants, immunity, and infection are difficult to study in natural systems, and empirical tests of possible directional relationships remain rare. We capitalized on extreme mercury variation in a diverse...

The biogeography of community assembly: latitude and predation drive variation in community trait distribution in a guild of epifaunal crustaceans

Collin Gross, Collin Gross, J Duffy, Kevin Hovel, Melissa Kardish, Pamela Reynolds, Christoffer Boström, Katharyn Boyer, Mathiew Cusson, Johan Eklöf, Aschwin Engelen, Klemens Eriksson, Joel Fodrie, John Griffin, Clara Hereu, Masakazu Hori, A Randall Hughes, Mikhail Ivanov, Pablo Jorgensen, Claudia Kruschel, Kun-Seop Lee, Jonathan Lefcheck, Karen McGlathery, Per-Olav Moksnes, Masahiro Nakaoka … & Jay Stachowicz
While considerable evidence exists of biogeographic patterns in the intensity of species interactions, the influence of these patterns on variation in community structure is less clear. Using a model selection approach on measures of trait dispersion in crustaceans associated with eelgrass (Zostera marina) spanning 30º of latitude in two oceans, we found that dispersion strongly increased with increasing predation and decreasing latitude. Ocean and epiphyte load appeared as secondary predictors; Pacific communities were more overdispersed...

Supplemental dataset from: Initial acoustoelastic measurements in olivine: Investigating the effect of stress on P- and S-wave velocities

Taryn Traylor, Pamela Burnley & Matthew Whitaker
It is well known that elasticity is a key physical property in the determination of the structure and composition of the Earth and provides critical information for the interpretation of seismic data. This study investigates the stress-induced variation in elastic wave velocities, known as the acoustoelastic effect, in San Carlos olivine. A recently developed experimental ultrasonic acoustic system, the Directly Integrated Acoustic System Combined with Pressure Experiments (DIASCoPE), was used with the D-DIA multi-anvil apparatus...

COVID-19 contact rates between mobile devices in Connecticut

Forrest Crawford, Sydney Jones, Matthew Cartter, Samantha Dean, Joshua Warren, Zehang Li, Jacqueline Barbieri, Jared Campbell, Patrick Kenney, Thomas Valleau & Olga Morozova
Close contact between people is the primary route for transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). We sought to quantify interpersonal contact at the population-level by using mobile device geolocation data. We computed the frequency of contact (within six feet) between people in Connecticut during February 2020 - January 2021 and aggregated counts of contact events by area of residence. When incorporated into a SEIR-type model of COVID-19 transmission, the contact...

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