95 Works

Data from: An early Miocene extinction in pelagic sharks

Elizabeth Sibert & Leah Rubin
Sharks populations have been decimated in recent decades due to over-fishing and other anthropogenic stressors, however the long-term impacts of such changes in marine predator abundance and diversity are poorly constrained. We present evidence for a previously unknown major extinction event in sharks that occurred in the Early Miocene, approximately 19 million years ago (Ma). During this interval, sharks virtually disappeared from open-ocean sediments, declining in abundance by >90%, and morphological diversity by >70%, an...

Integrative ichthyological species delimitation in the Greenthroat Darter complex (Percidae: Etheostomatinae)

Daniel MacGuigan, Christopher Hoagstrom, Sami Domisch, C. Hulsey & Thomas Near
Species delimitation is fundamental to deciphering the mechanisms that generate and maintain biodiversity. Alpha taxonomy historically relied on expert knowledge to describe new species using phenotypic and biogeographic evidence, which has the appearance of investigator subjectivity. In contrast, DNA‐based methods using the multispecies coalescent model (MSC) promise a more objective approach to describing biodiversity. However, recent criticisms suggest that under some conditions the MSC may over‐split lineages, identifying species that do not reflect biological reality....

Data from: Fossils improve phylogenetic analyses of morphological characters

Nicolás Mongiardino Koch, Russell Garwood & Luke Parry
Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here we use simulations to evaluate the performance of inference methods across different levels of fossil...

The first Silurian trilobite with three-dimensionally preserved soft parts reveals novel appendage morphology

Mark Sutton, Derek Siveter, Richard Fortey, Derek Briggs & David Siveter
The first Silurian trilobite known with soft parts preserved, a Dalmanites species, is described from the Herefordshire Lagerstätte. Biramous appendages and much of the alimentary system are evident. High-fidelity three-dimensional preservation reveals a novel, double arrangement of the exopod filaments, interconnected by a presumed membranous sheet. This morphology explains a misinterpretation of the exopod as supporting spiral structures, originally reported nearly 150 years ago. The new exopod morphology is considered primarily respiratory in function and...

A shift in ontogenetic timing produced the unique sauropod skull

Matteo Fabbri, Guillermo Navalón, Nicolás Mongiardino Koch, Michael Hanson, Holger Petermann & Bhart-Anjan Bhullar
Sauropod dinosaurs include the largest terrestrial vertebrates that have ever lived. Virtually every part of the sauropod body is heavily modified in association with gigantic size and associated physiological alterations. Sauropod skulls are no exception: they feature elongated, telescoped facial regions connected to tilted neurocrania and reoriented jaw adductor muscles. Several of these cranial features have been suggested to be adaptations for feeding on the one hand and the result of paedomorphic transformation near the...

Divergent patterns and spatial heterogeneity of soil nutrients in a complex and dynamic savanna landscape

Yong Zhou, Robert Taylor & Thomas Boutton
Many grassy ecosystems around the world are experiencing woody encroachment. These woody encroachers often cause nutrient enrichment in the plant-soil environment, potentially facilitating their growth and reproduction. However, studies of encroachment effects on nutrient distributions have been confined to a few major elements (e.g., N, and P) and limited in spatial extent. We analyzed 19 elements in dominant plants and in georeferenced soils across a subtropical savanna landscape experiencing woody encroachment to quantify their spatial...

Secondary Contact LTREB: Lake metadata

David Post & Eric Palkovacs
This dataset contains metadata for the core lakes of the Secondary Contact LTREB and other lakes that are occasionally sampled by the project.

Atmospheric and surface gravity wave data for role of surface gravity waves in aquaplanet ocean climates

Joshua Studholme, Margarita Markina & Sergey Gulev
This data corresponds to the runs analysed in the manscript: Role of Surface Gravity Waves in Aquaplanet Ocean Climates (JAMES, 2021). In this work, we present a set of idealised numerical experiments that demonstrate the thermodynamic and dynamic implications of surface gravity waves for the oceanic climate of an aquaplanet. We study the impact of accounting for modulations by such waves upon air-sea momentum fluxes, Langmuir circulation and the Stokes-Coriolis force. This dataset is made...

The past, present, and future of herbivore impacts on savanna vegetation

Ann Carla Staver, Joel Abraham, Gareth Hempson, Allison Karp & J Faith
1) Herbivory is a key process structuring vegetation in savannas, especially in Africa where large mammal herbivore communities remain intact. Exclusion experiments consistently show that herbivores impact savanna vegetation, but effect size variation has resisted explanation, limiting our understanding of the past, present, and future roles of herbivory in savanna ecosystems. 2) Synthesis of vegetation responses to herbivore exclusion shows that herbivory decreased grass abundance by 57.0% and tree abundance by 30.6% across African savannas....

Phylogeny and time scale of diversification in the fossil-rich Sunfishes and Black Basses (Teleostei: Percomorpha: Centrarchidae)

Thomas Near & Daemin Kim
Species of the North American freshwater fish lineage Centrarchidae are apex predators in their habitats and are among the world’s most popular sport fishes. Centrarchids boast a rich fossil record that extends from the latest Eocene to the Pleistocene. To investigate the phylogeny and timing of diversification of Centrarchidae, we deploy a dataset of DNA sequences of 16 nuclear genes sampled from nearly all of the recognized and undescribed species. We also utilize previously published...

Reptilian ear 3D morphometric data

Bhart-Anjan Bhullar
Reptiles, including birds, exhibit a range of behaviorally significant adaptations reflected in changes to the structure of the inner ear. These adaptations include capacity for flight and sensitivity to high-frequency sound. We used 3D morphometric analyses of a large sample of extant and extinct reptiles to investigate inner-ear correlates of locomotor ability and hearing acuity. Statistical analyses revealed three vestibular morphotypes, best explained by locomotor categories: quadrupeds, bipeds and simple fliers (including bipedal non-avialan dinosaurs),...

Chemical effects of snowmelt on an alpine lake in the Wind River Range, WY

Taylor Ganz & Gaboury Benoit
Nitrogen deposition from air pollution is increasingly reaching alpine lakes where the addition of nitrate and ammonium to sensitive surface waters can cause acidification and or eutrophication. Thirty years of sampling in the Wind River Range, WY have shown some lakes increasing in nitrogen. We sought to determine (1) if nutrient concentrations in Deep Lake increase during snowmelt when atmospheric deposition is released from the snowpack and (2) assess if the sampling season, location, meteorological...

High-speed videos of siphonophore tentilla and nematocyst discharge

Alejandro Damian-Serrano
Siphonophores are free-living predatory colonial hydrozoan cnidarians found in every ocean of the world. Siphonophore tentilla (tentacle side branches) are unique biological structures for prey capture, composed of a complex arrangement of cnidocytes (stinging cells) bearing different types of nematocysts (stinging capsules) and auxiliary structures. Tentilla present an extensive morphological and functional diversity across species. Tentilla have a precisely coordinated high-speed strike mechanism of synchronous unwinding and nematocysts discharge. Here we characterize the kinematic diversity...

Chinook salmon environmental data and allele frequency matrix

Yara Alshwairikh, Rebekah Horn, Travis Seaborn, Shawn Narum, Lisette Waits, William Swain, Steve Stephens-Cardenas, Jenny Olsson & Shayla Kroeze
Many species that undergo long breeding migrations, such as anadromous fishes, face highly heterogeneous environments along their migration corridors and at their spawning sites. These environmental challenges encountered at different life stages may act as strong selective pressures and drive local adaptation. However, the relative influence of environmental conditions along the migration corridor compared to the conditions at spawning sites on driving selection is still unknown. In this study, we performed genome-environment associations (GEA) to...

Evolution of bacterial cross-resistance to lytic phages and albicidin antibiotic

Kaitlyn Kortright
Due to concerns over the global increase of antibiotic-resistant bacteria, alternative antibacterial strategies, such as phage therapy, are increasingly being considered. However, evolution of bacterial resistance to new therapeutics is almost a certainty; indeed, it is possible that resistance to alternative treatments might result in an evolved trade-up such as enhanced antibiotic resistance. Here, we hypothesize that selection for Escherichia coli bacteria to resist phage T6, phage U115, or albicidin will result in a pleiotropic...

Large‐scale genome sampling reveals unique immunity and metabolic adaptations in bats

Diana Daniela Moreno Santillan, Tanya Lama, Yocelyn T Gutierrez Guerrero, Zixia Huang, Graham Hughes, Alexis Brown, Paul Donat, Huabin Zhao, Stephen Rossiter, Laurel Yohe, Joshua Potter, Emma Teeling, Sonja Vernes, Kalina Davies, Eugene Myers, Federico Hoffmann, Angelique Corthals, David Ray & Liliana Davalos
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large...

Spatial personalities: a meta-analysis of consistent individual differences in spatial behavior

Erica Stuber, Ben Carlson & Brett Jesmer
Individual variation in behavior, particularly consistent among-individual differences (i.e., personality), has important ecological and evolutionary implications for population and community dynamics, trait divergence, and patterns of speciation. Nevertheless, individual variation in spatial behaviors, such as home range behavior, movement characteristics, or habitat use has yet to be incorporated into the concepts or methodologies of ecology and evolutionary biology. To evaluate evidence for the existence of consistent among-individual differences in spatial behavior – which we refer...

Diverging conditions of current and potential future urban forest patches

Danica Doroski
Forested natural areas in cities provide a range of social, ecological, economic, and health benefits. Ensuring the delivery of these benefits requires an understanding of current and potential future forest conditions yet urban forest dynamics are not well understood. Here, we address this knowledge gap by examining forest structure and composition in 126 plots distributed across three forest patch sizes (large (95-126 ha), medium (1-19 ha), and small (0.05-0.65 ha) patches) in the city of...

In vivo imaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission

Pradeep Uchil, Kelsey Haugh, Mark Ladinsky, Irfan Ullah, Helen Stone, Ruoxi Pi, Alexandre Gilardet, Michael Grunst, Priti Kumar, Pamela Bjorkman & Walther Mothes
Early events in retrovirus transmission are determined by interactions between incoming viruses and frontline cells near entry sites. Despite their importance for retroviral pathogenesis, very little is known about these events. We developed a bioluminescence imaging (BLI)-guided multiscale imaging approach to study these events in vivo. Engineered murine leukemia reporter viruses allowed us to monitor individual stages of retrovirus life cycle including virus particle flow, virus entry into cells, infection and spread for retroorbital, subcutaneous...

Clinical trial eligibility in COVID-19 patients

Lauren Pischel
As the Coronavirus-2019 (COVID-19) pandemic continues, multiple therapies are rapidly being tested for efficacy in clinical trials. Clinical trials should be racially and ethnically representative of the population that will eventually benefit from these medications. There are multiple potential barriers to racial and ethnic minority enrollment in clinical trials, one of which could be that inclusion and exclusion criteria select for certain racial or ethnic groups disproportionately. In this observational cohort study at a single...

Detection histories for Lycalopex griseus, Lycalopex culpaeus, Leopardus guigna, and Canis familiaris and habitat destruction covariate data for Los Lagos Chile (2019)

Rumaan Malhotra, Jaime Jiménez & Nyeema Harris
In an increasingly anthropogenic world, species face multiple interacting threats. Habitat fragmentation and domestic dogs are two perturbations threatening terrestrial mammals globally. Our aim was to determine if (1) the spatial use of domestic dogs increases with habitat destruction and (2) whether domestic dogs and habitat destruction drive the spatial use of native carnivores in a heavily degraded agricultural landscape in the central valley/Andean foothills transition of Los Lagos, Chile. We implemented a camera trap...

Attention recruits frontal cortex in human infants

Cameron T Ellis, Lena J Skalaban, Tristan S Yates & Nicholas B Turk-Browne
Young infants learn about the world by overtly shifting their attention to perceptually salient events. In adults, attention recruits several brain regions spanning the frontal and parietal lobes. However, it is unclear whether these regions are sufficiently mature in infancy to support attention and, more generally, how infant attention is supported by the brain. We used event-related fMRI in 24 sessions from 20 awake behaving infants 3–12 months old while they performed a child-friendly attentional...

Positive long-term impacts of restoration on soils in an experimental urban forest

Danica Doroski & Elisabeth Ward
As urbanization increases worldwide, so too are investments in nature-based solutions that aim to mitigate urban stressors and counter the impacts of global climate change. Tree planting on degraded urban lands—or afforestation—is one form of nature-based solution that has been increasingly implemented in cities around the world. The benefits of afforestation are, however, contingent on the capacity of soils to support the growth of planted trees, which poses a challenge in some urban settings where...

Data from: Functional attractors in microbial community assembly

Sylvie Estrela, Jean Vila, Nanxi Lu, Djordje Bajic, Maria Rebolleda-Gomez, Chang-Yu Chang, Josh Goldford, Alicia Sanchez-Gorostiaga & Alvaro Sanchez
For microbiome biology to become a more predictive science, we must identify which descriptive features of microbial communities are reproducible and predictable, which are not, and why. We address this question by experimentally studying parallelism and convergence in microbial community assembly in replicate glucose-limited habitats. Here, we show that the previously observed family-level convergence in these habitats reflects a reproducible metabolic organization, where the ratio of the dominant metabolic groups can be explained from a...

Weak interactions between strong interactors in an old-field ecosystem: Control of nitrogen cycling by coupled herbivores and detritivores

Robert Buchkowski & Oswald Schmitz
Interactions between herbivores and detritivores are common in greenhouse and laboratory experiments. Such interactions are thought to cause feedbacks in real ecosystems where the combined actions of these animals create either high or low nutrient cycling rates. There is limited evidence from factorial field experiments to support these expectations. We present the results of a three-year experiment wherein we factorially manipulated grasshopper herbivores and earthworm detritivores in an old-field ecosystem and tested for significant interaction...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Yale University
  • University of Oxford
  • Institute of Oceanology. PP Shirshov Russian Academy of Sciences
  • National Autonomous University of Mexico
  • University of Florida
  • Princeton University
  • University of California Los Angeles
  • University of Pennsylvania
  • Stanford University
  • Utah State University