74 Works

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...

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...

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...

Rasch Measurement v. Item Response Theory: Knowing When to Cross the Line

Steven E. Stemler & Adam Naples
When students receive the same score on a test, does that mean they know the same amount about the topic? The answer to this question is more complex than it may first appear. This paper compares classical and modern test theories in terms of how they estimate student ability. Crucial distinctions between the aims of Rasch Measurement and IRT are highlighted. By modeling a second parameter (item discrimination) and allowing item characteristic curves to cross,...

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....

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...

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...

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),...

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...

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...

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...

The economics of direct nitrogen reduction technologies

Gal Hochman

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....

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.

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...

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...

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...

Data for: Resolving whole-plant economics from leaf, stem and root traits of 1467 Amazonian tree species

Jason Vleminckx
It remains unclear how evolutionary and ecological processes have shaped the wide variety of plant life strategies, especially in highly diverse ecosystems like tropical forests. Some evidence suggests that species have diversified across a gradient of ecological strategies, with different plant tissues converging to optimize resource use across environmental gradients. Alternative hypotheses propose that species have diversified following independent selection on different tissues, resulting in a decoupling of trait syndromes across organs. To shed light...

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...

Woody encroachment happens via intensification, not extensification, of species ranges in an African savanna

Yong Zhou, Morgan Tingley, Madelon Case, Corli Coetsee, Gregory Kiker, Rheinhardt Scholtz, Freek Venter & Carla Staver
Widespread woody encroachment is a prominent concern for savanna systems as it is often accompanied by losses in productivity and biodiversity. Extensive ecosystem-level work has advanced our understanding of its causes and consequences. However, there is still debate over whether local management can override regional and global drivers of woody encroachment, and it remains largely unknown how encroachment influences woody community assemblages. Here, we examined species-level changes in woody plant distributions and size structure from...

Ocean and ice with waves 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...

Data from: Mesozoic cupules and the origin of the angiosperm second integument

Gongle Shi, Fabiany Herrera, Patrick Herendeen, Elizabeth Clark & Peter Crane
This dataset is embargoed. Please contact Gongle Shi with any questions.

The distribution of Chrysaora melanaster and hydrographical conditions in the southeastern Bering Sea in 2018

Hongsheng Bi & Mary Beth Decker
Scyphozoan jellyfish are conspicuous components of marine ecosystems, which during a bloom, can impact food web structure and economically important fisheries. Jellyfish biomass in the southeastern Bering Sea (SEBS) is primarily comprised of Chrysaora melanaster and has varied widely over the past four decades, yet the underlying causes of these biomass fluctuations remain unclear. The present study investigated the spatial and seasonal dynamics of C. melanaster along the Alaska Peninsula in the SEBS using an...

Ericoid mycorrhizal shrubs alter the relationship between tree mycorrhizal dominance and soil carbon and nitrogen

Elisabeth Ward, Marlyse Duguid, Sara Kuebbing, James Lendemer, & Mark Bradford
1. Plant-fungal associations strongly influence forest carbon and nitrogen cycling. The prevailing framework for understanding these relationships is through the relative abundance of arbuscular (AM) versus ectomycorrhizal (EcM) trees. Ericoid mycorrhizal (ErM) shrubs are also common in forests and interactions between co-occurring ErM shrubs and AM and EcM trees could shift soil biogeochemical responses. Here we test hypotheses that the effects of ErM shrubs on soil carbon and nitrogen either extend or are redundant with...

Registration Year

  • 2021
    74

Resource Types

  • Dataset
    67
  • Text
    3
  • Journal Article
    2
  • Audiovisual
    1
  • Output Management Plan
    1

Affiliations

  • Yale University
    74
  • University of Oxford
    7
  • Institute of Oceanology. PP Shirshov Russian Academy of Sciences
    4
  • Pennsylvania State University
    3
  • University of Pennsylvania
    2
  • Stanford University
    2
  • Princeton University
    2
  • University of Michigan-Ann Arbor
    2
  • National Autonomous University of Mexico
    2
  • University of Sao Paulo
    2