99 Works

Varying impacts of logging frequency on tree communities and carbon storage across evergreen and deciduous tropical forests in the Andaman Islands, India

Akshay Surendra, Anand Osuri & Jayashree Ratnam
The majority of Earth’s tropical forests have been selectively logged; some on repeated occasions. Selective logging is known to affect forest structure, composition and function in various ways, but how such effects vary with logging frequency and across forest types remains unclear. In the Andaman Archipelago in India, we examined adult and pole-sized trees in baseline (unlogged since 1990s), once-logged (logged between 2007 and 2014) and twice-logged (logged in early 1990s and between 2007 and...

Ecological opportunity from innnovation, not islands, drove the Anole lizard adaptive radiation

Edward Burress
Islands are thought to facilitate adaptive radiation by providing release from competition and predation. Anole lizards are considered a classic example of this phenomenon: different ecological specialists (‘ecomorphs’) evolved in the Caribbean Greater Antilles (Cuba, Hispaniola, Jamaica, and Puerto Rico), resulting in convergent assemblages that are not observed in mainland Latin America. Yet, the role of islands in facilitating adaptive radiation is more often implied than directly tested, leaving uncertain the role of biogeography in...

Supplementary data and code for ‘Oscillatory Spatiotemporal Signal Detection in Climate Studies: A Multiple-Taper Spectral Domain Approach’ (Mann and Park 1999)

M.E. Mann & J. Park
This chapter introduces a methodology for signal detection and reconstruction of irregular spatiotemporal oscillatory signals—the multiple-taper spectrum estimation method (MTM)–singular-value decomposition (SVD) methodology. This methodology is offered as an alternative technique which avoids most of the problems encountered in traditional techniques and provides an efficient exploratory method for climate signal detection. The associated signal-detection parameter—the local fractional variance spectrum (LFV) spectrum—yields the correct null distribution for a very general class of spatiotemporal climate noise processes...

Introgression and species delimitation in the longear sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)

Daemin Kim, Bruce Bauer & Thomas Near
Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world’s most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, L. megalotis and L. peltastes, in the L. megalotis complex. Instead, evidence from...

Ocean and ice spin-up 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...

Retinotopic organization of visual cortex in human infants

Cameron Ellis, Tristan Yates, Lena Skalaban, Vikranth Bejjanki, Michael Arcaro & Nicholas Turk-Browne
Vision develops rapidly during infancy, yet how visual cortex is organized during this period is unclear. In particular, it is unknown whether functional maps that organize the mature adult visual cortex are present in the infant striate and extrastriate cortex. Here we test the functional maturity of infant visual cortex by performing retinotopic mapping with fMRI. Infants aged 5–23 months had retinotopic maps, with alternating preferences for vertical and horizontal meridians indicative of area boundaries...

An objective-based prioritization approach to support trophic complexity through ecological restoration

Emma Ladouceur, Jennifer McGowan, Patrick Huber, Hugh Possingham, Davide Scridel, Roel Van Klink, Peter Poschlod, Hans Cornelissen, Costantino Bonomi & Borja Jiménez-Alfaro
1. Reassembling ecological communities and rebuilding habitats through active restoration treatments requires curating the selection of plant species to use in seeding and planting mixes. Ideally, these mixes should be assembled based on attributes that support ecosystem function and services, promote plant and animal species interactions and ecological networks in restoration while balancing project constraints. Despite these critical considerations, it is common for species mixes to be selected opportunistically. Reframing the selection of seed mixes...

Clinical Trial Transparency and Data-Sharing Among Bio-Pharmaceutical Companies and the Role of Company Size, Location, and Product Type: A Cross-Sectional Descriptive Analysis

Sydney Axson, Michelle Mello, Deborah Lincow, Catherine Yang, Cary Gross, Joseph Ross & Jennifer Miller
Objective: To examine company characteristics associated with better transparency and to apply a tool used to measure and improve clinical trial transparency among large companies and drugs, to smaller companies and biologics. Design: Cross-sectional descriptive analysis. Setting and participants. Novel drugs and biologics FDA approved in 2016 and 2017, and their company sponsors. Using established Good Pharma Scorecard (GPS) measures, companies and products were evaluated on their clinical trial registration, results dissemination, and FDA Amendments...

An unanticipated role for sphingosine kinase-2 in bone and in the anabolic effect of parathyroid hormone: Supplementary figures

Joanne Walker, Gang-Qing Yao, Edwin Siu, Meiling Zhu, Christine Simpson & Karl Insogna
Sphingosine-1-phosphate (S1P) is an anabolic clastokine. SPHK is the rate-limiting enzyme in S1P production and has two isoforms. To evaluate the roles of SPHK1 and SPHK2 in bone, we examined the skeletal phenotype of mice with selective deletion of SPHK1 in osteoclasts (SPHK1-Oc-/-) and mice in which the SPHK2 gene was deleted in all tissues (SPHK2-/-). SPHK1-Oc-/- had normal bone mass. By contrast, SPHK2-/- female mice had a 14% lower spinal BMD (p<0.01) and males...

Ultraconserved elements data for Amarsipus and Pelagiaria

Richard Harrington, Matt Friedman, Masaki Miya, Thomas Near & Matthew Campbell
Amarsipus carlsbergi is a rare mesopelagic fish distributed in the Indian and Pacific Oceans, and is the only species classified in the family Amarsipidae. Since its description in 1969, phylogenetic hypotheses have varied regarding its relationship with other percomorph lineages, but most have indicated a close relationship with the traditional suborder Stromateoidei. Molecular phylogenies place families previously classified in Stromateoidei within a diverse clade– Pelagiaria– that includes fishes such as tunas, cutlassfishes, and pomfrets. A...

Forest phenoclusters for Argentina based on vegetation phenology and climate

Eduarda Silveira, Volker Radeloff, Guillermo Martínez Pastur, Sebastián Martinuzzi, Natalia Politi, Leonidas Lizarraga, Luis Rivera, Gregorio Gavier-Pizarro, He Yin, Yamina Rosas, Noelia Calamari, María Navarro, Yanina Sica, Ashley Olah, Julieta Bono & Anna Pidgeon
Forest biodiversity conservation and species distribution modeling greatly benefit from broad-scale forest maps depicting tree species or forest types rather than just presence and absence of forest, or coarse classifications. Ideally, such maps would stem from satellite image classification based on abundant field data for both model training and accuracy assessments, but such field-data does not exist in many parts of the globe. However, different forest types and tree species differ in their vegetation phenology,...

Thermal-metabolic phenotypes of the lizard Podarcis muralis differ across elevation, but converge in high elevation hypoxia

Brooke L Bodensteiner, Eric J Gangloff, Laura Kouyoumdjian, Martha M Muñoz & Fabien Aubret
In response to a warming climate, many montane species are shifting upslope to track the emergence of preferred temperatures. Characterizing patterns of variation in metabolic, physiological and thermal traits along an elevational gradient, and the plastic potential of these traits, is necessary to understand current and future responses to abiotic constraints at high elevations, including limited oxygen availability. We performed a transplant experiment with the upslope-colonizing common wall lizard (Podarcis muralis) in which we measured...

Data from: Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

Sylvie Estrela, Alicia Sanchez-Gorostiaga, Jean Vila & Alvaro Sanchez
A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, we investigate whether communities assembled in pairs of nutrients can be predicted from those assembled in every single nutrient alone. We first find that although the null, naturally additive model generally predicts well the family-level community composition, there exist systematic deviations from the additive...

Compartmentalization of cerebrospinal fluid inflammation across the spectrum of HIV infection

Richard Price, Magnus Gisslen, Sheila Keating, Serena Spudich, Victor Arechiga, Sophie Stephenson, Henrik Zetterberg, Clara Di Germanio, Kaj Blennow, Lars Hagberg, Philip Norris, Julia Peterson, Barbara Shacklett & Constantin Yiannoutsos
Objective: To characterize the evolution of central nervous system (CNS) inflammation in HIV-1 infection applying a panel of cerebrospinal fluid (CSF) inflammatory biomarkers to grouped subjects representing a broad spectrum of systemic HIV-1 immune suppression, CNS injury and viral control. Methods: This is a cross-sectional analysis of archived CSF and blood samples, assessing concentrations of 10 functionally diverse soluble inflammatory biomarkers by immunoassays in 143 HIV-1-infected subjects divided into 8 groups: untreated primary HIV-1 infection...

Selection for phage resistance reduces virulence of Shigella flexneri

Kaitlyn Kortright, Rachel Done, Benjamin Chan, Valeria Souza & Paul Turner
There is increasing interest in phage therapy as an alternative to chemical antibiotics for treating bacterial infections, especially using phages that select for evolutionary trade-offs between increased phage resistance and decreased fitness traits such as virulence in target bacteria. A vast repertoire of virulence factors allows the opportunistic bacterial pathogen, Shigella flexneri, to invade human gut epithelial cells, to replicate intracellularly, and to evade host immunity through intercellular spread; the latter is an infection stage...

The multidimensional (and contrasting) effects of environmental warming on a group of montane tropical lizards: Lizard and plant data

Martha M Munoz, Kenneth Feeley, Patrick Martin & Vincent Farallo
1. Mountains are cradles for biodiversity and crucibles for climate-driven species loss, particularly for tropical ectotherms. Constriction on activity and amplified heat stress are two key sources of warming-driven vulnerability in tropical montane ectotherms. These threats, however, might be counterbalanced if rising temperatures also release organisms from limits on activity induced by cold stress. 2. We used biophysical modeling to estimate activity patterns and thermal stress under warming in a group of summit-dwelling Anolis lizards...

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...

Monthly pCO2, gas transfer velocity and CO2 efflux rate in global streams and rivers (the GRADES river networks)

Shaoda Liu
The datasets contain monthly partial pressure of dissolved CO2 (pCO2, µatm), gas transfer velocity (k, m d-1), and CO2 efflux rate (g C m-2 d-1) estimates for global streams and rivers in both comma separated values (csv) and GeoTIFF formats. These datasets served as the base for monthly CO2 emission estimates for global streams and rivers and can be used to support regional terrestrial carbon balances. Original vector-version of products is based on the Global...

GMBA Mountain Inventory v2

Mark A. Snethlage, Jonas Geschke, Eva M. Spehn, Ajay Ranipeta, Nigel G. Yocco, Christian Körner, Walter Jetz, Markus Fischer & Davnah Urbach
A standardized delineation of the worlds’ mountains has many applications in research, education, and the science-policy interface. Here we provide a new inventory of 8616 mountain ranges developed under the auspices of the Global Mountain Biodiversity Assessment (GMBA). Building on an earlier compilation, the presented geospatial database uses a further advanced and generalized mountain definition and a semi-automated method to enable globally standardized, transparent delineations of mountain ranges worldwide. The inventory is presented on EarthEnv...

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...

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...

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 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...

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...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Yale University
  • University of Oxford
  • University of Florida
  • Princeton University
  • Institute of Oceanology. PP Shirshov Russian Academy of Sciences
  • Wayne State University
  • University of California Los Angeles
  • Cornell University
  • Affiliated Hospital of Nantong University
  • North West Agriculture and Forestry University