333 Works

Global analysis of environmental and socioeconomic factors associated with human burden of environmentally mediated pathogens

Susanne Sokolow, Isabel Jones, Chelsea Wood, Kevin Lafferty, Andres Garchitorena, Skylar Hopkins, Andrea Lund, Andrew MacDonald, Nicole Nova, Chris LeBoa, Alison Peel, Erin Mordecai, Meghan Howard, Julia Buck, David Lopez-Carr, Michele Barry, Matthew Bonds & Giulio De Leo
This repository contains four datasets that support repeatability of the analyses in the Sokolow et al. paper published in Lancet Planetary Health. Descriptions of the four datasets are included in the metadata document. This study found that 80% of pathogen species known to infect humans are environmentally mediated, causing about 40% of contemporary infectious-disease burden (global loss of 130 million years of healthy life annually). More than 91% of this environmentally-mediated disease burden occurs in...

Icelandic Volcanic Rocks Isotopic Database (IVID)

Sunna Harðardóttir, Simon Matthews, Sæmundur Ari Halldórsson & Matthew Jackson
We compile a new geochemical database (Icelandic Volcanic rocks Isotopic Database, IVID) which includes previously reported 87Sr/86Sr, 143Nd/144Nd, 176Hf/177Hf, 206Pb/204Pb, 207Pb/204Pb, 208Pb/204Pb, 187Os/188Os and 3He/4He data and major and trace element concentrations measured in Icelandic volcanic rocks. Isotopic compositions were evaluated, and filtered to identify the highest quality data and data most likely to represent mantle-derived compositions. The carefully filtered, comprehensive geochemical database is an important contribution to the geochemical community and can be used...

Eocene Terrane Accretion in Northern Cascadia Recorded by Brittle Left-lateral Slip on the San Juan Fault

Nicolas Harrichhausen, Kristin Morell, Christine Regalla, Emerson Lynch & Lucinda Leonard
The San Juan fault, on southern Vancouver Island, Canada, juxtaposes the oceanic Wrangellia and Pacific Rim terranes in the northern Cascadia forearc, and has been suggested to play a role in multiple Mesozoic--Cenozoic terrane accretion events. However, direct observations of the San Juan fault's kinematics have not been documented and its exact role in accommodating strain arising from terrane accretion is unknown. To test if, how, and when the San Juan fault accommodated accretion-related strain,...

Efficient Creation and Morphological Analysis of ABC Triblock Terpolymer Libraries

Elizabeth Murphy, Yan-Qiao Chen, Kaitlin Albanese, Jacob Blankenship, Allison Abdilla, Morgan Bates, Cheng Zhang, Christopher Bates & Craig Hawker
Multiblock copolymers with increasingly complex block sequences—for example, triblock terpolymers—offer unique opportunities to create nanostructured materials, but this potential has been hindered by a vast design space that complicates the exploration of structure–property relationships. Here, we report a versatile and scalable strategy to separate parent ABC and isomeric ACB triblock terpolymers into libraries of fractionated samples spanning a wide range of compositions. Using a combination of controlled polymerization and automated chromatography, the synthesis and separation...

Impossible Possible Machines

Christina Vagt
Arguing against the current paradigm of computationalism, the article revisits Alexandre Koyré’s history of European techno-rationality and 17th-century figures like Descartes and Galileo. Here, one finds the machine emerging at precisely the time and place in history where the gap between mathematical-geometrical idealization and the reality of bodies and experiments first appeared. Historically, the machine is rooted in theatrical mechanics of simulation, illusion, fiction, and deception. Structurally, it appears in between subject and object, the...

Additional file 2 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 2: Supplementary Table 1. TOGA status of 18430 ancestral placental mammal genes in muroid rodent genome assemblies. Supplementary Table 2. Positively selected genes and their mutation tolerance in humans according to gnomAD.

BEDMAP2 - Ice thickness, bed and surface elevation for Antarctica - standardised data points

Peter Fretwell, Alice Fremand, Julien Bodart, Hamish Pritchard, David Vaughan, Jonathan Bamber, N. Barrand, R.E. Bell, C Bianchi, Robert Bingham, Donald Blankenship, G. Casassa, Ginny Catania, D. Callens, H Conway, Alison Cook, Hugh Corr, D Damaske, V. Damn, Fausto Ferraccioli, Rene Forsberg, S. Fujita, Y. Gim, P. Gogineni, J. Griggs … & A. Zirizzotti
We present here the Bedmap2 ice thickness, bed and surface elevation standardised CSV data points that were used to create the Bedmap2 gridding products. The data consists of 25 million points coming from 68 individual surveys acquired in Antarctica. The associated datasets consist of: - Bedmap1 standardised CSV data points: https://doi.org/10.5285/f64815ec-4077-4432-9f55-0ce230f46029 - Bedmap3 standardised CSV data points: https://doi.org/10.5285/91523ff9-d621-46b3-87f7-ffb6efcd1847 - Bedmap2 statistically-summarised data points (shapefiles): https://doi.org/10.5285/0f90d926-99ce-43c9-b536-0c7791d1728b - Bedmap2 gridding products: https://doi.org/10.5285/fa5d606c-dc95-47ee-9016-7a82e446f2f2 This work is supported by...

Data for: Axisymmetric Displacement Flows in Flow-driven Fractures

Sri Savya Tanikella & Emilie Dressaire
The raw data presented in the associated manuscript entitled "Axisymmetric displacement flows in fluid-driven fractures" are included here. For experiments 1 through 16 (see table 3 for experimental parameters), we measure (1) the radius of the fracture during the formation of the pre-fracture, (2) the radius of the fracture during the displacement flow (i.e. when the second fluid is injected), and (3) the radial position of the interface during the two fluids, during the displacement...

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Abstract Background The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. Results We report a 2.5 Gb, chromosome-level reference genome assembly with...

Data from: Arthropod diversity in a tropical forest

Yves Basset, Lukas Cizek, Philippe Cuénoud, Raphael K. Didham, François Guilhaumon, Olivier Missa, Vojtech Novotny, Frode Ødegaard, Tomas Roslin, Jürgen Schmidl, Alexey K. Tishechkin, Neville N. Winchester, David W. Roubik, Henri-Pierre Aberlenc, Johannes Bail, Héctor Barrios, Jon R. Bridle, Gabriela Castaño-Meneses, Bruno Corbara, Gianfranco Curletti, Wesley Duarte Da Rocha, Domir De Bakker, Jacques H. C. Delabie, Alain Dejean, Laura L. Fagan … & Maurice Leponce
Most eukaryotic organisms are arthropods. Yet, their diversity in rich terrestrial ecosystems is still unknown. Here we produce tangible estimates of the total species richness of arthropods in a tropical rainforest. Using a comprehensive range of structured protocols, we sampled the phylogenetic breadth of arthropod taxa from the soil to the forest canopy in the San Lorenzo forest, Panama. We collected 6,144 arthropod species from 0.48 ha and extrapolated total species richness to larger areas...

Data from: The genetic basis and experimental evolution of inbreeding depression in Caenorhabditis elegans

Ivo M. Chelo, S. Carvalho, M. Roque, S. R. Proulx & Henrique Teotónio
Determining the genetic basis of inbreeding depression is important for understanding the role of selection in the evolution of mixed breeding systems. Here, we investigate how androdioecy (a breeding system characterized by partial selfing and outcrossing) and dioecy (characterized by obligatory outcrossing) influence the experimental evolution of inbreeding depression in Caenorhabditis elegans. We derived inbred lines from ancestral and evolved populations and found that the dioecious lineages underwent more extinction than androdioecious lineages. For both...

Data from: Independent origins of parasitism in Animalia

Sara B. Weinstein & Armand M. Kuris
Nearly half of all animals may have a parasitic lifestyle, yet the number of transitions to parasitism and their potential for species diversification remain unresolved. Based on a comprehensive survey of the animal kingdom, we find that parasitism has independently evolved at least 223 times in just 15 phyla, with the majority of identified independent parasitic groups occurring in the Arthropoda, at or below the level of Family. Metazoan parasitology is dominated by the study...

Data from: Spatial patterns of self-recruitment of a coral reef fish in relation to island-scale retention mechanisms

Ricardo Beldade, Sally J. Holbrook, Russell J. Schmitt, Serge Planes & Giacomo Bernardi
Oceanographic features influence the transport and delivery of marine larvae, and physical retention mechanisms, such as eddies, can enhance self-recruitment (i.e. the return of larvae to their natal population). Knowledge of exact locations of hatching (origin) and settlement (arrival) of larvae of reef animals provides a means to compare observed patterns of self-recruitment ‘connectivity’ with those expected from water circulation patterns. Using parentage inference based on multiple sampling years in Moorea, French Polynesia, we describe...

Data from: New England cod collapse and the climate

Kyle C. Meng, Kimberly L. Oremus & Steven D. Gaines
To improve fishery management, there is an increasing need to understand the long-term consequences of natural and anthropogenic climate variability for ecological systems. New England’s iconic cod populations have been in decline for several decades and have recently reached unprecedented lows. We find that 17% of the overall decline in Gulf of Maine cod biomass since 1980 can be attributed to positive phases of the North Atlantic Oscillation (NAO). This is a consequence of three...

Data from: Tiny vampires in ancient seas: evidence for predation via perforation in fossils from the 780–740 million-year-old Chuar Group, Grand Canyon, USA

Susannah M. Porter
One explanation for the early Neoproterozoic expansion of eukaryotes is the appearance of eukaryovorous predators—i.e. protists that preyed on other protists. Evidence for eukaryovory at this time, however, is indirect, based on inferences from character state reconstructions and molecular clocks, and on the presence of possible defensive structures in some protistan fossils. Here I describe 0.1–3.4 µm circular holes in seven species of organic-walled microfossils from the ~780–740 million-year-old Chuar Group, Grand Canyon, Arizona, USA,...

Data from: Integral Projection Models for host-parasite systems with an application to amphibian chytrid fungus

Mark Q. Wilber, Kate E. Langwig, Auston Marm Kilpatrick, Hamish I. McCallum & Cheryl J. Briggs
Host–parasite models are typically constructed under either a microparasite or macroparasite paradigm. However, this has long been recognized as a false dichotomy because many infectious disease agents, including most fungal pathogens, have attributes of both microparasites and macroparasites. We illustrate how Integral Projection Models (IPMs) provide a novel modelling framework to represent both types of pathogens. We build a simple host–parasite IPM that tracks both the number of susceptible and infected hosts and the distribution...

Data from: Climate modifies response of non-native and native species richness to nutrient enrichment

Habacuc Flores-Moreno, Peter B. Reich, Eric M. Lind, Lauren L. Sullivan, Eric W. Seabloom, Laura Yahdjian, Andrew S. MacDougall, Lara G. Reichmann, Juan Alberti, Selene Báez, Jonathan D. Bakker, Marc W. Cadotte, Maria C. Caldeira, Enrique J. Chaneton, Carla M. D'Antonio, Philip A. Fay, Jennifer Firn, Nicole Hagenah, W. Stanley Harpole, Oscar Iribarne, Kevin P. Kirkman, Johannes M. H. Knops, Kimberly J. La Pierre, Ramesh Laungani, Andrew D. B. Leakey … & Elizabeth T. Borer
Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of...

Data from: Benefits and challenges of scaling up expansion of marine protected area networks in the Verde Island Passage, Central Philippines

Vera Horigue, Robert L. Pressey, Morena Mills, Jana Brotanková, Reniel Cabral & Serge Andrefouet
Locally-established marine protected areas (MPAs) have been proven to achieve local-scale fisheries and conservation objectives. However, since many of these MPAs were not designed to form ecologically-connected networks, their contributions to broader-scale goals such as complementarity and connectivity can be limited. In contrast, integrated networks of MPAs designed with systematic conservation planning are assumed to be more effective—ecologically, socially, and economically—than collections of locally-established MPAs. There is, however, little empirical evidence that clearly demonstrates the...

Data from: Large-scale recovery of an endangered amphibian despite ongoing exposure to multiple stressors

Roland A. Knapp, Gary M. Fellers, Patrick M. Kleeman, David A. W. Miller, Vance T. Vredenburg, Erica Bree Rosenblum & Cheryl J. Briggs
Amphibians are one of the most threatened animal groups, with 32% of species at risk for extinction. Given this imperiled status, is the disappearance of a large fraction of the Earth’s amphibians inevitable, or are some declining species more resilient than is generally assumed? We address this question in a species that is emblematic of many declining amphibians, the endangered Sierra Nevada yellow-legged frog (Rana sierrae). Based on >7,000 frog surveys conducted across Yosemite National...

Data from: Resistance, tolerance and environmental transmission dynamics determine host extinction risk in a load-dependent amphibian disease

Mark Q. Wilber, Roland A. Knapp, Mary Toothman & Cheryl J. Briggs
While disease-induced extinction is generally considered rare, a number of recently emerging infectious diseases with load-dependent pathology have led to extinction in wildlife populations. Transmission is a critical factor affecting disease-induced extinction, but the relative importance of transmission compared to load-dependent host resistance and tolerance is currently unknown. Using a combination of models and experiments on an amphibian species suffering extirpations from the fungal pathogen Batrachochytrium dendrobatidis (Bd), we show that while transmission from an...

Data from: Biological and statistical processes jointly drive population aggregation: using host–parasite interactions to understand Taylor's power law

Pieter T. J. Johnson & Mark Q. Wilber
The macroecological pattern known as Taylor's power law (TPL) represents the pervasive tendency of the variance in population density to increase as a power function of the mean. Despite empirical illustrations in systems ranging from viruses to vertebrates, the biological significance of this relationship continues to be debated. Here we combined collection of a unique dataset involving 11 987 amphibian hosts and 332 684 trematode parasites with experimental measurements of core epidemiological outcomes to explicitly...

Data from: Divergence in pollen performance between Clarkia sister species with contrasting mating systems supports predictions of sexual selection

Susan J. Mazer, Brandon Thomas Hendrickson, Joseph P. Chellew, Lynn J. Kim, Jasen W. Liu, Jasper Shu, Manju V. Sharma & Susan Mazer
Animal taxa that differ in the intensity of sperm competition often differ in sperm production or swimming speed, arguably due to sexual selection on postcopulatory male traits affecting siring success. In plants, closely related self- and cross-pollinated taxa similarly differ in the opportunity for sexual selection among male gametophytes after pollination, so traits such as the proportion of pollen on the stigma that rapidly enters the style and mean pollen tube growth rate (PTGR) are...

Data from: Regulation of reproductive processes with Dynamic Energy Budgets

Erik B. Muller, Konstadia Lika, Roger M. Nisbet, Irvin R. Schultz, Jerome Casas, Andre Gergs, Cheryl A. Murphy, Diane Nacci & Karen H. Watanabe
1. Linking organismal level processes to underlying suborganismal mechanisms at the molecular, cellular and organ level constitutes a major challenge for predictive ecological risk assessments. This challenge can be addressed with the simple bioenergetic models in the family of Dynamic Energy Budget (DEB), which consist of a small number of state equations quantifying universal processes, such as feeding, maintenance, development, reproduction and growth. 2. Motivated by the need for process-based models to evaluate the impact...

Data from: Missing the people for the trees: identifying coupled natural-human system feedbacks driving the ecology of Lyme disease

Andrew J. MacDonald, Ashley E. Larsen & Andrew J. Plantinga
1. Infectious diseases are rapidly emerging and many are increasing in incidence across the globe. Processes of land-use change, notably habitat loss and fragmentation, have been widely implicated in emergence and spread of zoonoses such as Lyme disease, yet evidence remains equivocal. 2. Here we discuss and apply an innovative approach from the social sciences, instrumental variables, that seeks to tease out causality from observational data. Using this approach, we revisit the effect of forest...

Data from: Looking back to look ahead: a vision for soil denitrification research

Maya Almaraz, Michelle Wong & Wendy Yang
Denitrification plays a critical role in regulating ecosystem nutrient availability and anthropogenic reactive nitrogen (N) production. Its importance has inspired an increasing number of studies, yet it remains the most poorly constrained term in terrestrial ecosystem N budgets. We censused the peer-reviewed soil denitrification literature (1975 to 2015) to identify opportunities for future studies to advance our understanding despite the inherent challenges in studying the process. We found that only one-third of studies reported estimates...

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