194 Works

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: 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: 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: 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: 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: Flexibility of fetal tolerance: Immune function during pregnancy varies between ecologically distinct populations

Carmen Hové, Benjamin Trumble, Amy Anderson, Jonathan Stieglitz, Hillard Kaplan, Michael Gurven & Aaron Blackwell
Background and objectives: Among placental mammals, females undergo immunological shifts during pregnancy to accommodate the fetus (i.e. fetal tolerance). Fetal tolerance has primarily been characterized within post-industrial populations experiencing evolutionarily novel conditions (e.g. reduced pathogen exposure), which may shape maternal response to fetal antigens. This study investigates how ecological conditions affect maternal immune status during pregnancy by comparing the direction and magnitude of immunological changes associated with each trimester among the Tsimane (a subsistence population...

Polyethylene upcycling to long-chain alkylaromatics by tandem hydrogenolysis/aromatization

Fan Zhang, Manhao Zeng, Ryan Yappert, Jiakai Sun, Yu-Hsuan Lee, Anne LaPointe, Baron Peters, Mahdi Abu-Omar & Susannah Scott
The current scale of plastics production and the accompanying waste disposal problems represent a largely untapped opportunity for chemical upcycling. Tandem catalytic conversion by Pt/g-Al2O3 converts various polyethylene grades in high yields (up to 80 wt%) to low molecular-weight liquid/wax products, in the absence of added solvent or H2, with little production of light gases. The major components are valuable long-chain alkylaromatics and alkylnaphthenes (average ca. C30, Ð = 1.1). Coupling exothermic hydrogenolysis with endothermic...

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...

Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds

Samuel Verbanic, Yuning Shen, Juhee Lee, John Deacon & Irene Chen
Chronic wounds represent a large and growing disease burden. Infection and biofilm formation are two of the leading impediments of wound healing, suggesting an important role for the microbiome of these wounds. However, microbial taxa that may impact healing are poorly understood. Debridement is an effective treatment for chronic wounds, but the effect on the microbiome is unknown. Based on prior literature, we hypothesized that anaerobic organisms are exposed to the surface by debridement, contributing...

Kinetic sequencing (k-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters

Yuning Shen, Abe Pressman, Evan Janzen & Irene Chen
Characterizing genotype-phenotype relationships of biomolecules (e.g., ribozymes) requires accurate ways to measure activity for a large set of molecules. Kinetic measurement using high-throughput sequencing (e.g., k-Seq) is an emerging assay applicable in various domains that potentially scales up measurement throughput to over 106 unique nucleic acid sequences. However, maximizing the return of such assays requires understanding the technical challenges introduced by sequence heterogeneity and DNA sequencing. We characterized the k-Seq method in terms of model...

Disease hotspots or hot species? Infection dynamics in multi-host metacommunities controlled by species identity, not source location

Mark Wilber, Pieter Johnson & Cheryl Briggs
Pathogen persistence in host communities is influenced by processes operating at the individual host to landscape-level scale, but isolating the relative contributions of these processes is challenging. We developed theory to partition the influence of host species, habitat patches, and landscape connectivity on pathogen persistence within metacommunities of hosts and pathogens. We used this framework to quantify the contributions of host species composition and habitat patch identity on the persistence of an amphibian pathogen across...

Protecting the global ocean for biodiversity, food and climate

Enric Sala & Juan Mayorga
The ocean contains unique biodiversity, provides valuable food resources and is a major sink for anthropogenic carbon. Marine protected areas (MPAs) are an effective tool for restoring ocean biodiversity and ecosystem services1,2, but at present only 2.7% of the ocean is highly protected3. This low level of ocean protection is due largely to conflicts with fisheries and other extractive uses. To address this issue, here we developed a conservation planning framework to prioritize highly protected...

Data from: The future of food from the sea

Tracey Mangin, Christopher Costello, Ling Cao, Stefan Gelcich, Miguel A. Cisneros-Mata, Christopher M. Free, Halley E. Froehlich, Christopher D. Golden, Gakushi Ishimura, Jason Maier, Ilan Macadam-Somer, Michael C. Melnychuk, Masanori Miyahara, Carryn L. De Moor, Rosamond Naylor, Linda Nøstbakken, Elena Ojea, Erin O’Reilly, Ana M. Parma, Andrew J. Plantinga, Shakuntala H. Thilsted & Jane Lubchenco
Global food demand is on the rise and serious questions remain about whether supply can increase sustainably. Land-based expansion is possible, but may exacerbate climate change and biodiversity loss and compromise the delivery of other ecosystem services. As food from the sea represents only 17% of current edible meat production, we ask: How much food can we expect the ocean to sustainably produce by 2050? We examine the main food-producing sectors in the ocean—wild fisheries,...

A distributed circuit for associating environmental context to motor choice in retrosplenial cortex

Luis Franco & Michael Goard
During navigation, animals often use recognition of familiar environmental contexts to guide motor action selection. The retrosplenial cortex (RSC) receives inputs from both visual cortex and subcortical regions required for spatial memory, and projects to motor planning regions. However, it is not known whether RSC is important for associating familiar environmental contexts with specific motor actions. Here, we test this possibility by developing a task in which trajectories are chosen based on the context. We...

Data from: Phylogenetic conservatism in plant phenology

T. Jonathan Davies, Elizabeth M. Wolkovich, Nathan J. B. Kraft, Nicolas Salamin, Jenica M. Allen, Toby R. Ault, Julio L. Betancourt, Kjell Bolmgren, Elsa E. Cleland, Benjamin I. Cook, Theresa M. Crimmins, Susan J. Mazer, Gregory J. McCabe, Stephanie Pau, Jim Regetz, Mark D. Schwartz & Steven E. Travers
Phenological events – defined points in the life cycle of a plant or animal – have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism – the tendency...

Data from: Context-dependent effects of large wildlife declines on small mammal communities in central Kenya

Hillary S. Young, Douglas J. McCauley, Rodolfo Dirzo, Jacob R. Goheen, Bernard Agwanda, Cara Brook, Erik O. Castillo, Adam W. Ferguson, Stephen N. Kinyua, Molly M. McDonough, Todd M. Palmer, Robert M. Pringle, Truman P. Young & Kristofer M. Helgen
Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife...

Data from: Parasites affect food web structure primarily through increased diversity and complexity

Jennifer A. Dunne, Kevin D. Lafferty, Andrew P. Dobson, Ryan F. Hechinger, Armand M. Kuris, Neo D. Martinez, John P. McLaughlin, Kim N. Mouritsen, Robert Poulin, Karsten Reise, Daniel B. Stouffer, David W. Thieltges, Richard J. Williams & Claus Dieter Zander
Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite...

Engineering crack tortuosity in polymer-polymer composites through ordered pores

Megan Valentine, Craig Hawker, Luke Gockowski, Neil Dolinski, Roberto Chavez, Noy Cohen, Fabian Eisenreich, Stefan Hecht & Robert McMeeking
Multimaterial additive manufacturing (or 3D printing) is an enabling tool for exploring structure-property relationships. In this work, a recently developed multimaterial printing approach, solution mask liquid lithography (SMaLL), is used to produce polymer-polymer composites inspired by tough, hierarchical structures found in nature. Triphasic composites comprised of a hard exterior “cuticle”, a soft interior “core,” and controlled pore size/structure are printed in a single step and their mechanical properties evaluated. The results of these tests demonstrate...

Mixed-species herding levels the landscape of fear

Keenan Stears, Melissa Schmitt, Christopher Wilmers & Adrian Shrader
Prey antipredator behaviours are influenced by perceived predation risk in a landscape and social information gleaned from herd mates regarding predation risk. It is well documented that high-quality social information about risk can come from heterospecific herd mates. Here, we integrate social information with the landscape of fear to quantify how these landscapes are modified by mixed-species herding. To do this, we investigated zebra vigilance in single- and mixed-species herds across different levels of predation...

Data from: Mating system and historical climate conditions affect population mean seed mass: evidence for adaptation and a new component of the selfing syndrome in Clarkia

Susan Mazer, Isaac Park, Matthew Kimura, Aaron Yim, Emma Maul & Kristen Peach
1. The evolution of seed size may be influenced by intrinsic attributes of populations, such as mating system, and extrinsic factors, such as climate. Several hypotheses propose that the evolution of self-fertilization from an outcrossing progenitor will be accompanied by a reduction in seed size, but this prediction has not been rigorously tested. Many studies report that the mean seed size of populations or taxa is associated with long-term climate conditions. Here, we examined the...

Variations in the Intensity and Spatial Extent of Tropical Cyclone Precipitation

Danielle Touma, Samantha Stevenson, Suzana J. Camargo, Daniel E. Horton & Noah S. Diffenbaugh
The intensity and spatial extent of tropical cyclone precipitation (TCP) often shapes the risk posed by landfalling storms. Here we provide a comprehensive climatology of landfalling TCP characteristics as a function of tropical cyclone strength, using daily precipitation station data and Atlantic US landfalling tropical cyclone tracks from 1900-2017. We analyze the intensity and spatial extent of ≥ 1 mm/day TCP (Z1) and ≥ 50 mm/day TCP (Z50) over land. We show that the highest...

Conceptual, anthropological and cognitive issues surrounding religious experience. An interview with Ann Taves.

Ann Taves, Martin Fortier & Maddalena Canna
Cognitive Sciences of Religion scholar Ann Taves is the proponent of a ground-breaking building block approach (BBA) to religious experience. According to Taves, religious experience can be disaggregated into fundamental, constitutive components. Philosopher Martin Fortier and anthropologist Maddalena Canna explore the conceptual, anthropological and cognitive aspects of the foundations of religion, as disaggregated by Taves. In her analyses of the cognitive underpinnings of religion, Taves adopts a Predictive Coding Framework (PCF). The compatibility between PCF...

Distance decay relationships in foliar fungal endophytes are driven by rare taxa

Ryoko Oono, Emilie Lefevre & Anna Rasmussen
Foliar fungal endophytes represent a diverse and species-rich plant microbiome. Their biogeography provides essential clues to their cryptic relationship with hosts and the environment in which they disperse. We present species composition, diversity, and dispersal patterns of endophytic fungi associated with needles of Pinus taeda trees across regional scales in the absence of strong environmental gradients as well as within individual trees. An empirical designation of rare and abundant taxa enlightens us on the structure...

Double digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles

Ryoko Oono & Rodolfo Salas Lizana
The phylogenetic and population genetic structure of symbiotic microorganisms may correlate with important ecological traits that can be difficult to directly measure, such as host preferences or dispersal rates. This study develops and tests a low-cost double digest restriction site-associated DNA sequencing (ddRADseq) protocol to reveal among- and within-species genetic structure for Lophodermium, a genus of fungal endophytes whose evolutionary analyses have been limited by the scarcity of informative markers. The protocol avoids expensive barcoded...

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  • University of California, Santa Barbara
  • Stanford University
  • University of California, Santa Cruz
  • University of California, Davis
  • University of Washington
  • University of California System
  • University of California, San Diego
  • University of Hawaii at Manoa
  • University of California Los Angeles
  • United States Geological Survey