140 Works

Data from: Stimulus discriminability may bias value-based probabilistic learning

Iris Schutte, Heleen A. Slagter, Anne G.E. Collins, Michael J. Frank, J. Leon Kenemans & Anne G. E. Collins
Reinforcement learning tasks are often used to assess participants' tendency to learn more from the positive or more from the negative consequences of one's action. However, this assessment often requires comparison in learning performance across different task conditions, which may differ in the relative salience or discriminability of the stimuli associated with more and less rewarding outcomes, respectively. To address this issue, in a first set of studies, participants were subjected to two versions of...

Data from: Biomass resilience of Neotropical secondary forests

Lourens Poorter, Frans Bongers, T. Mitchell Aide, Angélica M. Almeyda Zambrano, Patricia Balvanera, Justin M. Becknell, Vanessa Boukili, Pedro H. S. Brancalion, Eben N. Broadbent, Robin L. Chazdon, Dylan Craven, Jarcilene S. De Almeida-Cortez, George A. L. Cabral, Ben H. J. De Jong, Julie S. Denslow, Daisy H. Dent, Saara J. DeWalt, Juan M. Dupuy, Sandra M. Durán, Mario M. Espírito-Santo, María C. Fandino, Ricardo G. César, Jefferson S. Hall, José Luis Hernandez-Stefanoni, Catarina C. Jakovac … & Danaë M. A. Rozendaal
Land-use change occurs nowhere more rapidly than in the tropics, where the imbalance between deforestation and forest regrowth has large consequences for the global carbon cycle1. However, considerable uncertainty remains about the rate of biomass recovery in secondary forests, and how these rates are influenced by climate, landscape, and prior land use2, 3, 4. Here we analyse aboveground biomass recovery during secondary succession in 45 forest sites and about 1,500 forest plots covering the major...

Data from: Incompressible fluid plays a mechanical role in the development of passive muscle tension

David A. Sleboda & Thomas J. Roberts
Over short time scales, muscle fibres maintain a nearly constant volume of intracellular fluid. This fluid is essential to normal biochemical function, but its role in determining the mechanical properties of muscle has been considered in only a few theoretical analyses. Here we investigate the mechanical role of fluid in a fundamental property of muscle, its development of passive tension in response to stretch. We test a model of muscle structure in which incompressible fluid...

Data from: Targeted approach to identify genetic loci associated with evolved dioxin tolerance in Atlantic Killifish (Fundulus heteroclitus)

Dina A. Proestou, Patrick Flight, Denise Champlin & Diane Nacci
Background: The most toxic aromatic hydrocarbon pollutants are categorized as dioxin-like compounds (DLCs) to which extreme tolerance has evolved independently and contemporaneously in (at least) four populations of Atlantic killifish (Fundulus heteroclitus). Surprisingly, the magnitude and phenotype of DLC tolerance is similar among these killifish populations that have adapted to varied, but highly aromatic hydrocarbon-contaminated urban/industrialized estuaries of the US Atlantic coast. Multiple tolerant and neighboring sensitive killifish populations were compared with the expectation that...

Tracking the Near East origins and European dispersal of the house mouse

Thomas CUCCHI, Katerina Papayianni, Sophie Cersoy, Laetitia Aznar-Cormano, Antoine Zazzo, Régis Debruyne, Rémi Berthon, Adrian Bălășescu, Alan Simmons, François Valla, Yannis Hamilakis, Fanis Mavridis, Marjan Mashkour, Jamshid Darvish, Roohollah Siahsarvi, Fereidoun Biglari, Cameron A. Petrie, Lloyd Weeks, Alireza Sardari, Sepideh Maziar, Christiane Denys, David Orton, Emma Jenkins, Melinda Zeder, Jeremy B. Searle … & Jean-Denis Vigne
The house mouse (Mus musculus) is one of the most invasive mammals and an evolutionary model. However, the timing and components of its origin and dispersal remain poorly documented. To track its synanthropisation and subsequent biological invasion during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, dating between 40,000 and 3,000 cal. BP, combining geometric morphometris numerical taxonomy with ancient mitochondrial DNA...

The bite force-gape relationship as an avenue of biomechanical adaptation to trophic niche in two salmonid fishes

Elska B. Kaczmarek & Nicholas J. Gidmark
All skeletal muscles produce their largest forces at a single optimal length, losing force when stretched or shortened. In vertebrate feeding systems, this fundamental force-length relationship translates to variation in bite force across gape, which affects the food types that can be eaten effectively. We measured the bite force-gape curves of two sympatric species: king salmon (Oncorhynchus tshawytscha) and pink salmon (O. gorbuscha). Cranial anatomical measurements are not significantly different between species, however, peak bite...

Data from: Covariation of diet and gut microbiome in African megafauna

Tyler R. Kartzinel, Julianna C. Hsing, Paul M. Musili, Bianca R. P. Brown & Robert M. Pringle
A major challenge in biology is to understand how phylogeny, diet, and environment shape the mammalian gut microbiome. Yet most studies of non-human microbiomes have relied on relatively coarse dietary categorizations and have focused either on individual wild populations or on captive animals that are sheltered from environmental pressures, which may obscure the effects of dietary and environmental variation on microbiome composition in diverse natural communities. We analyzed plant and bacterial DNA in fecal samples...

Optimizing Coastal Restoration with the Stress Gradient Hypothesis

Hallie S Fischman, Sinead M Crotty & Christine Angelini
Restoration efforts have been escalating worldwide in response to widespread habitat degradation. However, coastal restoration attempts notoriously vary in their ability to establish resilient, high-functioning ecosystems. Conventional restoration attempts disperse transplants in competition-minimizing arrays, yet recent studies suggest that clumping transplants to maximize facilitative interactions may improve restoration success. Here, we modify the Stress Gradient Hypothesis to generate predictions about where each restoration design will perform best across environmental stress gradients. We then test this...

Data from: Nonnative old-field species inhabit early-season phenological niches and exhibit unique sensitivity to climate

Rachel Reeb, Isabel Acevedo, Mason Heberling & Sara Kuebbing
Native and nonnative plant species can exhibit differences in the timing of their reproductive phenology as well as their phenological sensitivity to climate. These contrasts may influence species’ interactions and the invasion potential of nonnative species; however, a limited number of phenology studies expressly consider phenological mismatches among native and nonnative species over broad spatial or temporal scales. To fill this knowledge gap, we used two complementary approaches: first, we quantified the flowering phenology of...

Data for: A coordinate-system-independent method for comparing joint rotational mobilities

Armita Razieh Manafzadeh & Stephen Miles Gatesy
Three-dimensional studies of range of motion currently plot joint poses in an "Euler space" whose axes are angles measured in the joint's three rotational degrees of freedom. Researchers then compute the volume of a pose cloud to measure rotational mobility. However, pairs of poses that are equally different from one another in orientation are not always plotted equally far apart in Euler space. This distortion causes a single joint's mobility to change when measured based...

Topological structure and dynamics of three-dimensional active nematics

Guillaume Duclos, Thomas Powers, Aparna Baskaran, Zvonimir Dogic, Vincenzo Vitelli, Federico Toschi, Raymond Adkins, Debarghya Banerjee, Matthew Peterson, Minu Varghese, Itamar Kolvin, Robert Pelcovits, Sebastian Streichan, Daniel Beller, Arvind Baskaran, Michael Hagan, Matthew S. E. Peterson, Robert A. Pelcovits, Thomas R. Powers, Michael F. Hagan & Sebastian J. Streichan
Topological structures are effective descriptors of the nonequilibrium dynamics of diverse many-body systems. For example, motile, point-like topological defects capture the salient features of two-dimensional active liquid crystals composed of energy-consuming anisotropic units. We dispersed force-generating microtubule bundles in a passive colloidal liquid crystal to form a three-dimensional active nematic. Light-sheet microscopy revealed the temporal evolution of the millimeter-scale structure of these active nematics with single-bundle resolution. The primary topological excitations are extended, charge-neutral disclination...

Data from: Fluctuating, warm temperatures decrease the effect of a key floral repressor on flowering time in Arabidopsis thaliana

Liana T. Burghardt, Daniel E. Runcie, Amity M. Wilczek, Martha D. Cooper, Judith L. Roe, Stephen M. Welch & Johanna Schmitt
The genetic basis of growth and development is often studied in constant laboratory environments; however, the environmental conditions that organisms experience in nature are often much more dynamic. We examined how daily temperature fluctuations, average temperature, day length and vernalization influence the flowering time of 59 genotypes of Arabidopsis thaliana with allelic perturbations known to affect flowering time. For a subset of genotypes, we also assessed treatment effects on morphology and growth. We identified 17...

Data from: Investigating processes of neotropical rain forest tree diversification by examining the evolution and historical biogeography of the Protieae (Burseraceae)

Paul Van Antwerp Fine, Felipe Zapata & Douglas C. Daly
Andean uplift and the collision of North and South America are thought to have major implications for the diversification of the Neotropical biota. However, few studies have investigated how these geological events may have influenced diversification. We present a multilocus phylogeny of 102 Protieae taxa (73% of published species), sampled pantropically, to test hypotheses about the relative importance of dispersal, vicariance, habitat specialization, and biotic factors in the diversification of this ecologically dominant tribe of...

Data from: Ecomorphological determinations in the absence of living analogs: the predatory behavior of the marsupial lion (Thylacoleo carnifex) as revealed by elbow-joint morphology

Borja Figueirido, Alberto Martín-Serra & Christine M. Janis
Thylacoleo carnifex, or the "pouched lion" (Mammalia: Marsupialia: Diprotodontia: Thylacoleonidae) was a carnivorous marsupial that inhabited Australia during the Pleistocene. Although today all authors agree that Thylacoleo had a hypercarnivorous diet, the way in which it killed its prey remains uncertain. Here we use geometric morphometrics to capture the shape of the elbow joint (i.e., the posterior articular surface of the distal humerus) in a wide sample of extant mammals of known behavior to determine...

Data from: The prevalence of MS in the United States: a population-based estimate using health claims data

Mitchell T. Wallin, William J. Culpepper, Jonathan D. Campbell, Lorene M. Nelson, Annette Langer-Gould, Ruth Ann Marrie, Gary R. Cutter, Wendy E. Kaye, Laurie Wagner, Helen Tremlett, Stephen L. Buka, Piyameth Dilokthornsakul, Barbara Topol, Lie H. Chen & Nicholas G. LaRocca
Objective: To generate a national multiple sclerosis (MS) prevalence estimate for the United States by applying a validated algorithm to multiple administrative health claims (AHC) datasets. Methods: A validated algorithm was applied to private, military, and public AHC datasets to identify adult cases of MS between 2008 and 2010. In each dataset, we determined the 3-year cumulative prevalence overall and stratified by age, sex, and census region. We applied insurance-specific and stratum-specific estimates to the...

Data from: Prediction of forest aboveground net primary production from high-resolution vertical leaf-area profiles

K. C. Cushman & James R. Kellner
Temperature and precipitation explain about half the variation in aboveground net primary production (ANPP) among tropical forest sites, but determinants of remaining variation are poorly understood. Here we test the hypothesis that the amount of leaf area, and its vertical arrangement, predicts ANPP when other variables are held constant. Using measurements from airborne lidar in a lowland Neotropical rain forest, we quantify vertical leaf-area profiles and develop models of ANPP driven by leaf area and...

Data from: Targeting global conservation funding to limit immediate biodiversity declines

Anthony Waldron, Arne O. Mooers, Daniel C. Miller, Nate Nibbelink, David Redding, Tyler S. Kuhn, J. Timmons Roberts & John L. Gittleman
Inadequate funding levels are a major impediment to effective global biodiversity conservation and are likely associated with recent failures to meet United Nations biodiversity targets. Some countries are more severely underfunded than others and therefore represent urgent financial priorities. However, attempts to identify these highly underfunded countries have been hampered for decades by poor and incomplete data on actual spending, coupled with uncertainty and lack of consensus over the relative size of spending gaps. Here,...

Data from: The effect of population bottlenecks on mutation rate evolution in asexual populations

Yevgeniy Raynes, Angela L. Halstead & Paul D. Sniegowski
In the absence of recombination, a mutator allele can spread through a population by hitchhiking with beneficial mutations that appear in its genetic background. Theoretical studies over the past decade have shown that the survival and fixation probability of beneficial mutations can be severely reduced by population size bottlenecks. Here, we use computational modelling and evolution experiments with the yeast S. cerevisiae to examine whether population bottlenecks can affect mutator dynamics in adapting asexual populations....

Clinging ability is related to particular aspects of foot morphology in salamanders

Erica Baken & Mary Kate O'Donnell
The interaction between morphology, performance, and ecology has long been studied in order to explain variation in the natural world. Within arboreal salamanders, diversification in foot morphology and microhabitat use are thought to be linked by the impact of foot size and shape on clinging and climbing performance, resulting in an ability to access new habitats. We examine whether various foot shape metrics correlate with stationary cling performance and microhabitat to explicitly quantify this performance...

Data from: Activation of autophagy during normothermic machine perfusion of discarded livers is associated with improved hepatocellular function

Anders Ohman, Siavash Raigani, John Santiago, Megan Heaney, Joan Boylan, Nicola Parry, Cailah Carroll, Sofia Baptista, Korkut Uygun, Phillip Gruppuso, Jennifer Sanders & Heidi Yeh
Liver transplantation is hampered by a severe shortage of donor organs. Normothermic machine perfusion (NMP) of donor livers allows dynamic preservation in addition to viability assessment prior to transplantation. Little is known about the injury and repair mechanisms induced during NMP. To investigate these mechanisms, we examined gene and protein expression changes in a cohort of discarded human livers, stratified by hepatocellular function, during NMP. Six human livers acquired through donation after circulatory death (DCD)...

Social and abiotic factors differentially affect plumage ornamentation of young and old males in an Australian songbird

Joseph F. Welklin, Samantha M. Lantz, Sarah Khalil, Nicole M. Moody, Jordan Karubian & Michael S. Webster
Both abiotic environmental conditions and variation in social environment are known to impact the acquisition of sexual signals. However, the influences of abiotic environmental and social factors are rarely compared to each other. Here we test the relative importance of these factors in determining whether and when male red-backed fairywrens (Malurus melanocephalus) moult into a known sexual signal, ornamented breeding plumage. One-year-old male red-backed fairywrens vary in whether or not they acquire ornamentation, whereas males...

Ecological and behavioral mechanisms of density-dependent habitat expansion in a recovering African ungulate population

Justine A. Becker, Matthew Hutchinson, Arjun Potter, Shinkyu Park, Jennifer Guyton, Kyler Abernathy, Victor Americo, Ana Gledis Da Conceiçāo, Tyler Kartzinel, Luca Kuziel, Naomi Leonard, Eli Lorenzi, Nuno Martins, Johan Pansu, William Scott, Maria Stahl, Kai Torrens, Marc Stalmans, Ryan Long & Robert Pringle
Major disturbances can temporarily remove factors that otherwise constrain population abundance and distribution. During such windows of relaxed top-down and/or bottom-up control, ungulate populations can grow rapidly, eventually leading to resource depletion and density-dependent expansion into less-preferred habitats. Although many studies have explored the demographic outcomes and ecological impacts of these processes, fewer have examined the individual-level mechanisms by which they occur. We investigated these mechanisms in Gorongosa National Park, where the Mozambican Civil War...

Canopy height distributions and estimated above-ground biomass across a tropical rain forest landscape in Costa Rica, 1992-2018

David Clark, Deborah Clark & James Kellner
This publication presents four related data sets that describe canopy height distributions and estimated above-ground biomass across an old-growth tropical rain forest landscape at the La Selva Biological Station, Costa Rica, from 1992 – 2018. One data set contains measured forest heights that were taken annually from 1999-2018 at 231 points per plot in 18 0.50 ha forest inventory plots (9 plots in 1999, 18 thereafter). The second data set contains data from an annual...

Ecological consequences of large herbivore exclusion in an African savanna: 12 years of data from the UHURU experiment

Jesse Alston, Courtney Reed, Leo Khasoha, Bianca Brown, Gilbert Busienei, Nathaniel Carlson, Tyler Coverdale, Megan Dudenhoeffer, Marissa Dyck, John Ekeno, Abdikadir Hassan, Rhianna Hohbein, Rhiannon Jakopak, Buas Kimiti, Samson Kurukura, Peter Lokeny, Allison Louthan, Simon Musila, Paul Musili, Tosca Tindall, Sarah Weiner, Tyler Kartzinel, Todd Palmer, Robert Pringle & Jacob Goheen
Diverse communities of large mammalian herbivores (LMH), once widespread, are now rare. LMH exert strong direct and indirect effects on community structure and ecosystem functions, and measuring these effects is important for testing ecological theory and for understanding past, current, and future environmental change. This in turn requires long-term experimental manipulations, owing to the slow and often nonlinear responses of populations and assemblages to LMH removal. Moreover, the effects of particular species or body-size classes...

Data from: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification

Bianca Saladin, Andrew B. Leslie, Rafael O. Wueest, Glenn Litsios, Elena Conti, Nicolas Salamin & Niklaus E. Zimmermann
Background: The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies, mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular phylogeny that makes use of the rich pine fossil record, and this study is the first to estimate the divergence...

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