334 Works

Data for: Environmental and anthropogenic constraints on animal space use drive extinction risk worldwide

Myriam R. Hirt, Andrew D. Barnes, Alessandro Gentile, Laura J. Pollock, Benjamin Rosenbaum, Wilfried Thuiller, Marlee A. Tucker & Ulrich Brose
Animals require a certain amount of habitat to persist and thrive, and habitat loss is one of the most critical drivers of global biodiversity decline. While habitat requirements have been predicted by relationships between species traits and home range size, little is known about constraints imposed by environmental conditions and human impacts on a global scale. Our meta-analysis of 395 vertebrate species shows that global climate gradients in temperature and precipitation exert indirect effects via...

DNA sequences of transgenes detected via environmental DNA (raw ABI files, processed FASTA files, and reference alignments)

Charles Xu, Claire Ramsay, Mitra Cowan, Mehrnoush Dehghani, Paul Lasko & Rowan Barrett
We demonstrate that simple, non-invasive environmental DNA (eDNA) methods can detect transgenes of genetically modified (GM) animals from terrestrial and aquatic sources in invertebrate and vertebrate systems. We detected transgenic fragments between 82-234 bp through targeted PCR amplification of environmental DNA extracted from food media of GM fruit flies (Drosophila melanogaster), feces, urine, and saliva of GM laboratory mice (Mus musculus), and aquarium water of GM tetra fish (Gymnocorymbus ternetzi). With rapidly growing accessibility of...

Data to Prior exposure to stress allows the maintenance of an ecosystem cycle following severe acidification

Sofia Van Moorsel, Justin Marleau, Andrew Gonzalez, Owen Petchey, Charles Bazerghi & Jorge Negrin Dastis
This freshwater mesocosm study was conducted in 19 out of 110 mesocosms at the Large Experimental Array of Ponds (LEAP) at the Gault Nature Reserve in Mont-St-Hilaire, QC, Canada (45°32' N, 73°08' W, 122 m a.s.l.) between May and October 2018 for a total of 147 days. On 24 May 2018, the mesocosms (1100L stock tanks, Rubbermaid, Huntersville, NC, USA) were filled with approximately 1000 liters of unfiltered lake water via a pipeline from oligotrophic...

Supplemental material: Astrocyte biomarkers in Alzheimer’s disease: a systematic review and meta-analysis

Bruna Bellaver, João Pedro Ferrari-Souza, Lucas Uglione Da Ros, Stephen F. Carter, Elena Rodriguez-Vieitez, Agneta Nordberg, Luc Pellerin, Pedro Rosa-Neto, Douglas Teixeira Leffa & Eduardo R. Zimmer
Objective: To perform a systematic review and meta-analysis to determine whether fluid and imaging astrocyte biomarkers are altered in Alzheimer's disease (AD). Methods: PubMed and Web of Science databases were searched for articles reporting fluid or imaging astrocyte biomarkers in AD. Pooled effect sizes were determined with mean differences (SMD) using the Hedge’s G method with random-effects to determine biomarker performance. Adapted questions from QUADAS-2 were applied for quality assessment. A protocol for this study...

Temporally varying disruptive selection in the medium ground finch (Geospiza fortis).

Marc-Olivier Beausoleil, Luke Frishkoff, Leithen M'Gonigle, Joost Raeymaekers, Sarah Knutie, Luis De León, Sarah Huber, Jaime Chaves, Dale Clayton, Jennifer Koop, Jeffrey Podos, Diana Sharpe, Andrew Hendry & Rowan Barrett
Disruptive natural selection within populations exploiting different resources is considered to be a major driver of adaptive radiation and the production of biodiversity. Fitness functions, which describe the relationships between trait variation and fitness, can help to illuminate how this disruptive selection leads to population differentiation. However, a single fitness function represents only a particular selection regime over a single specified time period (often a single season or a year), and therefore might not capture...

Global meta-analysis of how marine upwelling affects herbivory

Andrew Sellers, Brian Leung & Mark Torchin
Aim: Nutrient subsidies support high primary productivity, increasing herbivore abundance and influencing their top-down control of producers. Wind-driven upwelling events deliver cold nutrient-rich water to coastlines, supporting highly productive marine environments. Results from studies comparing ecological processes across upwelling regimes are mixed: some reveal weaker herbivory in upwelling regions, while others report a positive relationship between upwelling and herbivory. In this synthesis we examine the influence of upwelling on top-down control of producers across the...

Data from: The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications

Khanh Huy Bui, Ichikawa Muneyoshi, Daniel Dai, Katya Peri, Ahmad Abdelzaher Zaki Khalifa, Muneyoshi Ichikawa, Shintaroh Kubo, Corbin Steven Black, Thomas S McAlear, Simon Veyron, Shun Kai Yang, Javier Vargas, Susanne Bechstedt & Jean-François Trempe
Microtubules are cytoskeletal structures involved in stability, transport and organization in the cell. The building blocks, the α- and β-tubulin heterodimers, form protofilaments that associate laterally into the hollow microtubule. Microtubule also exists as highly stable doublet microtubules in the cilia where stability is needed for ciliary beating and function. The doublet microtubule maintains its stability through interactions at its inner and outer junctions where its A- and B-tubules meet. Here, using cryo-electron microscopy, bioinformatics...

Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)

Meredith M. Doellman, Glen R. Hood, Jacob Gersfeld, Amanda Driscoe, Charles C.Y. Xu, Ryan N. Sheehy, Noah Holmes, Wee L. Yee & Jeffrey L. Feder
Insect pests destroy ~15% of all USA crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), is a major invasive pest threatening the multibillion-dollar apple industry in the Pacific Northwest USA. The fly is also sympatric with a benign but morphologically similar and genetically closely related species,...

Coping with the commute: behavioural responses to wind conditions in a foraging seabird

Philip Collins, Jonathan Green, Kyle Elliott, Peter Shaw, Lorraine Chivers, Scott Hatch & Lewis Halsey
Movement is a necessary yet energetically expensive process for motile animals. Yet how individuals modify their behaviour to take advantage of environmental conditions and hence optimise energetic costs during movement remains poorly understood. This is especially true for animals that move through environments where they cannot easily be observed. We examined the behaviour during commuting flights of black-legged kittiwakes Rissa tridactyla breeding on Middleton Island, Alaska in relation to wind conditions they face. By simultaneously...

Education is associated with Aβ burden in preclinical familial and sporadic Alzheimer’s disease

Julie Gonneaud, Christophe Bedetti, Alexa Pichet Binette, Tammie Benzinger, John Morris, Randall Bateman, Judes Poirier, John Breitner & Sylvia Villeneuve
Objective. To determine whether years of education and the ε4 risk allele at APOE influence β-amyloid pathology similarly in asymptomatic individuals with a family history of sporadic Alzheimer’s disease (AD) and pre-symptomatic autosomal dominant AD mutation carriers. Methods. We analyzed cross-sectional data from 106 asymptomatic individuals with a parental history of sporadic AD (PREVENT-AD cohort; age=67.28±4.72 years) and 117 pre-symptomatic autosomal dominant AD mutation carriers (DIAN cohort; age=34.00±9.43 years). All participants underwent structural MRI and...

Data from: DG-CA3 circuitry mediates hippocampal representations of latent information

Alexandra T. Keinath, Andrés Nieto-Posadas, Jennifer C. Robinson & Mark P. Brandon
Survival in complex environments necessitates a flexible navigation system that incorporates memory of recent behavior and associations. Yet, how the hippocampal spatial circuit represents latent information independent of sensory inputs and future goals has not been determined. To address this, we imaged the activity of large ensembles in subregion CA1 via wide-field fluorescent microscopy during a novel behavioral paradigm. Our results demonstrated that latent information is represented through reliable firing rate changes during unconstrained navigation....

Data from: Draft genome of the American eel (Anguilla rostrata)

Scott A. Pavey, Martin Laporte, Eric Normandeau, Jérémy Gaudin, Louis Létourneau, Sébastien Boisvert, Jacques Corbeil, Céline Audet & Louis Bernatchez
Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American Eel. This genome...

Data from: Exploring an alternative explanation for the second phase of viral decay: infection of short-lived cells in a drug-limited compartment during HAART

Steven Sanche, Thibault Mesplède, Nancy Sheehan, Jun Li, Fahima Nekka & Nancy L. Sheehan
Most HIV-infected patients who initiate combination antiretroviral therapy experience a viral load decline in several phases. These phases are characterized by different rates of viral load decay that decrease when transitioning from one phase to the next. There is no consensus as to the origin of these phases. One hypothesis put forward is that short- and long-lived infected cells are responsible for the first and second phases of decay, respectively. However, significant differences in drug...

Data from: Multilocus approaches for the measurement of selection on correlated genetic loci

Zachariah Gompert, Scott P. Egan, Rowan D. H. Barrett, Jeffrey L. Feder & Patrik Nosil
The study of ecological speciation is inherently linked to the study of selection. Methods for estimating phenotypic selection within a generation based on associations between trait values and fitness (e.g. survival) of individuals are established. These methods attempt to disentangle selection acting directly on a trait from indirect selection caused by correlations with other traits via multivariate statistical approaches (i.e. inference of selection gradients). The estimation of selection on genotypic or genomic variation could also...

Data from: New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts

David J. Weston, Richard A. Russell, Elizabeth Batty, Kirsten Jensen, David A. Stephens, Niall M. Adams & Paul S. Freemont
The nuclei of higher eukaryotic cells display compartmentalization and certain nuclear compartments have been shown to follow a degree of spatial organization. To date, the study of nuclear organization has often involved simple quantitative procedures that struggle with both the irregularity of the nuclear boundary and the problem of handling replicate images. Such studies typically focus on inter-object distance, rather than spatial location within the nucleus. The concern of this paper is the spatial preference...

Data from: Using simulations to evaluate Mantel-based methods for assessing landscape resistance to gene flow

Katherine A. Zeller, Tyler G. Creech, Katie L. Millette, Rachel S. Crowhurst, Robert A. Long, Helene H. Wagner, Niko Balkenhol & Erin L. Landguth
Mantel-based tests have been the primary analytical methods for understanding how landscape features influence observed spatial genetic structure. Simulation studies examining Mantel-based approaches have highlighted major challenges associated with the use of such tests and fueled debate on when the Mantel test is appropriate for landscape genetics studies. We aim to provide some clarity in this debate using spatially explicit, individual-based, genetic simulations to examine the effects of the following on the performance of Mantel-based...

Data from: Disentangling invasion processes in a dynamic shipping - boating network

Anaïs Lacoursière-Roussel, Christopher W. McKindsey, Dan G. Bock, Melania E. Cristescu, Frédéric Guichard, Philippe Girard & Pierre Legendre
The relative importance of multiple vectors to the initial establishment, spread, and population dynamics of invasive species remains poorly understood. This study used molecular methods to clarify the roles of commercial shipping and recreational boating in the invasion by the cosmopolitan tunicate, Botryllus schlosseri. We evaluated i) single vs. multiple introduction scenarios, ii) the relative importance of shipping and boating to primary introductions, iii) the interaction between these vectors for spread (i.e., the presence of...

Data from: Constraints on speciation suggested by comparing lake-stream stickleback divergence across two continents

Daniel Berner, Marius Roesti, Andrew P. Hendry & Walter Salzburger
Adaptation to ecologically distinct environments can coincide with the emergence of reproductive barriers. The outcome of this process is highly variable and can range along a continuum from weak population differentiation all the way to complete, genome-wide divergence. The factors determining how far diverging taxa will move along this continuum remain poorly understood but are most profitably investigated in taxa under replicate divergence. Here we explore determinants of progress toward speciation by comparing phenotypic and...

Data from: Revised Airlie House consensus guidelines for design and implementation of ALS clinical trials

Leonard H Van Den Berg, Eric Sorenson, Gary Gronseth, Eric A. Macklin, Jinsy Andrews, Robert H. Baloh, Michael Benatar, James D. Berry, Adriano Chio, Philippe Corcia, Angela Genge, Amelie K. Gubitz, Catherine Lomen-Hoerth, Christopher J. McDermott, Erik P. Pioro, Jeffrey Rosenfeld, Vincenzo Silani, Martin R. Turner, Markus Weber, Benjamin Rix Brooks, Robert G. Miller & Hiroshi Mitsumoto
Objective: To revise the 1999 Airlie House consensus guidelines for the design and implementation of preclinical therapeutic studies and clinical trials in amyotrophic lateral sclerosis (ALS). Methods: A consensus committee comprising 140 key members of the international ALS community (ALS researchers, clinicians, patient representatives, research funding representatives, industry and regulatory agencies) addressed nine areas of need within ALS research: 1. Pre-clinical studies; 2. Biological and phenotypic heterogeneity; 3. Outcome measures; 4. Disease-modifying and symptomatic interventions;...

Data from: Using adaptive traits to consider potential consequences of temporal variation in selection: male guppy colour through time and space

Kiyoko M. Gotanda & Andrew P. Hendry
Temporal variation in selection is typically evaluated by estimating and comparing selection coefficients in natural populations. Meta-analyses of these coefficients have yielded important insights, but selection coefficients are limited in several respects, including low statistical power, imperfect fitness surrogates, and uncertainty regarding consequences for trait change. A complementary approach without these limitations is to examine temporal variation in adaptive traits themselves, which is mechanistically easier and more directly relevant to evolutionary consequences. We illustrate this...

Data from: Experimental adaptation to marine conditions by a freshwater alga

Josianne Lachapelle, Graham Bell & Nick Colegrave
The marine-freshwater boundary has been suggested as one of the most difficult to cross for organisms. Salt is a major ecological factor and provides an unequalled range of ecological opportunity because marine habitats are much more extensive than freshwater habitats, and because salt strongly affects the structure of microbial communities. We exposed experimental populations of the freshwater alga Chlamydomonas reinhardtii to steadily increasing concentrations of salt. About 98% of the lines went extinct. The ones...

Data from: Does plasticity enhance or dampen phenotypic parallelism? A test with three lake-stream stickleback pairs.

Krista B. Oke, Mehvish Bukhari, Renaud Kaeuffer, Gregor Rolshausen, Katja Räsänen, Daniel I. Bolnick, Catherine L. Peichel & Andrew P. Hendry
Parallel (and convergent) phenotypic variation is most often studied in the wild, where it is difficult to disentangle genetic versus environmentally-induced effects. As a result, the potential contributions of phenotypic plasticity to parallelism (and non-parallelism) are rarely evaluated in a formal sense. Phenotypic parallelism could be enhanced by plasticity that causes stronger parallelism across populations in the wild than would be expected from genetic differences alone. Phenotypic parallelism could be dampened if site-specific plasticity induced...

Data for Interindividual variation in maximum aerobic metabolism varies with gill morphology and myocardial bioenergetics in Gulf killifish

Bernard Rees, Jessica Reemeyer & Brian Irving
This study asked whether interindividual variation in maximum and standard aerobic metabolic rates of the Gulf killifish, Fundulus grandis, correlate with gill morphology and cardiac mitochondrial bioenergetics, traits reflecting critical steps in the O2 transport cascade from the environment to the tissues. Maximum metabolic rate (MMR) was positively related to body mass, total gill filament length, and myocardial oxygen consumption during maximum oxidative phosphorylation (multiple R2 = 0.836). Standard metabolic rate (SMR) was positively related...

Environmental nucleic acids: a field-based comparison for monitoring freshwater habitats using eDNA and eRNA

Joanne Littlefair, Michael Rennie & Melania Cristescu
Nucleic acids released by organisms and isolated from environmental substrates are increasingly being used for molecular biomonitoring. While environmental DNA (eDNA) has received attention recently, the potential of environmental RNA as a biomonitoring tool remains less explored. Several recent studies using paired DNA and RNA metabarcoding of bulk samples suggest that RNA might better reflect “metabolically active” parts of the community. However, such studies mainly capture organismal eDNA and eRNA. For larger eukaryotes, isolation of...

Telomere length correlates with physiological and behavioural responses of a long-lived seabird to an ecologically-relevant challenge

Z Morgan Benowitz-Fredericks, Lindsay Lacey, Shannon Whelan, Alexis Will, Scott Hatch & Alexander Kitaysky
Determinants of individual variation in reallocation of limited resources towards self-maintenance versus reproduction are not well known. We tested the hypothesis that individual heterogeneity in long-term “somatic state” a) explains variation in endocrine and behavioural responses to environmental challenges, and b) is associated with variation in strategies for allocating to self-maintenance versus reproduction. We used relative telomere length as an indicator of somatic state and experimentally generated an abrupt short-term reduction of food availability (withdrawal...

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