67 Works

Data from: A practical introduction to random forest for genetic association studies in ecology and evolution

Marine S.O. Brieuc, Charles D. Waters, Daniel P. Drinan, Kerry Ann Naish & Marine S. O. Brieuc
Large genomic studies are becoming increasingly common with advances in sequencing technology, and our ability to understand how genomic variation influences phenotypic variation between individuals has never been greater. The exploration of such relationships first requires the identification of associations between molecular markers and phenotypes. Here we explore the use of Random Forest (RF), a powerful machine learning algorithm, in genomic studies to discern loci underlying both discrete and quantitative traits, particularly when studying wild...

Data from: Parental habituation to human disturbance over time reduces fear of humans in coyote offspring

Christopher J. Schell, Julie K. Young, Elizabeth V. Lonsdorf, Rachel M. Santymie, Jill M. Mateo & Rachel M. Santymire
A fundamental tenet of maternal effects assumes that maternal variance over time should have discordant consequences for offspring traits across litters. Yet, seldom are parents observed across multiple reproductive bouts, with few studies considering anthropogenic disturbances as an ecological driver of maternal effects. We observed captive coyote (Canis latrans) pairs over two successive litters to determine whether among-litter differences in behavior (i.e., risk-taking) and hormones (i.e., cortisol and testosterone) corresponded with parental plasticity in habituation....

Data from: Genetic signals of artificial and natural dispersal linked to colonization of South America by non-native Chinook salmon (Oncorhynchus tshawytscha)

Daniel Gomez-Uchida, Diego Cañas-Rojas, Carla M. Riva-Rossi, Javier E. Ciancio, Miguel A. Pascual, Billy Ernst, Eduardo Aedo, Selim S. Musleh, Francisca Valenzuela-Aguayo, Thomas P. Quinn, James E. Seeb & Lisa W. Seeb
Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non-native populations. Yet, our understanding of how artificial (human-mediated) and natural dispersal pathways of non-native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the widespread colonization of Chinook salmon Oncorhynchus tshawytscha in South America, mediated by both dispersal pathways, to address these issues using data from a panel of polymorphic SNPs. First, genetic diversity and the...

Data from: The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life

Walter Jetz & R. Alexander Pyron
Human activities continue to erode the tree of life, requiring us to prioritize research and conservation. Amphibians represent key victims and bellwethers of global change, and the need for action to conserve them is drastically outpacing knowledge. We provide a phylogeny incorporating nearly all extant amphibians (7,238 species). Current amphibian diversity is composed of both older, depauperate lineages and extensive, more recent tropical radiations found in select clades. Frog and salamander diversification increased strongly after...

Data from: Geometric morphometrics reveal altered corpus callosum shape in pyridoxine-dependent epilepsy

Gabriela Oesch, A. Murat Maga, Seth D. Friedman, Sandra L. Poliachik, Christopher B. Budech, Jason N. Wright, Levinus A. Bok & Sidney M. Gospe
Objective: To evaluate the features and maturational changes in overall callosal shape in patients with pyridoxine-dependent epilepsy (PDE). Methods: Measurements were conducted through landmark based geometric morphometrics applied on cerebral MRIs of PDE patients and age-matched control subjects. The outline of the corpus callosum was manually traced in the midsagittal plane. 300 semi-landmarks along the outline were collected and underwent statistical generalized Procrustes analysis. An allometric regression was applied to evaluate the callosal shape due...

Data from: Scale‐dependent spatial patterns in benthic communities around a tropical island seascape

Eoghan A. Aston, Gareth J. Williams, J. A. Mattias Green, Andrew J. Davies, Lisa M. Wedding, Jamison M. Gove, Jean-Baptiste Jouffray, Timothy T. Jones & Jeanette Clark
Understanding and predicting patterns of spatial organization across ecological communities is central to the field of landscape ecology, and a similar line of inquiry has begun to evolve sub‐tidally among seascape ecologists. Much of our current understanding of the processes driving marine community patterns, particularly in the tropics, has come from small‐scale, spatially‐discrete data that are often not representative of the broader seascape. Here we expand the spatial extent of seascape ecology studies and combine...

Data from: Sexual dimorphism modifies habitat‐associated divergence: evidence from beach and creek breeding sockeye salmon

Krista B. Oke, Elena Motivans, Thomas P. Quinn & Andrew P. Hendry
Studies of parallel or convergent evolution (the repeated, independent evolution of similar traits in similar habitats) rarely explicitly quantify the extent of parallelism (i.e., variation in the direction and/or magnitude of divergence) between the sexes; instead they often investigate both sexes together or exclude one sex. However, differences in male and female patterns of divergence could contribute to overall variation in the extent of parallelism among ecotype pairs, especially in sexually dimorphic traits. Failing to...

Data from: Origins of East Asian Summer Monsoon Seasonality

John Chiang, Wenwen Kong, Chi-Hua Wu & David Battisti
Climatological model output used in Chiang et al. (2019), "Origins of East Asian Summer Monsoon Seasonality".

Data from: Intercomparison of photogrammetry software for three-dimensional vegetation modelling

Alexandra Probst, Demetrios Gatziolis & Nikolay Strigul
Photogrammetry-based 3D reconstruction of objects is becoming increasingly appealing in research areas unrelated to computer vision. It has the potential to facilitate the assessment of forest inventory-related parameters by enabling or expediting resource measurements in the field. We hereby compare several implementations of photogrammetric algorithms (CMVS/PMVS, CMPMVS, MVE, OpenMVS, SURE, and Agisoft PhotoScan) with respect to their performance in vegetation assessment. The evaluation is based on (a) a virtual scene where the precise location and...

Data from: Genomewide association analyses of fitness traits in captive-reared Chinook salmon: applications in evaluating conservation strategies

Charles D. Waters, Jeffrey J. Hard, Marine S.O. Brieuc, David E. Fast, Kenneth I. Warheit, Curtis M. Knudsen, William J. Bosch, Kerry A. Naish & Marine S. O. Brieuc
A novel application of genome-wide association analyses is to use trait-associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive- and wild-origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus...

Data from: History dependence in insect flight decisions during odor tracking

Rich Pang, Floris Van Breugel, Michael Dickinson, Jeffrey A. Riffell & Adrienne Fairhall
Natural decision-making often involves extended decision sequences in response to variable stimuli with complex structure. As an example, many animals follow odor plumes to locate food sources or mates, but turbulence breaks up the advected odor signal into intermittent filaments and puffs. This scenario provides an opportunity to ask how animals use sparse, instantaneous, and stochastic signal encounters to generate goal-oriented behavioral sequences. Here we examined the trajectories of flying fruit flies (Drosophila melanogaster) and...

Data from: Artificial selection on reproductive timing in hatchery salmon drives a phenological shift and potential maladaptation to climate change

Michael D. Tillotson, Heidy K. Barnett, Mary E. Buthimethee, Michele E. Koehler & Thomas P. Quinn
The timing of breeding migration and reproduction links generations and substantially influences individual fitness. In salmonid fishes, such phenological events (seasonal return to fresh water and spawning) vary among populations but are consistent among years, indicating local adaptation in these traits to prevailing environmental conditions. Changing reproductive phenology has been observed in many populations of salmonids, and is sometimes attributed to adaptive responses to climate change. The sockeye salmon spawning in the Cedar River near...

Data from: Taxonomy-based hierarchical analysis of natural mortality: polar and sub-polar phocid seals

Irina S. Trukhanova, Paul B. Conn & Peter L. Boveng
Knowledge of life‐history parameters is frequently lacking in many species and populations, often because they are cryptic or logistically challenging to study, but also because life‐history parameters can be difficult to estimate with adequate precision. We suggest using hierarchical Bayesian analysis (HBA) to analyze variation in life‐history parameters among related species, with prior variance components representing shared taxonomy, phenotypic plasticity, and observation error. We develop such a framework to analyze U‐shaped natural mortality patterns typical...

Data from: Accounting for observation processes across multiple levels of uncertainty improves inference of species distributions and guides adaptive sampling of environmental DNA

Amy J. Davis, Kelly E. Williams, Nathan P. Snow, Kim M. Pepin & Antoinette J. Piaggio
Understanding factors that influence observation processes is critical for accurate assessment of underlying ecological processes. When indirect methods of detection, such as environmental DNA, are used to determine species presence, additional levels of uncertainty from observation processes need to be accounted for. We conducted a field trial to evaluate observation processes of a terrestrial invasive species (wild pigs- Sus scrofa) from DNA in water bodies. We used a multi-scale occupancy analysis to estimate different levels...

Data from: Heat tolerance is more variable than cold tolerance across species of Iberian lizards after controlling for intraspecific variation

Salvador Herrando-Pérez, Camila Monasterio, Wouter Beukema, Verónica Gomes, Francisco Gomes Ferri-Yáñez, Josabel Belliure, Steven L. Chown, Lauren B Buckley, David R. Vieites & Miguel B. Araújo
The widespread observation that heat tolerance is less variable than cold tolerance (‘cold-tolerance asymmetry’) leads to the prediction that species exposed to temperatures near their thermal maxima should have reduced evolutionary potential for adapting to climate warming. However, the prediction is largely supported by species-level global studies based on single estimates of both physiological metrics per taxon. We ask if cold-tolerance asymmetry holds for Iberian lizards after accounting for intraspecific variation in critical thermal maxima...

Data from: Variation in growth and developmental responses to supraoptimal temperatures near latitudinal range limits of gypsy moth Lymantria dispar (L.), an expanding invasive species

Lily M. Thompson, Trevor M. Faske, Nana Banahene, Dominique Grim, Salvatore J. Agosta, Dylan Parry, Patrick C. Tobin, Derek M. Johnson & Kristine L. Grayson
Variation in thermal performance within and between populations provides the potential for adaptive responses to increasing temperatures associated with climate change. Organisms experiencing temperatures above their optimum on a thermal performance curve exhibit rapid declines in function and these supraoptimal temperatures can be a critical physiological component of range limits. The gypsy moth, Lymantria dispar (L.) (Lepidoptera: Erebidae), is one of the best-documented biological invasions and factors driving its spatial spread are of significant ecological...

Data from: Urban nectarivorous bird communities in Cape Town, South Africa, are structured by ecological generalisation and resource distribution

Anina Coetzee, Phoebe Barnard & Anton Pauw
Biological communities are increasingly faced with novel urban habitats and their response may depend on a combination of biological and habitat traits. The response of pollinator species to urban habitats are of particular importance because all species involved in the pollination mutualism may be affected. Nectarivorous bird communities worldwide show varying tolerances to urban areas, but studies from Africa are lacking. We investigated nectarivorous bird communities in a medium-sized South African city and asked which...

Data from: Population responses of common ravens to reintroduced gray wolves

Lauren E. Walker, John M. Marzluff, Matthew C. Metz, Aaron J. Wirsing, L. Monika Moskal, Daniel R. Stahler & Douglas W. Smith
1. Top predators have cascading effects throughout the food web but their impacts on scavenger abundance are largely unknown. Gray wolves (Canis lupus) provide carrion to a suite of scavenger species, including the common raven (Corvus corax). Ravens are wide-ranging and intelligent omnivores that commonly take advantage of anthropogenic food resources. In areas where they overlap with wolves, however, ravens are numerous and ubiquitous scavengers of wolf-acquired carrion. 2. We aimed to determine whether subsidies...

Data from: Geomagnetic field influences upward movement of young Chinook salmon emerging from nests

Nathan F. Putman, Michelle M. Scanlan, Amanda M. Pollock, Joseph P. O'Neil, Ryan B. Couture, Joseph S. Stoner, Thomas P. Quinn, Kenneth J. Lohmann, David L.G. Noakes & David L. G. Noakes
Organisms use a variety of environmental cues to orient their movements in three-dimensional space. Here, we show that the upward movement of young Chinook salmon (Oncorhynchus tshawytscha) emerging from gravel nests is influenced by the geomagnetic field. Fish in the ambient geomagnetic field travelled farther upwards through substrate than did fish tested in a field with the vertical component inverted. This suggests that the magnetic field is one of several factors that influences emergence from...

Data from: Animals alter precipitation legacies: trophic and ecosystem engineering effects on plant community temporal dynamics

Joshua B. Grinath, Nicolas Deguines, John W. Chesnut, Laura R. Prugh, Justin S. Brashares & Katharine N. Suding
1. Multi-year precipitation ‘legacies’ can have stronger effects on plant community composition than rainfall in the current growing season, but variation in the magnitude of these effects is not fully understood. Direct interactions between plants and animals, such as herbivory, and indirect interactions, such as ecosystem engineering (via changes in the physical environment), may influence precipitation legacies by altering mechanisms of lagged effects. However, the role of direct and indirect plant-animal interactions in determining the...

Data from: Large mammal declines and the incipient loss of mammal-bird mutualisms in an African savanna ecosystem

Nathan Diplock, Kate Johnston, Antoine Mellon, Laura Mitchell, Madison Moore, Daniel Schneider, Alyssa Taylor, Jess Whitney, Kera Zegar, John Kioko & Christian Kiffner
Over the past half-century, large mammal populations have declined substantially throughout East Africa, mainly due to habitat loss and unsustainable direct exploitation. While it has been acknowledged that the loss of large mammals can have direct and cascading effects on community composition and ecosystem characteristics, limited quantitative work has been done on how declines of large herbivore populations impacts the abundance of mutualistic symbionts. Using a space-for-time observational approach, we quantified the large mammal community...

Data from: Influence of a growth hormone transgene on the genetic architecture of growth-related traits: a comparative analysis between transgenic and wild-type coho salmon

Miyako Kodama, Kerry A. Naish & Robert H. Devlin
Genetic engineering has been increasingly applied to many commercially important plant and animal species, generating phenotypic changes that are not observed in natural populations and creating genetic interactions that have not experienced natural selection. The degree to and way in which such human-induced genetic variation interacts with the rest of the genome is currently largely unknown. Integrating such information into ecological and risk assessment frameworks is crucial to understand the potential effects of genetically modified...

Data from: Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

Dorothee Hodapp, Elizabeth T. Borer, W. Stanley Harpole, Eric M. Lind, Eric W. Seabloom, Peter B. Adler, Juan Alberti, Carlos A. Arnillas, Jonathan D. Bakker, Lori Biederman, Marc Cadotte, Elsa E. Cleland, Scott Collins, Philip A. Fay, Jennifer Firn, Nicole Hagenah, Yann Hautier, Oscar Iribarne, Johannes M.H. Knops, Rebecca L. McCulley, Andrew MacDougall, Joslin L. Moore, John W. Morgan, Brent Mortensen, Kimberly J. La Pierre … & Johannes M. H. Knops
Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta-diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major...

Data from: Optimal foraging or surplus killing: selective consumption and discarding of salmon by brown bears

Alexandra E. Lincoln & Thomas P. Quinn
Selective consumption of prey by predators, observed in many animals, is often attributed to optimal foraging. Consistent with this idea, brown bears (Ursus arctos) often exhibit partial consumption, feeding exclusively on lipid-rich tissues of Pacific salmon (Oncorhynchus spp.), and discarding remains. However, bears also kill and abandon salmon without consuming any tissue. These discarded fish may be consistent with optimal foraging choices if they are of poor quality and if bears have easy access to...

Data from: Estimating infection prevalence: best practices and their theoretical underpinnings

Ian F. Miller, India Schneider-Crease, Charles L. Nunn & Michael P. Muehlenbein
Accurately estimating infection prevalence is fundamental to the study of population health, disease dynamics, and infection risk factors. Prevalence is estimated as the proportion of infected individuals (“individual-based estimation”), but is also estimated as the proportion of samples from which the disease-causing organisms are recovered (“anonymous estimation”). The latter method is often used when researchers lack information on individual host identity, which can occur during noninvasive sampling of wild populations or when the individual that...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Washington
  • Utah State University
  • Duke University
  • University of Minnesota
  • University of California, Berkeley
  • Alaska Fisheries Science Center
  • United States Department of Agriculture
  • McGill University
  • University of Oslo
  • Monash University