392 Works

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 Musleh, Francisca Valenzuela-Aguayo, Thomas P. Quinn, James E. Seeb, Lisa W. Seeb & Selim S. Musleh
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: Precipitation alters interactions in a grassland ecological community

Nicolas Deguines, Justin S. Brashares & Laura R. Prugh
Climate change is transforming precipitation regimes world-wide. Changes in precipitation regimes are known to have powerful effects on plant productivity, but the consequences of these shifts for the dynamics of ecological communities are poorly understood. This knowledge gap hinders our ability to anticipate and mitigate the impacts of climate change on biodiversity. Precipitation may affect fauna through direct effects on physiology, behaviour or demography, through plant-mediated indirect effects, or by modifying interactions among species. In...

Data from: A new Late Cretaceous iguanomorph from North America and the origin of New World Pleurodonta (Squamata, Iguania)

David G. DeMar, Jack L. Conrad, Jason J. Head, David J. Varricchio & Gregory P. Wilson
Iguanomorpha (stem + crown Iguania) is a diverse squamate clade with members that predominate many modern American lizard ecosystems. However, the temporal and palaeobiogeographic origins of its constituent crown clades (e.g. Pleurodonta (basilisks, iguanas, and their relatives)) are poorly constrained, mainly due to a meagre Mesozoic-age fossil record. Here, we report on two nearly complete skeletons from the Late Cretaceous (Campanian) of North America that represent a new and relatively large-bodied and possibly herbivorous iguanomorph...

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: 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: 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: 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: 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: 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 & Kerry A. Naish
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: 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: 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: 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: 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: Phylogeny and new taxonomy of the Booted Eagles (Accipitriformes: Aquilinae)

Heather R. L. Lerner, Les Christidis, Anita Gamauf, Carole Griffiths, Elisabeth Haring, Christopher J. Huddleston, Sonia Kabra, Annett Kocum, Meade Krosby, Kirsti Kvaloy, David Mindell, Pamela Rasmussen, Nils Rov, Rachel Wadleigh, Michael Wink & Jan Ove Gjershaug
We present a phylogeny of all booted eagles (38 extant and one extinct species) based on analysis of published sequences from seven loci. We find molecular support for five major clades within the booted eagles: Nisaetus (10 species), Spizaetus (4 species), Clanga (3 species), Hieraaetus (6 species) and Aquila (11 species), requiring generic changes for 14 taxa. Additionally, we recommend that the Long-crested Eagle (Lophaetus occipitalis) and the Black Eagle (Ictinaetus malaiensis) remain in their...

Data from: Tracing the dynamics of gene transcripts after organismal death

Alexander E. Pozhitkov, Rafik Neme, Tomislav Domazet-Lošo, Brian G. Leroux, Shivani Soni, Diethard Tautz & Peter A. Noble
In life, genetic and epigenetic networks precisely coordinate the expression of genes—but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes and pathways are involved. We studied this by identifying mRNA transcripts that apparently increase in relative abundance after death, assessing their functions, and comparing their abundance profiles through postmortem time in two species, mouse and zebrafish. We found mRNA transcript profiles of 1063 genes became...

Data from: Spatial and temporal dynamics and value of nature-based recreation, estimated via social media

Laura J. Sonter, Keri B. Watson, Spencer A. Wood & Taylor H. Ricketts
Conserved lands provide multiple ecosystem services, including opportunities for nature-based recreation. Managing this service requires understanding the landscape attributes underpinning its provision, and how changes in land management affect its contribution to human wellbeing over time. However, evidence from both spatially explicit and temporally dynamic analyses is scarce, often due to data limitations. In this study, we investigated nature-based recreation within conserved lands in Vermont, USA. We used geotagged photographs uploaded to the photo-sharing website...

Data from: Forty years of seagrass population stability and resilience in an urbanizing estuary

Andrew Olaf Shelton, Tessa B. Francis, Blake E. Feist, Gregory D. Williams, Adam Lindquist, Phillip S. Levin, Philip S. Levin & Andrew O. Shelton
Coasts and estuaries contain among the most productive and ecologically important habitats in the world and face intense pressure from current and projected human activities, including coastal development. Seagrasses are a key habitat feature in many estuaries perceived to be in widespread decline owing to human actions. We use spatio-temporal models and a 41-year time series from 100s of km of shoreline which includes over 160 000 observations from Puget Sound, Washington, USA, to examine...

Data from: Genetic signatures of ecological diversity along an urbanization gradient

Ryan P. Kelly, James L. O'Donnell, Natalie C. Lowell, Andrew O. Shelton, Jameal F. Samhouri, Shannon M. Hennessey, Blake E. Feist & Gregory D. Williams
Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore...

Data from: Multiple natural enemies cause distance-dependent mortality at the seed-to-seedling transition

Evan C. Fricke, Joshua J. Tewksbury & Haldre S. Rogers
Specialised natural enemies maintain forest diversity by reducing tree survival in a density- or distance-dependent manner. Fungal pathogens, insects and mammals are the enemy types most commonly hypothesised to cause this phenomenon. Still, their relative importance remains largely unknown, as robust manipulative experiments have generally targeted a single enemy type and life history stage. Here, we use fungicide, insecticide and physical exclosure treatments to isolate the impacts of each enemy type on two life history...

Data from: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

James Starrett, Shahan Derkarabetian, Marshal Hedin, , John E. McCormack, Brant C. Faircloth & Robert W. Bryson
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic...

Data from: Use of glacial fronts by narwhals (Monodon monoceros) in West Greenland

Kristin L. Laidre, Twila Moon, Donna D.W. Hauser, Richard McGovern, Mads Peter Heide-Joergensen, Rune Dietz, Benjamin Hudson, Donna D. W. Hauser & Ben Hudson
Glacial fronts are important summer habitat for narwhals (Monodon monoceros), however, no studies have quantified which glacial properties attract whales. We investigated the importance of glacial habitats using telemetry data from n=15 whales in September 1993-1994 and 2006-2007 in Melville Bay, West Greenland. For 41 marine-terminating glaciers, we estimated 1) narwhal presence/absence, 2) number of 24 h periods spent at glaciers, and 3) the fraction of narwhals that visited each glacier (at 5, 7, and...

Data from: Morphological and functional maturity of the oral jaws covary with offspring size in Trinidadian guppies

Terry R. Dial, Luz Patricia Hernandez & Elizabeth L. Brainerd
Large size of individual offspring is routinely selected for in highly competitive environments, such as in low-predation populations of the Trinidadian guppy (Poecilia reticulata). Large guppy offspring outcompete their smaller conspecifics, but the functional mechanisms underlying this advantage are unknown. We measured jaw kinematics during benthic feeding and cranial musculoskeletal morphologies in neonates and juveniles from five populations of Trinidadian guppy and found that both kinematics and morphologies vary substantially with neonatal size. Rotation at...

Data for allometric equations of Chrysolepis sempervirens, Cornus sericea, Corylus cornuta ssp. californica, and Leucothoe davisiae.

James A. Lutz, J. A. Freund, A. J. Larson, M. E. Swanson, T. J. Furniss, K. M. L. Becker, E. M. Blomdahl, C. A. Cansier, S. J. Germain & S. M. A. Jeronimo

Data from: The oceanic biological pump: rapid carbon transfer to depth at continental margins during winter

Laurenz Thomsen, Jacopo Aguzzi, Corrado Costa, Fabio De Leo, Andrea Ogston & Autun Purser
The oceanic biological pump is responsible for the important transfer of CO2-C as POC “Particulate Organic Carbon” to the deep sea. It plays a decisive role in the Earth’s carbon cycle and significant effort is spent to quantify its strength. In this study we used synchronized daily time-series data of surface chlorophyll-a concentrations from the NASA’s MODIS satellite in combination with hourly to daily observations from sea surface buoys and from an Internet Operated Vehicle...

Data from: A phylogenomic perspective on the biogeography of skinks in the Plestiodon brevirostris group inferred from target enrichment of ultraconserved elements

, Charles W. Linkem, Carlos J. Pavón-Vázquez, Adrián Nieto-Montes De Oca, John Klicka, John E. McCormack & Robert W. Bryson
Aim: The aim of our study was to reconstruct ancestral geographic distributions from time-calibrated phylogenies generated from phylogenomic data to answer three broad questions about the biogeography of skinks in the Plestiodon brevirostris group: (1) Are biogeographic patterns correlated with the formation of the Trans-Mexican Volcanic Belt? (2) Do different methods of phylogenetic estimation result in different topologies? If so, (3) are biogeographic reconstructions impacted by the use of different phylogenetic trees? Location: Mexico. Methods:...

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