70 Works

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: Primary productivity explains size variation across the Pallid bat’s (Antrozous pallidus) western geographic range

Rochelle M. Kelly, Rachel Friedman & Sharlene E. Santana
1. Body size is associated with many aspects of the life history, ecology, and physiology of animals. Within a species, body size can vary substantially across space and time, and the mechanisms generating these patterns have been the focus of evolutionary and ecology research. 2. Bergmann’s Rule predicts a negative relationship between body size and temperature across the geographic range of endothermic animals; larger animals have a lower surface to volume ratio, which would allow...

Data from: Leapfrogging the Mexican highlands: influence of biogeographical and ecological factors on the diversification of highland species

Itzue W. Caviedes-Solis & Adam D. Leaché
In order to understand the processes that generate and maintain diversity, it is important to disentangle the roles of ecology and geography in speciation. We investigated the biogeographical and ecological factors that influenced the diversification of tree frogs (genus Sarcohyla) in the Mexican highlands, a region with high levels of endemism. Using single nucleotide polymorphism data for 58 samples, we found support for seven distinct genetic clusters within the Sarcohyla bistincta species complex, corresponding to...

Data from: Environmental drivers of forest structure and stem turnover across Venezuelan tropical forests

Emilio Vilanova, Hirma Ramirez-Angulo, Armando Torres-Lezama, Gerardo Aymard, Luis Gámez, Cristabel Durán, Lionel Hernández, Rafael Herrera, Geertje Van Der Heijden, Oliver L. Phillips & Gregory J. Ettl
Using data from 50 long-term permanent plots from across Venezuelan forests in northern South America, we explored large-scale patterns of stem turnover, aboveground biomass (AGB) and woody productivity (AGWP), and the relationships between them and with potential climatic drivers. We used principal component analysis coupled with generalized least squares models to analyze the relationship between climate, forest structure and stem dynamics. Two major axes associated with orthogonal temperature and moisture gradients effectively described more than...

Data from: Quantifying uncertainty due to fission-fusion dynamics as a component of social complexity

Gabriel Ramos-Fernandez, Andrew J. King, Jacinta C. Beehner, Thore J. Bergman, Margaret C. Crofoot, Anthony Di Fiore, Julia Lehmann, Colleen M. Schaffner, Noah Snyder-Mackler, Klaus Zuberbühler, Filippo Aureli & Denis Boyer
Groups of animals (including humans) may show flexible grouping patterns, in which temporary aggregations or subgroups come together and split, changing composition over short temporal scales, i.e. fission and fusion). A high degree of fission-fusion dynamics may constrain the regulation of social relationships, introducing uncertainty in interactions between group members. Here we use Shannon's entropy to quantify the predictability of subgroup composition for three species known to differ in the way their subgroups come together...

Data from: A genomic evaluation of taxonomic trends through time in coast horned lizards (genus Phrynosoma)

Adam D. Leache, Matt T. McElroy, Anna Trinh & Matthew T. McElroy
Determining the boundaries between species and deciding when to describe new species are challenging practices that are particularly difficult in groups with high levels of geographic variation. The coast horned lizards (Phrynosoma blainvillii, P. cerroense, and P. coronatum) have an extensive geographic distribution spanning many distinctive ecological regions ranging from northern California to the Cape Region of Baja California, Mexico, and populations differ substantially with respect to external morphology across much of this range. The...

Data from: Self-reported functional status predicts post-operative outcomes in non-cardiac surgery patients with pulmonary hypertension

Aalap C. Shah, Kevin Ma, David Faraoni, Daniel C.S. Oh, G. Alec Rooke, Gail A. Van Norman & Daniel C. S. Oh
BACKGROUND: Pulmonary hypertension (PHTN) is associated with increased post-procedure morbidity and mortality. Pre-procedure echocardiography (ECHO) is a widely used tool for evaluation of these patients, but its accuracy in predicting post-procedure outcomes is unproven. Self-reported exercise tolerance has not been evaluated for operative risk stratification of PHTN patients. OBJECTIVE: We analyzed whether self-reported exercise tolerance predicts outcomes (hospi-tal length-of-stay [LOS], mortality and morbidity) in PHTN patients (WHO Class I - V) under-going anesthesia and surgery....

Data from: Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs

Jennifer Firn, James M. McGree, Eric Harvey, Habacuc Flores-Moreno, Martin Schütz, Yvonne M. Buckley, Elizabeth T. Borer, Eric W. Seabloom, Kimberly J. La Pierre, Andrew M. MacDougall, Suzanne M. Prober, Carly J. Stevens, Lauren L. Sullivan, Erica Porter, Emma Ladouceur, Charlotte Allen, Karine H. Moromizato, John W. Morgan, W. Stanley Harpole, Yann Hautier, Nico Eisenhauer, Justin P. Wright, Peter B. Adler, Carlos Alberto Arnillas, Jonathan D. Bakker … & Anita C. Risch
Leaf traits are frequently measured in ecology to provide a ‘common currency’ for predicting how anthropogenic pressures impact ecosystem function. Here, we test whether leaf traits consistently respond to experimental treatments across 27 globally distributed grassland sites across 4 continents. We find that specific leaf area (leaf area per unit mass)—a commonly measured morphological trait inferring shifts between plant growth strategies—did not respond to up to four years of soil nutrient additions. Leaf nitrogen, phosphorus...

Nanoparticle-mediated delivery of Tanshinone IIA reduces adverse cardiac remodeling following myocardial infarctions in a mice model: role of NF-κB pathway

Shuai Mao, Lei Wang, Peipei Chen, Yong Lan, Rui Guo & Minzhou Zhang
Our previous works have shown that tanshinone IIA inhibited maladaptive extracellular matrix remodeling in cardiac fibroblasts implicating its potential role in treating of pathologic cardiac remodeling. However, the intrinsically poor solubility and bioavailability of tanshinone IIA hindered its clinical application. Here we develop monomethoxy-poly (ethylene glycol)-poly (lactic acid)-D-α-Tocopheryl polyethylene glycol 1000 succinate (mPEG-PLA-TPGS) nanoparticle incorporating tanshinone IIA (tanshinone IIA-NPs) and study its efficacy in post-infarction left ventricular (LV) remodeling. Male C57BL/6 mice underwent left coronary...

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: 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: A global test of the cold-climate hypothesis for the evolution of viviparity of squamate reptiles

Liang Ma, Lauren B. Buckley, Raymond B. Huey & Wei-Guo Du
Aim The evolution of viviparity in squamate reptiles has attracted considerable scientific attention since the beginning of last century. The cold climate hypothesis posits that cold regions favor viviparity (and therefore the incidence of viviparous squamates is increased in these regions) because viviparous females can use thermoregulatory behavior to shorten embryonic developmental time and to reduce exposure of embryos to stressful temperatures. However, a rigorous global-scale test of the impact of viviparity on the developmental...

Registration Year

  • 2018
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Affiliations

  • University of Washington
    70
  • The Ohio State University
    4
  • Charité - University Medicine Berlin
    3
  • Yunnan University
    3
  • Sun Yat-sen University
    3
  • Zhejiang University
    3
  • Guangdong University of Foreign Studies
    3
  • Utah State University
    3
  • Air Force Medical University
    3
  • Fudan University Shanghai Cancer Center
    3