1,276 Works

Newick trees for \"Within-patient phylogenetic reconstruction reveals early events in Barrett's Esophagus\"

Mary Kuhner & Lucian Smith
Newick format within-patient phylogenetic trees for a Barrett's Esophagus WGS dataset

Data from - Ecological insights from three decades of animal movement tracking across a changing Arctic

Gil Bohrer, Sarah Davidson, Eliezer Gurarie, Scott LaPoint, Peter Mahoney, Emma Grier, Ophélie Couriot, Allicia Kelly, Bryan Bedrosian, Jerrold Belant, Travis Booms, Bridget Borg, Stan Boutin, Erica Craig, Tracy Davison, Robert Domenech, James Hodson, Kyle Joly, Nicholas Larter, A. David M. Latham, Stephen Lewis, Carol McIntyre, Tricia Miller, Kelsey Russell, Dale Seip … & Judy Williams
We provide here the data used in analysis of 3 test cases, presented in the manuscript "Ecological insights from three decades of animal movement tracking across a changing Arctic". We utilized the new Arctic Animal Movement Archive (AAMA), a growing collection of 201 standardized terrestrial and marine animal tracking studies from 1991–present. The AAMA supports public data discovery, preserves fundamental baseline data for the future, and facilitates efficient, collaborative data analysis. With three AAMA-based case...

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: 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: 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: 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: On the comparative biology of mammalian telomeres: telomere length co-evolves with body mass, lifespan and cancer risk

Michael Le Pepke & Dan T. A. Eisenberg
Telomeres, the short repetitive DNA sequences that cap the ends of linear chromosomes, shorten during cell division and are implicated in senescence in most species. Telomerase can rebuild telomeres but is repressed in many mammals that exhibit replicative senescence, presumably as a tumor suppression mechanism. It is therefore important to understand the co-evolution of telomere biology and life-history traits that has shaped the diversity of senescence patterns across species. Gomes et al. (2011) produced a...

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 to replicate: Forecasting community reassembly using climate-linked spatio-temporal ecosystem models

James Thorson, Mayumi Arimitsu, Lewis Barnett, Wei Cheng, Lisa Eisner, Alan Haynie, Albert Hermann, Kirstin Holsman, David Kimmel, Mike Lomas, Jon Richar & Elizabeth Siddon
Ecosystems are increasingly impacted by human activities, altering linkages among physical and biological components. Spatial community reassembly occurs when these human impacts modify the spatial overlap between system components, and there is need for practical tools to forecast spatial community reassembly at landscape scales using monitoring data. To illustrate a new approach, we extend a generalization of empirical orthogonal function (EOF) analysis, which involves a spatio-temporal ecosystem model that approximates coupled physical, biological, and human...

Data from: The utility of climatic water balance for ecological inference depends on vegetation physiology assumptions

Derek Young, Sean Jeronimo, Derek Churchill, Van Kane & Andrew Latimer
This repository contains the data and code supporting the analyses in the corresponding paper in Global Ecology and Biogeography (GEB). The abstract of the paper is as follows: Background: In modeling and explaining spatial vegetation patterns, ecologists have increasingly favored the use of climatic water balance variables, including actual evapotranspiration (AET) and climatic water deficit (CWD), for representing the hydrologic and energetic environment experienced by plants. Much of the interest in these variables lies in...

Supplemental material for: NINDS consensus diagnostic criteria for Traumatic Encephalopathy Syndrome

Douglas Katz, Charles Bernick, David Dodick, Jesse Mez, Megan Mariani, Charles Adler, Michael Alosco, Laura Balcer, Sarah Banks, William Barr, David Brody, Robert Cantu, Kristen Dams-O'Connor, Yonas Geda, Barry Jordan, Thomas McAllister, Elaine Peskind, Ronald Petersen, Jennifer Wether, Ross Zafonte, Eimear Foley, Debra Babcock, Walter Koroshetz, Ann McKee, Martha Shenton … & Robert Stern
Objective: To develop evidence-informed, expert consensus research diagnostic criteria for Traumatic Encephalopathy Syndrome (TES), the clinical disorder associated with neuropathologically diagnosed Chronic Traumatic Encephalopathy (CTE). Methods: A panel of 20 expert clinician-scientists in neurology, neuropsychology, psychiatry, neurosurgery, and physical medicine and rehabilitation, from 11 academic institutions, participated in a modified Delphi procedure to achieve consensus, initiated at the First NINDS Consensus Workshop to Define the Diagnostic Criteria for TES, April, 2019. Prior to consensus, panelists...

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: 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: 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: 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: Effects of Bark Beetle Outbreaks on Forest Landscape Pattern in the Southern Rocky Mountains, U.S.A.

Kyle Rodman, Robert Andrus, Cori Butkiewicz, Teresa Chapman, Nathan Gill, Brian Harvey, Dominik Kulakowski, Niko Tutland, Thomas Veblen & Sarah Hart
Since the late 1990s, extensive outbreaks of native bark beetles (Curculionidae: Scolytinae) have affected coniferous forests throughout Europe and North America, driving changes in carbon storage, wildlife habitat, nutrient cycling, and water resource provisioning. Remote sensing is a crucial tool for quantifying the effects of these disturbances across broad landscapes. In particular, Landsat time series (LTS) are increasingly used to characterize outbreak dynamics, including the presence and severity of bark beetle-caused tree mortality, though broad-scale...

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: Local range boundaries versus large-scale tradeoffs: climatic and competitive constraints on tree growth

Leander D. L. Anderegg & Janneke HilleRisLambers
Species often respond to human‐caused climate change by shifting where they occur on the landscape. To anticipate these shifts, we need to understand the forces that determine where species currently occur. We tested whether a long‐hypothesised trade‐off between climate and competitive constraints explains where tree species grow on mountain slopes. Using tree rings, we reconstructed growth sensitivity to climate and competition in range centre and range margin tree populations in three climatically distinct regions. We...

Wildfire smoke affects detection of birds in Washington state

Olivia Sanderfoot
Wildfire smoke is likely to have direct health effects on birds, as well as influence movement, vocalization, and other avian behaviors. These behavioral changes may affect if and how birds are observed in the wild, although research on the effects of wildfire smoke on bird behavior is limited. To evaluate how wildfire smoke affects detection of birds, we combined data from eBird, an online community science program, with data from an extensive network of air...

Shifting trends: detecting changes in cetacean population dynamics in shifting habitat

Charlotte Boyd & Andre Punt
The ability to monitor population dynamics and detect major changes in population trend is essential for wildlife conservation and management. However, this is often challenging for cetaceans as surveys typically cover only a portion of a population’s range and conventional stock assessment methods cannot then distinguish whether apparent changes in abundance reflect real changes in population size or shifts in distribution. We developed and tested methods for estimating population size and trend and detecting changes...

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...

Genomic and immunogenic changes of Piscine novirhabdovirus (Viral hemorrhagic septicemia virus) over its evolutionary history in the Laurentian Great Lakes

Carol Stepien, Megan Niner, Carol Stepien, Douglas W. Leaman & Bartolomeo Gorgoglione
A unique and highly virulent subgenogroup (VHSV-IVb) of Piscine novirhabdovirus, also known as Viral Hemorrhagic Septicemia Virus (VHSV), suddenly appeared in the Laurentian Great Lakes, causing large mortality outbreaks in 2005 and 2006, and affecting >32 freshwater fish species to date. Periods of apparent dormancy have punctuated smaller and more geographically-restricted outbreaks in 2007, 2008, and 2017. In this study, we conduct the largest whole genome sequencing analysis of VHSV-IVb to date, evaluating its evolutionary...

Data for tree mortality calibration of satellite and LiDAR-derived fire severity estimates.

N. Macriss, T.J. Furniss, S.M.A. Jeronimo, E. L. Crowley, O. W. Germain, S. Germain, V. R. Kane, A. J. Larson & James A. Lutz
The 55 JFSP plots were established to capture forest types, fire histories, and severity levels beyond those found within the YFPD. The plots were square 50 m × 50 m plots established in Pinus ponderosa, Pinus jeffreyi, and Abies concolor – Pinus lambertiana forest types between 1,431 m and 2,250 m elevation. Plots were installed post-fire based on a randomly chosen locations stratified by burn severity levels as calculated from the differenced Normalized Burn Ratio...

Data from: Leaf shape tracks transitions across forest-grassland boundaries in the grass family (Poaceae)

Timothy Jay Gallaher, Dean C. Adams, Lakshmi Attigala, Sean V. Burke, Joseph M. Craine, Melvin R. Duvall, Phillip C. Klahs, Emma Sherratt, William P. Wysocki & Lynn G. Clark
Grass leaf shape is a strong indicator of their habitat. Linear leaves predominate in open areas and more ovate leaves distinguish forest-associated grasses. This pattern among extant species suggests that ancestral shifts between forest and open habitats may have coincided with changes in leaf shape or size. We tested relationships between habitat, climate, photosynthetic pathway and leaf shape and size in a phylogenetic framework to evaluate drivers of leaf shape and size variation over the...

A new diterpenoid alkaloid from Delphinium gyalanum C. Marquand & Airy Shaw

Xinyu Li, Meizhen Ye, Feng Gao, Xianli Zhou, Lin Chen & Shuai Huang
A new C19-diterpenoid alkaloid named gyalanutine A (1) and fourteen known compounds 2-15 were isolated from the plant of Delphinium gyalanum C. Marquand & Airy Shaw. Compound 1 displayed an unusual lycoctonine-type C19-diterpenoid alkaloid skeleton with the cleavage of N-C19 and C7-C17 bonds, and the construction of the N-C7 bond. Structures were identified by multiple spectroscopic analyses including 1 D, 2 D NMR, IR and HR-ESI-MS. Compounds were tested for acetylcholinesterase inhibitory and anti-inflammatory activity.

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