103 Works

Species and environmental datasets from Sierra Nevada, CA (USA) streams in lake-stream networks

Matthew Green, David Herbst, Kurt Anderson & Marko Spasojevic
A major goal of community ecology is understanding the processes responsible for generating biodiversity patterns along spatial and environmental gradients. In stream ecosystems, system specific conceptual frameworks have dominated research describing biodiversity change along longitudinal gradients of river networks. However, support for these conceptual frameworks has been mixed, mainly applicable to specific stream ecosystems and biomes, and these frameworks have placed less emphasis on general mechanisms driving biodiversity patterns. Rethinking biodiversity patterns and processes in...

Micro and macroclimatic constraints on the activity of a vulnerable tortoise: a mechanistic approach under a thermal niche view

Rafael A. Lara-Resendiz, Donald Miles, Philip Rosen & Barry Sinervo
1. Thermal constraints imposed by the environment limit the activity time of ectotherms and have been a central issue in ecophysiology. Assessing these restrictions is key to determining the vulnerability of species to changing thermal niches and developing conservation strategies. 2. We generate an explicit tortoise model of thermal constraints at both micro and macroclimate scales based on thermophysiology parameters and environmental operative temperatures during a biologically significant period. As a study model, we use...

Standardizing protocols for determining the cause of mortality in wildlife studies

Bogdan Cristescu, Mark Elbroch, Tavis Forrester, Maximilian Allen, Derek Spitz, Christopher Wilmers & Heiko Wittmer
Mortality site investigations of telemetered wildlife are important for cause-specific survival analyses and understanding underlying causes of observed population dynamics. Yet eroding ecoliteracy and a lack of quality control in data collection can lead researchers to make incorrect conclusions, which may negatively impact management decisions for wildlife populations. We reviewed a random sample of 50 peer-reviewed studies published between 2000 and 2019 on survival and cause-specific mortality of ungulates monitored with telemetry devices. This concise...

Antarctic minke whale acoustic data

Ari Friedlaender
Acoustic signaling is the predominant form of communication among cetaceans. Understanding the behavioral state of calling individuals can provide insights into the specific function of sound production; in turn, this information can aid the evaluation of passive monitoring data sets to estimate species presence, density, and behavior. Antarctic minke whales are the most numerous baleen whale species in the Southern Ocean. However, our knowledge of their vocal behavior is limited. Utilizing the first animal-borne audio-video...

Sea otters in a California estuary: Detecting temporal and spatial dynamics with volunteer monitoring

Kerstin Wasson, Ron Eby, Susan Rosso, John Copriviza, Robert Scoles, Yohn Gideon, Joseph Mancino, Karl Mayer & Julie Yee
Volunteer monitoring can support conservation of imperiled wildlife, by providing higher resolution data in space and time than those available from professional scientists. However, concerns have been raised that data collected by amateurs are inaccurate or inconsistent and thus do not allow for robust detection of spatial or temporal trends. We evaluated the rigor and value of volunteer monitoring data for one iconic wildlife species, the southern sea otter (Enhydra lutris nereis), in Elkhorn Slough...

Rare species biodiversity, socio-demographics and local and landscape characteristics in Northern California community urban gardens

Theresa Ong, Brenda Lin, Azucena Lucatero, Hamutahl Cohen, Peter Bichier, Monika Egerer, Alana Danieu, Shalene Jha & Stacy Philpott
Cities are sometimes characterized as homogenous with species assemblages composed of abundant, generalist species having similar ecological functions. Under this assumption, rare species, or species observed infrequently, would have especially high conservation value in cities for their potential to increase functional diversity. Management to increase the number of rare species in cities could be an important conservation strategy in a rapidly urbanizing world. However, most studies of species rarity define rarity in relatively pristine environments...

Sandy seeds: Armor or invisibility cloak? Mucilage-bound sand physically protects seeds from rodents and invertebrates

Eric LoPresti, Vincent Pan, Cecilia Girvin, Gabhriel Barber, Sierra Jaeger & John Orrock
Seeds represent a stage of a plant’s life cycle that is extremely vulnerable to predation, which, unlike most vegetative herbivory, is fatal to the individual. As such, understanding the distribution and abundance of plants may rely upon understanding seed defenses: characteristics of seeds that make them more difficult for granivores to locate, make them less beneficial for granivores to consume, or both. Seeds that produce mucilage are widespread and found across many families and species....

Multi-state diel occupancy model

Kimberly Rivera, Brian Gerber, Mason Fidino, Seth Magle, Zach Farris & Asia Murphy
Current methods to model species habitat use through space and diel time are limited. Development of such models is critical when considering rapidly changing habitats where species are forced to adapt to anthropogenic change, often by shifting their diel activity across space. We use an occupancy modeling framework to specify the multi-state diel occupancy model (MSDOM), which can evaluate species diel activity against continuous response variables which may impact diel activity within and across seasons...

Additional file 2 of HIV awareness, pre-exposure prophylaxis perceptions and experiences among people who exchange sex: qualitative and community based participatory study

Yasaswi Kislovskiy, Sarah Erpenbeck, Jamie Martina, Courtney Judkins, Elizabeth Miller & Judy C. Chang
Additional file 2.

Additional file 7 of HIV awareness, pre-exposure prophylaxis perceptions and experiences among people who exchange sex: qualitative and community based participatory study

Yasaswi Kislovskiy, Sarah Erpenbeck, Jamie Martina, Courtney Judkins, Elizabeth Miller & Judy C. Chang
Additional file 7.

Native annual forb and vegetation data for ten paired grazed and ungrazed prairies in coastal California grasslands at two time periods 15 years apart

Josephine Lesage, Karen Holl & Grey Hayes
Livestock grazing is often used as a land management tool to maximize vegetation diversity in grassland ecosystems worldwide. Prior research has shown that cattle grazing benefits native annual forb species in California’s coastal prairies, but drought and increasing aridity may alter this relationship. In 2016 and 2017, we resurveyed the vegetation structure, native annual forb cover, and native annual forb richness in ten grazed and ungrazed prairies that were originally measured in 2000 and 2001...

Data from: Identification of a minority population of LMO2+ breast cancer cells that integrate into the vasculature and initiate metastasis.

Shaheen Sikandar & Gunsagar Gulati
Metastasis is responsible for the majority of breast cancer-related deaths, however, identifying the cellular determinants of metastasis has remained challenging. Here, we identified a minority population of immature THY1+/VEGFA+ tumor epithelial cells in human breast tumor biopsies that display angiogenic features and are marked by the expression of the oncogene, LMO2. Higher abundance of LMO2+ basal cells correlated with tumor endothelial content and predicted poor distant recurrence-free survival in patients. Using MMTV-PyMT/Lmo2CreERT2 mice, we demonstrated...

Anticipating fluctuations of bigeye tuna in the Pacific Ocean from three-dimensional ocean biogeochemistry

Fernando González Taboada, Jong-Yeon Park, Barbara Muhling, Desiree Tommasi, Kisei Tanaka, Ryan Rykaczewski, Charles Stock & Jorge L. Sarmiento
1. Subseasonal to decadal ocean forecasting can make significant contributions to achieving effective management of living marine resources in a changing ocean. Most applications rely on indirect proxies, however, often measured at the ocean surface and lacking a direct mechanistic link to the dynamics of marine populations. 2. Here we take advantage of three-dimensional, dynamical reconstructions and forecasts of ocean biogeochemistry based on a global Earth System Model to hindcast and assess the capacity to...

Population-specific vulnerability to ocean change in a multi-stressor environment

Emily Donham, Iris Flores, Alexis Hooper, Evan O'Brien, Kate Vylet, Yuichiro Takeshita, Jan Freiwald & Kristy Kroeker
Variation in environmental conditions across a species’ range can alter their responses to environmental change through local adaptation and acclimation. Evolutionary responses, however, may be challenged in ecosystems with tightly coupled environmental conditions, where changes in the covariance of environmental factors may make it more difficult for species to adapt to global change. Here, we conduct a 3-month-long mesocosm experiment and find evidence for local adaptation/acclimation in populations of red sea urchins, Mesocentrotus franciscanus, to...

Data from: Puma responses to unreliable human cues suggest an ecological trap in a fragmented landscape

Anna Nisi, John Benson & Christopher C. Wilmers
Animals’ fear of people is widespread across taxa and can mitigate the risk of human-induced mortality, facilitating coexistence in human-dominated landscapes. However, humans can be unpredictable predators and anthropogenic cues that animals perceive may not be reliable indicators of the risk of being killed. In these cases, animal fear responses may be ineffective and may even exacerbate the risk of anthropogenic mortality. Here, we explore these questions using a 10-year dataset of movement and mortality...

Using seabird and whale distribution models to estimate spatial consumption of krill to inform fishery management

Victoria Warwick-Evans, Natalie Kelly, Luciano Dalla Rosa, Ari Friedlaender, Jefferson Hinke, Jeong-Hoon Kim, Nobuo Kokubun, Jarrod Santora, Eduardo Secchi, Elisa Seyboth & Philip Trathan
Ecosystem dynamics at the north-west Antarctic Peninsula are driven by interactions between physical and biological processes. For example, baleen whale populations are recovering from commercial harvesting against the backdrop of rapid climate change, including reduced sea-ice extent and changing ecosystem composition. Concurrently, the commercial harvesting of Antarctic krill is increasing, with the potential to increase the likelihood for competition with and between krill predators and the fishery. However, understanding the ecology, abundance, and spatial distribution...

Data From: Applying empirical dynamic modeling to distinguish abiotic and biotic drivers of population fluctuations in sympatric fishes

Ben Wasserman, Tanya Rogers, Stephan Munch & Eric Palkovacs
Fluctuations in the population abundances of interacting species are widespread. Such fluctuations could be a response to abiotic factors, biotic interactions, or a combination of the two. Correctly identifying the drivers are critical for effective population management. However, such effects are not always static in nature. Nonlinear relationships between abiotic factors and biotic interactions make it difficult to parse true effects. We used a type of nonlinear forecasting, empirical dynamic modeling, to investigate the context-dependent...

Environmental gradients, covering coastal central California, which are relevant to modeling habitat suitability of Deinandra increscens subsp. villosa

Ariel Simons, Rachel Meyer & Van Wishingrad
Species distribution models (SDMs) are often used to predict areas of suitable habitat for a species across a geographic extent, or to predict range changes due to climate change. These models rely on presence-only data for individuals distributed across a landscape, together with environmental conditions at the points at which individuals occur, in order to predict suitable habitats outside of the observed area. ​​MaxEnt has been commonly used to model the distribution of species when...

Black rockfish otolith and early life history data

Hamilton Fennie
Understanding how future ocean conditions will affect populations of marine species is integral to predicting how climate change will impact both ecosystem function and fisheries management. Fish population dynamics are driven by variable survival of the early life stages, which are highly sensitive to environmental conditions. As global warming generates extreme ocean conditions (i.e., marine heatwaves) we can gain insight into how larval fish growth and mortality will change in warmer conditions. The California Current...

Data for: Mobbing for matings: dynamics, plumage correlates, and fitness impacts of conspicuous group extra-pair behaviors in the lark bunting

Bruce Lyon
The widespread occurrence of extra-pair paternity (EPP) in birds adds rich complexity to our understanding of sexual selection and mating system evolution. Extra-pair matings are typically cryptic so for most species we lack the detailed behavioral observations needed to fully determine whether both sexes benefit from EPP and, when trait correlations with EPP are found, whether they reflect female choice or male intrasexual competition. Here we examine behavioral and morphological correlates of EPP in the...

Short-finned pilot whales exhibit behavioral plasticity in foraging strategies mediated by their environment

Jeanne M. Shearer, Frants H. Jensen, Nicola J. Quick, Ari Friedlaender, Brandon Southall, Douglas P. Nowacek, Matthew Bowers, Heather J. Foley, Zachary T. Swaim, Danielle M. Waples & Andrew J. Read
Predators adapt their foraging behavior to exploit a variety of prey in a range of environments. Short-finned pilot whales are wide-ranging predators in tropical and sub-tropical oceans, but most previous studies of their foraging ecology have been conducted near oceanic islands. We deployed sound and movement recording tags on 43 short-finned pilot whales off Cape Hatteras, North Carolina, USA, to measure their foraging behavior in a continental shelf-break ecosystem and investigate how variation in the...

Additional file 2 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 2. Amendments to the pre-registered protocol.

Additional file 3 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 3. Code and data. IPD from co-authors who agreed to share it, results of all analyses presented in the paper, and R code files necessary to reproduce the analysis and figures.

Additional file 5 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 5: Figure S1. Assessment of publication bias. A Funnel plots. Symbols show the effect of the menstrual cycle (x-axis) and the standard error of that effect (y-axis, reversed). Each symbol shows an individual study. Vertical solid line shows no effect. Vertical dashed line shows the meta-estimate of effect. Diagonal dashed lines enclose the region expected to include 95% of studies based on the estimated meta-effect and the standard errors. B Results of Egger’s...

Landscape structure, bird, and vegetation recruitment in restoration plantations

Karen Holl, Miriam San Jose, Francis Joyce, Rakan Zahawi, Leland Werden & J. Leighton Reid
Reversing large-scale habitat degradation and deforestation goes beyond what can be achieved by site-level ecological restoration and a landscape ecology perspective is fundamental. Here we assess the relative importance of tree cover and its configuration on forest-dependent birds and late-successional tree seedlings in restoration sites in southern Costa Rica. The abundance and species richness of birds increased in landscapes with more corridors, higher tree cover, and lower levels of fragmentation, highlighting the importance of riparian...

Registration Year

  • 2022
    103

Resource Types

  • Dataset
    67
  • Text
    27
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    8
  • Journal Article
    1

Affiliations

  • University of California, Santa Cruz
    103
  • University of Washington
    14
  • University of Toronto
    13
  • Harvard University
    13
  • Massachusetts General Hospital
    12
  • Fred Hutchinson Cancer Research Center
    12
  • London School of Hygiene & Tropical Medicine
    12
  • Karolinska University Hospital
    12
  • George Washington University
    12
  • University of Vermont
    12