27 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...

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...

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...

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...

Morphological measurements of arm loss for eight octopus species

Kelley Voss
Sublethal predation is prevalent in multi-limbed marine invertebrates and holistically quantifying their injuries has potential to provide important ecological and physiological insights including the rate of trophic energy transfer. We demonstrate the utility of an Injury Severity Index (ISI) to holistically describe the magnitude of appendage injury in invertebrates, using data collected from octopuses in museums and the field. ISI, when applied to octopus, quantifies the numbers of arms lost and the proportion of tissue...

Quantification of thermal impacts across freshwater life stages to improve temperature management for anadromous salmonids

Alyssa FitzGerald & Benjamin Martin
Water temperature is the major controlling factor that shapes the physiology, behavior, and ultimately, survival of aquatic ectotherms. Here we examine temperature effects on the survival of Chinook salmon (Oncorhynchus tshawytscha), a species of high economic and conservation importance. We implement a framework to assess how incremental changes in temperature impact survival across populations that is based on thermal performance models for three freshwater life stages of Chinook salmon. These temperature-dependent models were combined with...

Photographs of 15-day wound closure progress in C57BL/6J mice

Hsin-Ya Yang, Michelle Bagood, Hector Carrion & Rivkah Isseroff
Evaluating and tracking wound size is a fundamental metric for the wound assessment process. Good location and size estimates can enable proper diagnosis and effective treatment. Traditionally, laboratory wound healing studies include a collection of images at uniform time intervals exhibiting the wounded area and the healing process in the test animal, often a mouse. These images are then manually observed to determine key metrics —such as wound size progress— relevant to the study. However,...

Vocal behavior in spotted seals (Phoca largha) and implications for passive acoustic monitoring

Jillian Sills & Colleen Reichmuth
Passive acoustic methods enable remote monitoring of marine species and habitats. These methods can be applied to investigate distribution and abundance of populations, to evaluate behavioral and physiological states of individuals, and to inform management efforts for animals that live in hard-to-reach places. Spotted seals (Phoca largha) inhabit high-latitude, light-limited sub-Arctic and Arctic waters and move seasonally with unstable sea ice. They are high trophic level predators vulnerable to changing conditions associated with environmental warming....

Physiological responses of narwhals to anthropogenic noise: a case study with seismic airguns and vessel traffic in the Arctic

Terrie Williams, Susanna Blackwell, Outi Tervo, Eva Garde, Mikkel Strander Sinding, Beau Richter & Mads Peter Heide-Jørgensen
Limited polar geographical range, narrowly defined migratory routes, and deep-diving behaviors make narwhals exceptionally vulnerable to anthropogenic disturbances including oceanic noise. Although behavioral studies indicate marked responses of cetaceans to disturbance, the link between fear reactions and possible injury from noise exposure is limited for most species. To address this, we deployed custom-made heart rate-accelerometer-depth recorders on 13 adult narwhals in Scoresby Sound, East Greenland across a five-year period (2014-2018). Physiological responses of the cetaceans...

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...

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...

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...

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...

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...

Cyclin F drives proliferation through SCF-dependent degradation of the retinoblastoma-like tumor suppressor p130/RBL2

Wayne Stallaert, Taylor Enrico, Elizaveta Wick, Peter Ngoi, Michael Emanuele, Seth Rubin, Nicholas Brown, Jeremy Purvis, Taylor P Enrico, Elizaveta T Wick, Xianxi Wang, Seth M Rubin, Nicholas G Brown, Jeremy E Purvis & Michael J Emanuele
Cell cycle gene expression programs fuel proliferation and are universally dysregulated in cancer. The retinoblastoma (RB)-family of proteins, RB1, RBL1/p107, and RBL2/p130, coordinately represses cell cycle gene expression, inhibiting proliferation, and suppressing tumorigenesis. Phosphorylation of RB-family proteins by cyclin-dependent kinases is firmly established. Like phosphorylation, ubiquitination is essential to cell cycle control, and numerous proliferative regulators, tumor suppressors, and oncoproteins are ubiquitinated. However, little is known about the role of ubiquitin signaling in controlling RB-family...

Soil chemistry and dry season intensity, Panama Canal Area

Benjamin L. Turner & Richard Condit
Woody plant species were surveyed at 72 locations near the Panama Canal, spanning geological formations and a rainfall gradient. Soil chemistry, and dry season intensity at all the sites. Response of tree species to environmental gradients was estimated. The soil and climate data are provided in a single table here. Tree distributions are published at Condit et al. (2013a), including a data archive in Condit et al. (2013b). Note that the PNAS article incorrectly cites...

Demographic response to light environment of all species in the Barro Colorado plot: recruitment, growth, and mortality

Nadja Rüger, Stephen P. Hubbell & Richard Condit
We measured growth, death, and recruitment of 250,000 individual trees of 300 species in the Barro Colorado 50-ha plot in Panama. To understand how light limits demography, we also carried out a detailed map of the light environment across the 50 hectares, providing an estimate of the light at the top of every tree in the plot (Rüger et al. 2009, 2011ab, 2012, 2018, 2020). These tables combine results from the three main studies on...

Coupled changes in pH, temperature and dissolved oxygen impact the physiology and ecology of herbivorous kelp forest grazers

Emily Donham, Lauren Strope, Scott Hamilton & Kristy Kroeker
Understanding species’ responses to upwelling may be especially important in light of ongoing environmental change. Upwelling frequency and intensity are expected to increase in the future, while ocean acidification and deoxygenation are expected to decrease the pH and dissolved oxygen of upwelled waters. However, the acute effects of a single upwelling event and the integrated effects of multiple upwelling events on marine organisms are poorly understood. Here, we use in situ measurements of pH, temperature,...

Cedar Creek Tree Plot, Minnesota: Neighbor influence on growth and survival in a burned oak landscape

Mark A. Davis & Richard Condit
The 16-ha Cedar Creek plot had all trees at least 2 cm dbh measured every 5 years from 1990 to 2015. Additional censuses were carried out every year, but trees were only checked for survival in those intervening censuses. The six growth censuses are thus numbered 1, 6, 11, 16, 21, 26. Data included here were used in Davis and Condit (2022). More details on methods and other uses of the data appear Davis (2021)...

Data from: Accounting for variation in temperature and oxygen availability when quantifying marine ecosystem metabolism

Matthew Bracken, Luke Miller, Sarah Mastroni, Stephany Lira & Cascade Sorte
Given human modification of Earth’s ecosystems, it is essential to understand how these changes are influencing ecosystem functioning, including net and gross community production and community respiration. These responses are often estimated by measuring oxygen production in the light (net community production) and consumption in the dark (community respiration). These values can then be combined to estimate gross community production. However, the method used to create “dark” conditions – either experimental darkening during the day...

On the spread of microbes that manipulate reproduction in marine invertebrates

Matthew Kustra & Tyler Carrier
Bacterial symbionts are functionally integral to animal reproduction and development, some of which have evolved additional mechanisms to override these host programs. One habitat that is increasingly recognized to contain phylogenetically related lineages of reproductive manipulators is the ocean. The reproduction of marine invertebrates often occurs by free-spawning instead of by the physical contact of copulation in terrestrial systems. We developed an integrated model to understand whether and when microbes that manipulate host reproduction by...

Breeding site fidelity is lower in polygamous shorebirds and male-biased in monogamous species

Eunbi Kwon, Mihai Valcu, Margherita Cragnolini, Martin Bulla, Bruce Lyon & Bart Kempenaers
Sex-bias in breeding dispersal is considered the norm in many taxa, and the magnitude and direction of such sex-bias is expected to correlate with the social mating system. We used local return rates in shorebirds as an index of breeding site fidelity, and hence as an estimate of the propensity for breeding dispersal, and tested whether variation in site fidelity and in sex-bias in site fidelity relates to the mating system. Among 111 populations of...

Resilient consumers accelerate the plant decomposition in a naturally acidified seagrass ecosystem

Juhyung Lee, Maria Cristina Gambi, Kristy Kroeker, Marco Munari, Kabir Peay & Fiorenza Micheli
Anthropogenic stressors are predicted to alter biodiversity and ecosystem functioning worldwide. However, scaling up from species to ecosystem responses poses a challenge, as species and functional groups can exhibit different capacities to adapt, acclimate, and compensate under changing environments. We used a naturally acidified seagrass ecosystem (the endemic Mediterranean Posidonia oceanica) as a model system to examine how ocean acidification (OA) modifies the community structure and functioning of plant detritivores, which play vital roles in...

Plasticity and evolution shape the scaling of metabolism and excretion along a geothermal temperature gradient

Javiera Benavente, David Fryxell, Michael Kinnison, Eric Palkovacs & Kevin Simon
Physiological rates are heavily dependent on temperature and body size. Most current predictions of organisms’ response to environmental warming are based on the assumption that key physiological rates like metabolism and excretion scale independently with body size and temperature and will not evolve. However, temperature is a significant driver for phenotypic variability in the allometric scaling and thermal sensitivity of physiological rates within ectotherm species, suggesting that evolution may play a role in shaping these...

Burrowing crabs and physical factors hasten marsh recovery at panne edges

Kathryn Beheshti, Charlie Endris, Peter Goodwin, Annabelle Pavlak & Kerstin Wasson
Salt marsh loss is projected to increase as sea-level rise accelerates with global climate change. Salt marsh loss occurs along both lateral creek and channel edges and in the marsh interior, when pannes expand and coalesce. Often, edge loss is attributed to erosive processes whereas dieback in the marsh interior is linked to excessive inundation or deposition of wrack, but remains poorly understood. We conducted a two-year field investigation in a central California estuary to...

Registration Year

  • 2022

Resource Types

  • Dataset


  • University of California, Santa Cruz
  • Moss Landing Marine Laboratories
  • San Diego State University
  • National Oceanic and Atmospheric Administration
  • Max Planck Institute for Ornithology
  • Victoria University of Wellington
  • Stanford University
  • The University of Texas at Austin
  • Korea Polar Research Institute
  • Oregon Department of Fish and Wildlife