314 Works

Data from: A century of sprawl in the United States

Christopher Barrington-Leigh & Adam Millard-Ball
The urban street network is one of the most permanent features of cities. Once laid down, the pattern of streets determines urban form and the level of sprawl for decades to come. We present a high-resolution time series of urban sprawl, as measured through street network connectivity, in the United States from 1920 to 2012. Sprawl started well before private car ownership was dominant and grew steadily until the mid-1990s. Over the last two decades,...

Data from: Algal toxin impairs sea lion memory and hippocampal connectivity, with implications for strandings

Peter F. Cook, Colleen Reichmuth, Andrew A. Rouse, Laura A. Libby, Sophie E. Dennison, Owen T. Carmichael, Kris T. Kruse-Elliott, Josh Bloom, Baljeet Singh, Vanessa A. Fravel, Lorraine Barbosa, Jim J. Stuppino, William G. Van Bonn, Frances M. D. Gulland & Charan Ranganath
Domoic acid (DA) is a naturally occurring neurotoxin known to harm marine animals. DA-producing algal blooms are increasing in size and frequency. Although chronic exposure is known to produce brain lesions, the influence of DA toxicosis on behavior in wild animals is unknown. We showed, in a large sample of wild sea lions, that spatial memory deficits are predicted by the extent of right dorsal hippocampal lesions related to natural exposure to DA and that...

Data from: Ocean acidification affects fish spawning but not paternity at CO2 seeps

Marco Milazzo, Carlo Cattano, Suzanne H. Alonzo, Andrew Foggo, Michele Gristina, Riccardo Rodolfo-Metalpa, Mauro Sinopoli, Davide Spatafora, Kelly A. Stiver & Jason M. Hall-Spencer
Fish exhibit impaired sensory function and altered behaviour at levels of ocean acidification expected to occur owing to anthropogenic carbon dioxide emissions during this century. We provide the first evidence of the effects of ocean acidification on reproductive behaviour of fish in the wild. Satellite and sneaker male ocellated wrasse (Symphodus ocellatus) compete to fertilize eggs guarded by dominant nesting males. Key mating behaviours such as dominant male courtship and nest defence did not differ...

Data from: Range and niche shifts in response to past climate change in the desert horned lizard (Phrynosoma platyrhinos)

Tereza Jezkova, Jef Jaeger, Viktoria Oláh-Hemmings, K. Bruce Jones, Rafael A. Lara-Resendiz, Daniel G. Mulcahy, Brett R. Riddle & Jef R. Jaeger
During climate change, species are often assumed to shift their geographic distributions (geographic ranges) in order to track environmental conditions – niches – to which they are adapted. Recent work, however, suggests that the niches do not always remain conserved during climate change but shift instead, allowing populations to persist in place or expand into new areas. We assessed the extent of range and niche shifts in response to the warming climate after the Last...

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...

Data from: Patterns of genomic divergence and signals of selection in sympatric and allopatric northeastern Pacific and Sea of Cortez populations of the sargo (Anisotremus davidsonii) and longjaw mudsucker (Gillichthys mirabilis)

Eric Garcia, Brian Simison & Giacomo Bernardi
Studying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, USA, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands...

Supplemental material for Climate forcing by battered-and-breaded fillets and crab-flavored sticks from Alaska pollock

Brandi McKuin, Jordan Watson, Alan Haynie & J. Elliott Campbell
Detailed supplemental datasets: inputs and output information and emission factors for ingredients, non-ingredient materials, and embodied energy of pollock products.

Northern elephant seal UAS mass estimates

Roxanne Beltran
Unmanned aerial system (UAS) photogrammetry offers a method that is safer for both animals and researchers and is logistically simpler than traditional weighing methods (Fiori et al. 2017). Additionally, UAS photogrammetry facilitates larger sample sizes because it allows measurement at larger spatial scales, thereby increasing statistical power (Sweeney et al. 2015). However, UAS photogrammetry requires calibration and validation prior to use in order to assess the error relative to known mass measurements. Species-specific calibration of...

Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge

Alisa Vershinina, Peter Heintzman, Duane Froese, Grant Zazula, Molly Cassatt-Johnstone, Love Dalén, Clio Der Sarkissian, Shelby Dunn, Luca Ermini, Cristina Gamba, Pamela Groves, Joshua Kapp, Daniel Mann, Andaine Seguin-Orlando, John Southon, Mathias Stiller, Matthew Wooller, Gennady Baryshnikov, Dmitry Gimranov, Eric Scott, Elizabeth Hall, Susan Hewitson, Irina Kirillova, Pavel Kosintsev, Fedor Shidlovsky … & Beth Shapiro
The Bering Land Bridge (BLB) last connected Eurasia and North America during the Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and...

An escape theory model for directionally moving prey and an experimental test in juvenile Chinook salmon

Megan Sabal, Joseph Merz, Suzanne Alonzo & Eric Palkovacs
Prey evaluate risk and make decisions based on the balance between the costs of predation and those of engaging in antipredator behavior. Economic escape theory has been valuable in understanding responses of stationary prey under predation risk; however, current models are not applicable for directionally moving prey. Here we present an extension of existing escape theory that predicts how much predation risk is perceived by directionally moving prey. Perceived risk is measured by the extent...

Census data from 65 tree plots in Panama, 1994-2015

Richard Condit, Rolando Pérez, Salomón Aguilar & Suzanne Lao
These are data from 65 tree plots in Panama established over 1994-2014; 43 of the plots have been recensused, while 22 plots have just a single census. Details of census methods are described in Condit (1998) and Condit et al. (2013). The 65 plots here are mostly 1 ha in area, though several are 0.32 ha, one is 4 ha, and one is 6 ha. Those two larger censuses are the Sherman and Cocoli plots...

A sample of Saturn interior density profiles derived with MCMC and gravity-based likelihood.

Naor Movshovitz, Jonathan Fortney, Chris Mankovich, Daniel Thorngren & Ravit Helled
We ran a Markov-Chain Monte Carlo algorithm to derive the posterior distribution of density profiles for Saturn, where the likelihood function was a chi-squared distributed distance of each curve's gravity coefficients from the values reported for that planet by the Cassini radio science team (Iess et al., 2019). The result is a large sample of interior profiles of Saturn consistent with observation and minimally constrained by model assumptions. This sample is archived here in sufficiently...

The promise and the perils of resurveying to understand global change impacts

Katharine Stuble, Sharon Bewick, Mark Fisher, Matthew Forister, Susan Harrison, Arthur Shapiro, Andrew Latimer & Laurel Fox
Historical datasets can be useful tools to aid in understanding the impacts of global change on natural ecosystems. Resampling of historically sampled sites (“snapshot resampling”) has often been used to detect long-term shifts in ecological populations and communities, because it allows researchers to avoid long-term monitoring costs and investigate a large number of potential trends. But recent simulation-based research has called the reliability of resampling into question, and its utility has not been comprehensively evaluated....

Results of high-performance computing parameter sweeps associated with the Zimbabwe agro-pastoral management model

M.V. Eitzel, Jon Solera, K.B. Wilson, Kleber Neves, Aaron Fisher, André Veski, Oluwasola Omoju, Abraham Mawere Ndlovu & Emmanuel Mhike Hove
This dataset includes all the results of the model runs used to explore the parameters in the Zimbabwe Agro-Pastoral Management Model, archived at ComSES.net (https://doi.org/10.25937/ta23-sn46). This model has been created with and for the researcher-farmers of the Muonde Trust (http://www.muonde.org/), a registered Zimbabwean non-governmental organization dedicated to fostering Indigenous innovation. The results in this dataset were generated using the BehaviorSpace functionality in NetLogo, running headless on a high-performance computing cluster (499,200 runs). The dataset includes...

Data from: Geographic structuring of Antarctic penguin populations

Jarrod Santora, Michelle LaRue & David Ainley
We hypothesized that regional spatial organization of Antarctic penguin breeding populations was affected by social factors, i.e., proximity and size of adjacent colonies, and by physical factors, i.e., availability of breeding habitat and proximity of polynyas and submarine canyons where prey is abundant. The hypothesis of Furness & Birkhead (1984), that forage competition and density-dependence affect geographic structure of seabird populations, was tested previously for Antarctic penguins when biologging to quantify colony foraging areas was...

Increased frequency of extreme precipitation events in the North Atlantic during the PETM: Observations and theory

William Rush
Climate model simulations of the PETM (Paleocene-Eocene Thermal Maximum) warming have mainly focused on replicating the global thermal response through greenhouse forcing, i.e. CO2, at levels compatible with observations. Comparatively less effort has gone into assessing the skill of models to replicate the response of the hydrologic cycle to the warming, particularly on regional scales. Here we have assembled proxy records of regional precipitation, focusing on the Mid-Atlantic Coasts of North America (New Jersey) and...

Patterns of speciation are similar across mountainous and lowland regions for a Neotropical plant radiation (Costaceae: Costus)

Oscar M. Vargas, Brittany Goldston, Dena Louise Grossenbacher & Kathleen M. Kay
High species richness and endemism in tropical mountains are recognized as major contributors to the latitudinal diversity gradient. The processes underlying mountain speciation, however, are largely untested. The prevalence of steep ecogeographic gradients and the geographic isolation of populations by topographic features are predicted to promote speciation in mountains. We evaluate these processes in a species-rich Neotropical genus of understory herbs that range from the lowlands to montane forests and have higher species richness in...

Variation in resting strategies across trophic levels and habitats in mammals

Roxanne Beltran, Ishana Shukla & A. Marm Kilpatrick
Mammals must carefully balance rest with other behaviors that influence fitness (e.g., foraging, finding a mate) while minimizing predation risk. However, factors influencing resting strategies and the degree to which resting strategies are driven by the activities of predators and/or prey remain largely unknown. Our goal was to examine how mammalian resting strategies varied with trophic level, body mass, and habitat. We reviewed findings from 127 publications and classified the resting strategies of terrestrial and...

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...

Restoration interventions mediate tropical tree recruitment dynamics over time

Andy Kulikowski, Rakan Zahawi, Kai Zhu, Leland Werden & Karen Holl
Forest restoration is increasingly heralded as a global strategy to conserve biodiversity and mitigate climate change, yet long-term studies that compare the effects of different restoration strategies on tree recruit demographics are lacking. We measured tree recruit survival and growth annually in three restoration treatments ‒ natural regeneration, applied nucleation, and tree plantations ‒ replicated at 13 sites in southern Costa Rica, and evaluated the changes over a decade. Early-successional seedlings had 14% higher survival...

Data for: Modeling short-term energetic costs of sonar disturbance to cetaceans using high resolution foraging data

Max Czapanskiy, Matthew Savoca, William Gough, Paolo Segre, Danuta Wisniewska, David Cade & Jeremy Goldbogen
Anthropogenic noise is a pervasive and increasing source of disturbance to wildlife. Marine mammals exhibit behavioral and physiological responses to naval sonar and other sound sources. The lost foraging opportunities and elevated locomotor effort associated with sonar disturbance likely carry energetic costs, which may lead to population-level consequences. We modeled the energetic costs associated with behavioral responses using (1) empirical datasets of cetacean feeding rates and prey characteristics and (2) allometry of swimming performance and...

Data from: Local tropical forest restoration strategies affect tree recruitment more strongly than does landscape forest cover

Karen D. Holl, John Leighton Reid, José Miguel Chaves-Fallas, Federico Oviedo-Brenes & Rakan A. Zahawi
Developing restoration strategies that accelerate natural successional processes and are resource‐efficient is critical to facilitating tropical forest recovery across millions of hectares of deforested lands in the tropics. We compared tree recruitment after a decade in three restoration treatments (natural regeneration, applied nucleation/island tree planting and plantation) and nearby reference forest in the premontane rain forest zone in southern Costa Rica. The study was replicated at 13 sites with a range of surrounding forest cover,...

Dataset S1 - Noelaerhabdaceae organic carbon isotope culture data compilation

Samuel Phelps, Gwenn Hennon, Sonya Dyhrman, María Hernández-Limón, Olivia Williamson & Pratigya Polissar
The carbon isotope fractionation in algal organic matter (Ep), including the long-chain alkenones produced by the coccolithophorid family Noelaerhabdaceae, is used to reconstruct past atmospheric CO2 levels. The conventional proxy linearly relates Ep to changes in cellular carbon demand relative to diffusive CO2 supply, with larger Ep values occurring at lower carbon demand relative to supply (i.e. abundant CO2). However, the response of Gephyrocapsa oceanica, one of the dominant alkenone producers of the last few...

Heterogeneous genetic basis of age at maturity in salmonid fishes

Charles Waters, Anthony Clemento, Tutku Aykanat, John Garza, Kerry-Ann Naish, Shawn Narum & Craig Primmer
Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications to conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains under-explored. We address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmon (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait...

Data from: Factors explaining variability in woody above-ground biomass accumulation in restored tropical forest

Karen D. Holl & Rakan A. Zahawi
Secondary forests comprise an increasing area of the tropics and play an important role in global carbon cycling. We compare above-ground biomass accumulation of both planted and naturally regenerating trees, as well as C in the top soil layer, in three restoration treatments replicated at 14, six to eight year old restoration sites in southern Costa Rica. Restoration strategies include: control (no planting), planting tree islands, and conventional, mixed-species tree plantations. We evaluate the importance...

Registration Year

  • 2022
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Resource Types

  • Dataset


  • University of California, Santa Cruz
  • Stanford University
  • University of California, Davis
  • Southwest Fisheries Science Center
  • University of California, Berkeley
  • University of California, Santa Barbara
  • University of California Los Angeles
  • Organization For Tropical Studies
  • Yale University
  • University of California System