242 Works

The CALFISH database: A century of California's non-confidential fisheries landings and participation data

Christopher M. Free, Camila Vargas Poulsen, Lyall F. Bellquist, Sophia N. Wassermann & Kiva L. Oken
California's commercial and recreational fisheries support vibrant coastal economies and communities. Maintaining healthy fishing communities into the future requires a detailed understanding of their past. The California Department of Fish and Wildlife (CDFW) has been monitoring statewide fisheries landings and participation since 1916 and releases confidential versions of this data through authorized data requests and non-confidential summaries of this data in its quasi-annual landings reports. The non-confidential data published in the landings reports provide a...

Parasites in kelp-forest food webs increase food-chain length, complexity, and specialization, but reduce connectance

Dana Morton & Kevin Lafferty
We explored whether parasites are important in kelp forests by examining their effects on a high-quality, high-resolution kelp-forest food web. After controlling for generic effects of network size, parasites affected kelp-forest food web structure in some ways consistent with other systems. Parasites increased the trophic span of web, increasing top predator vulnerability and the longest chain length. Unique links associated with parasites, such as concomitant predation (consumption of parasites along with their hosts by predators)...

A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing.

Ryoko Oono
High-throughput sequencing technology has helped microbial community ecologists explore ecological and evolutionary patterns at unprecedented scales. The benefits of a large sample size still typically outweigh that of greater sequencing depths per sample for accurate estimations of ecological inferences. However, excluding or not sequencing rare taxa may mislead the answers to the questions ‘how and why are communities different?’ This study evaluates the confidence intervals of ecological inferences from high-throughput sequencing data of foliar fungal...

Double digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles

Ryoko Oono & Rodolfo Salas Lizana
The phylogenetic and population genetic structure of symbiotic microorganisms may correlate with important ecological traits that can be difficult to directly measure, such as host preferences or dispersal rates. This study develops and tests a low-cost double digest restriction site-associated DNA sequencing (ddRADseq) protocol to reveal among- and within-species genetic structure for Lophodermium, a genus of fungal endophytes whose evolutionary analyses have been limited by the scarcity of informative markers. The protocol avoids expensive barcoded...

Data from: Experimental evidence of frequency-dependent selection on group behaviour

Jonathan N. Pruitt, Brendan L. McEwen, Steven T. Cassidy, Gabriella M. Najm & Noa Pinter-Wollman
Evolutionary ecologists often seek to identify the mechanisms maintaining intraspecific variation. In social animals, whole groups can exhibit between-group differences in their collective traits. We examined whether negative frequency-dependent selection (i.e., a rare-type advantage) could help to maintain between-group variation. We engineered neighborhoods of social spider colonies bearing bold or shy foraging phenotypes and monitored their fecundity in situ. We found that bold colonies enjoyed a rare-type advantage that is lost as the frequency of...

Mixed-species herding levels the landscape of fear

Keenan Stears, Melissa Schmitt, Christopher Wilmers & Adrian Shrader
Prey antipredator behaviours are influenced by perceived predation risk in a landscape and social information gleaned from herd mates regarding predation risk. It is well documented that high-quality social information about risk can come from heterospecific herd mates. Here, we integrate social information with the landscape of fear to quantify how these landscapes are modified by mixed-species herding. To do this, we investigated zebra vigilance in single- and mixed-species herds across different levels of predation...

Habitats and fish communities at mesophotic depths in the Mexican Pacific

Jordan A. Hollarsmith, Georgina Ramirez-Ortiz, Tallulah Winquist, Manuel Velasco-Lozano, Katherine DuBois, Hector Bonilla, Kyle Neumann & Ted Grosholz
Aim: Mesophotic ecosystems, found at the limit of light penetration in the ocean, are rich in biodiversity and harbor unique ecological communities. However, they remain among the least studied habitat zones on earth due to high costs and technological limitations. Here, we characterize mesophotic communities in two marine reserves across a range of habitat types, depths, and temperatures using submersible technologies, with the goal of understanding the processes that structure these communities across biogeographic regions....

Data from: Mating system and historical climate conditions affect population mean seed mass: evidence for adaptation and a new component of the selfing syndrome in Clarkia

Susan Mazer, Isaac Park, Matthew Kimura, Aaron Yim, Emma Maul & Kristen Peach
1. The evolution of seed size may be influenced by intrinsic attributes of populations, such as mating system, and extrinsic factors, such as climate. Several hypotheses propose that the evolution of self-fertilization from an outcrossing progenitor will be accompanied by a reduction in seed size, but this prediction has not been rigorously tested. Many studies report that the mean seed size of populations or taxa is associated with long-term climate conditions. Here, we examined the...

Engineering crack tortuosity in polymer-polymer composites through ordered pores

Megan Valentine, Craig Hawker, Luke Gockowski, Neil Dolinski, Roberto Chavez, Noy Cohen, Fabian Eisenreich, Stefan Hecht & Robert McMeeking
Multimaterial additive manufacturing (or 3D printing) is an enabling tool for exploring structure-property relationships. In this work, a recently developed multimaterial printing approach, solution mask liquid lithography (SMaLL), is used to produce polymer-polymer composites inspired by tough, hierarchical structures found in nature. Triphasic composites comprised of a hard exterior “cuticle”, a soft interior “core,” and controlled pore size/structure are printed in a single step and their mechanical properties evaluated. The results of these tests demonstrate...

Data from: Prozac in the water: chronic fluoxetine exposure and predation risk interact to shape behaviors in an estuarine crab

Joseph R. Peters, Elise F. Granek, Catherine E. De Rivera & Matthew Rollins
Predators exert considerable top-down pressure on ecosystems by directly consuming prey or indirectly influencing their foraging behaviors and habitat use. Prey is, therefore, forced to balance predation risk with resource reward. A growing list of anthropogenic stressors such as rising temperatures and ocean acidification has been shown to influence prey risk behaviors and subsequently alter important ecosystem processes. Yet, limited attention has been paid to the effects of chronic pharmaceutical exposure on risk behavior or...

Data from: Physiological plasticity and local adaptation to elevated pCO2 in calcareous algae: an ontogenetic and geographic approach

Jacqueline L. Padilla-Gamiño, Juan D. Gaitán-Espitia, Morgan W. Kelly & Gretchen E. Hofmann
To project how ocean acidification will impact biological communities in the future, it is critical to understand the potential for local adaptation and the physiological plasticity of marine organisms throughout their entire life cycle, as some stages may be more vulnerable than others. Coralline algae are ecosystem engineers that play significant functional roles in oceans worldwide, and are considered vulnerable to ocean acidification. Using different stages of coralline algae, we tested the hypothesis that populations...

Data from: Herbivore size matters for productivity-richness relationships in African savannas

Deron E. Burkepile, Richard W. S. Fynn, Dave I. Thompson, Nathan P. Lemoine, Sally E. Koerner, Stephanie Eby, Nicole Hagenah, Kevin R. Wilcox, Scott L. Collins, Kevin P. Kirkman, Alan K. Knapp & Melinda D. Smith
1.Productivity and herbivory often interact to shape plant community composition and species richness with levels of production mediating the impact of herbivory. Yet, differences in herbivore traits such as size, feeding guild, and dietary requirements may result in different impacts of diverse herbivore guilds across productivity gradients. 2.We used size-selective herbivore exclosures to separate the effects of herbivory by larger herbivores, such as elephant, Burchell's zebra, and blue wildebeest from those of medium/smaller herbivores, such...

Data from: Combining fish and benthic communities into multiple regimes reveals complex reef dynamics

Mary K. Donovan, Alan M. Friedlander, Joey Lecky, Jean-Baptiste Jouffray, Gareth J. Williams, Lisa M. Wedding, Larry B. Crowder, Ashley L. Erickson, Nick A. J. Graham, Jamison M. Gove, Carrie V. Kappel, Kendra Karr, John N. Kittinger, Albert V. Norström, Magnus Nyström, Kirsten L. L. Oleson, Kostantinos A. Stamoulis, Crow White, Ivor D. Williams & Kimberly A. Selkoe
Coral reefs worldwide face an uncertain future with many reefs reported to transition from being dominated by corals to macroalgae. However, given the complexity and diversity of the ecosystem, research on how regimes vary spatially and temporally is needed. Reef regimes are most often characterised by their benthic components; however, complex dynamics are associated with losses and gains in both fish and benthic assemblages. To capture this complexity, we synthesised 3,345 surveys from Hawai‘i to...

Data from: Parasites affect food web structure primarily through increased diversity and complexity

Jennifer A. Dunne, Kevin D. Lafferty, Andrew P. Dobson, Ryan F. Hechinger, Armand M. Kuris, Neo D. Martinez, John P. McLaughlin, Kim N. Mouritsen, Robert Poulin, Karsten Reise, Daniel B. Stouffer, David W. Thieltges, Richard J. Williams & Claus Dieter Zander
Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite...

Data from: Fear of feces? Trade-offs between disease risk and foraging drive animal activity around raccoon latrines

Sara B. Weinstein, Chad W. Moura, Jon Francis Mendez & Kevin D. Lafferty
Fear of predation alters prey behavior, which can indirectly alter entire landscapes. A parasite-induced ecology of fear might also exist if animals avoid parasite-contaminated resources when infection costs outweigh foraging benefits. To investigate whether animals avoid parasite contaminated sites, and if such avoidance balances disease costs and foraging gains, we monitored animal behavior at raccoon latrines — sites that concentrate both seeds and pathogenic parasite eggs. Using wildlife cameras, we documented over 40 potentially susceptible...

Data from: Limited trophic partitioning among sympatric delphinids off a tropical oceanic atoll

Hillary Young, Katherine Nigro, Douglas J. McCauley, Lisa T. Ballance, Erin M. Oleson & Simone Baumann-Pickering
Understanding trophic relationships among marine predators in remote environments is challenging, but it is critical to understand community structure and dynamics. In this study, we used stable isotope analysis of skin biopsies to compare the isotopic, and thus, trophic niches of three sympatric delphinids in the waters surrounding Palmyra Atoll, in the Central Tropical Pacific: the melon-headed whale (Peponocephala electra), Gray’s spinner dolphin (Stenella longirostris longirostris), and the common bottlenose dolphin (Tursiops truncatus). δ15N values...

Data from: Simulating regimes of chemical disturbance and testing impacts in the ecosystem using a novel programmable dosing system

Mark Anthony Browne, Paul R. Brooks, Robert Clough, Andrew S. Fisher, Mariana Mayer Pinto & Tasman P. Crowe
Pollution is a global issue at the frontier between ecology, environmental science, management, engineering and policy. Legislation requires experiments to determine how much contamination an ecosystem can absorb before there are structural or functional changes. Yet, existing methods cannot realistically simulate regimes of chemical disturbance and determine impacts to assemblages in ecosystems. This is because they lack ecologically relevant species and biotic interactions, are logistically difficult to set-up, and lack environmentally relevant regimes of chemical...

Data from: Context-dependent effects of large wildlife declines on small mammal communities in central Kenya

Hillary S. Young, Douglas J. McCauley, Rodolfo Dirzo, Jacob R. Goheen, Bernard Agwanda, Cara Brook, Erik O. Castillo, Adam W. Ferguson, Stephen N. Kinyua, Molly M. McDonough, Todd M. Palmer, Robert M. Pringle, Truman P. Young & Kristofer M. Helgen
Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife...

Data from: Transitions between phases of genomic differentiation during stick-insect speciation

Rüdiger Riesch, Moritz Muschick, Dorothea Lindtke, Romain Villoutreix, Aaron A. Comeault, Timothy E. Farkas, Kay Lucek, Elizabeth Hellen, Víctor Soria-Carrasco, Stuart R. Dennis, Clarissa F. De Carvalho, Rebecca J. Safran, Cristina P. Sandoval, Jeff Feder, Regine Gries, Bernard J. Crespi, Gerhard Gries, Zach Gompert & Patrik Nosil
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to...

Data from: Long-term, high frequency in situ measurements of intertidal mussel bed temperatures using biomimetic sensors

Brian Helmuth, Francis Choi, Allison Matzelle, Jessica L. Torossian, Scott L. Morella, K. A. S. Mislan, Lauren Yamane, Denise Strickland, P. Lauren Szathmary, Sarah Gilman, Alyson Tockstein, Thomas J. Hilbish, Michael T. Burrows, Anne Marie Power, Elizabeth Gosling, Nova Mieszkowska, Christopher D. G. Harley, Michael Nishizaki, Emily Carrington, Bruce Menge, Laura Petes, Melissa M. Foley, Angela Johnson, Megan Poole, Mae M. Noble … & Gerardo Zardi
At a proximal level, the physiological impacts of global climate change on ectothermic organisms are manifest as changes in body temperatures. Especially for plants and animals exposed to direct solar radiation, body temperatures can be substantially different from air temperatures. We deployed biomimetic sensors that approximate the thermal characteristics of intertidal mussels at 71 sites worldwide, from 1998-present. Loggers recorded temperatures at 10–30 min intervals nearly continuously at multiple intertidal elevations. Comparisons against direct measurements...

Data from: Gene co-expression modules underlying polymorphic and monomorphic zooids in the colonial hydrozoan, Hydractinia symbiolongicarpus

M. Sabrina Pankey, Brian R. Johnson, Eric J. Ronne, Artyom Kopp, Richard K. Grosberg & David C. Plachetzki
Advances in sequencing technology have forced a quantitative revolution in Evolutionary Biology. One important feature of this renaissance is that comprehensive genomic resources can be obtained quickly for almost any taxon, thus speeding the development of new model organisms. Here, we analyze 20 RNA-seq libraries from morphologically, sexually, and genetically distinct polyp types from the gonochoristic colonial hydrozoan, Hydractinia symbiolongicarpus (Cnidaria). Analyses of these data using weighted gene co-expression networks highlight deeply conserved genetic elements...

Data from: Social tipping points in animal societies in response to heat stress

Grant Navid Doering, Inon Scharf, Holly V. Moeller & Jonathan N. Pruitt
Living systems sometimes experience abrupt tipping points in response to stress. Here we investigate the factors contributing to the appearance of such abrupt state transitions in animal societies. We first construct a mathematical account of how the personality compositions of societies could alter their propensity to shift from calm to violent states in response to thermal stress. To evaluate our model, we subjected experimental societies of the spider Anelosimus studiosus to heat stress. We demonstrate...

Data from: Protection of large predators in a marine reserve alters size-dependent prey mortality

Rebecca L. Selden, Steven D. Gaines, Scott L. Hamilton & Robert R. Warner
Where predator–prey interactions are size-dependent, reductions in predator size owing to fishing has the potential to disrupt the ecological role of top predators in marine ecosystems. In southern California kelp forests, we investigated the size-dependence of the interaction between herbivorous sea urchins and one of their predators, California sheephead (Semicossyphus pulcher). Empirical tests examined how differences in predator size structure between reserve and fished areas affected size-specific urchin mortality. Sites inside marine reserves had greater...

Data from: Slower environmental change hinders adaptation from standing genetic variation

Thiago S. Guzella, Snigdhadip Dey, Ivo M. Chelo, Ania Pino-Querido, Veronica F. Pereira, Stephen R. Proulx & Henrique Teotónio
Evolutionary responses to environmental change depend on the time available for adaptation before environmental degradation leads to extinction. Explicit tests of this relationship are limited to microbes where adaptation usually depends on the sequential fixation of de novo mutations, excluding standing variation for genotype-by-environment fitness interactions that should be key for most natural species. For most natural species evolving from standing genetic variation, adaptation at slower rates of environmental change may be impeded since the...

Data from: The effect of keystone individuals on collective outcomes can be mediated through interactions or behavioral persistence

Noa Pinter-Wollman, Carl Nick Keiser, Roy Wollman & Jonathan Pruitt
Collective behavior emerges from interactions among group members who often vary in their behavior. The presence of just one or a few keystone individuals, such as leaders or tutors, may have a large effect on collective outcomes. These individuals can catalyze behavioral changes in other group members, thus altering group composition and collective behavior. The influence of keystone individuals on group function may lead to trade-offs between ecological situations, because the behavioral composition they facilitate...

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