41 Works

Data from: Does population size affect genetic diversity? A test with sympatric lizard species

Michael T. J. Hague & Eric J. Routman
Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution...

A basic ddRADseq two-enzyme protocol performs well in herbarium and silica-dried tissues across four genera

Ingrid Jordon-Thaden, James Beck, Catherine Rushworth, Michael Windham, Nicolas Diaz, Jason Cantley, Chris Martine & Carl Rothfels
Premise of the study: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of broad datasets with taxonomic and geographic sampling not otherwise possible. Here we evaluate the utility of a basic restriction site-associated DNA (ddRADseq) protocol with DNAs from four genera extracted from both silica-dried and herbarium tissue. Methods: DNAs from Draba, Boechera, Solidago, and Ilex were processed with a double-digest restriction-site associated DNA sequencing (ddRADseq) protocol. The...

Data from: Thermal niche evolution across replicated Anolis lizard adaptive radiations

Alex R. Gunderson, D. Luke Mahler & Manuel Leal
Elucidating how ecological and evolutionary mechanisms interact to produce and maintain biodiversity is a fundamental problem in evolutionary ecology. We investigate this issue by focusing on how physiological evolution affects performance and species coexistence along the thermal niche axis in replicated radiations of Anolis lizards, groups best known for resource partitioning based on morphological divergence. We find repeated divergence in thermal physiology within these radiations, and that this divergence significantly affects performance within natural thermal...

Data from: Infection with Batrachochytrium dendrobatidis is common in tropical lowland habitats: implications for amphibian conservation

Hector Zumbado-Ulate, Adrián García-Rodríguez, Vance T. Vredenburg & Catherine Searle
Numerous species of amphibians declined in Central America during the 1980s and 1990s. These declines mostly affected highland stream amphibians and have been primarily linked to chytridiomycosis, a deadly disease caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd). Since then, the majority of field studies on Bd in the Tropics have been conducted in midland and highland environments (>800 m) mainly because the environmental conditions of mountain ranges match the range of ideal abiotic conditions...

Analyzing coastal fog effects on carbon and water fluxes in a California agricultural system using approaches in biometeorology, remote sensing, and plant physiology

Sara Baguskas, Andrew Oliphant, Rachel Clemesha & Michael Loik
In coastal California, the peak growing season of economically important crops is concurrent with fog events, which buffer drought stress during the dry season. Coastal fog patterns are changing, so we quantified its effects on the energy, water, and carbon fluxes of an economically important cropland at multiple spatial and temporal scales. Our study site was a strawberry farm located in the fog-belt of the Salinas Valley, California. We used GOES-satellite total albedo to detect...

Phytoplankton prey of an abundant estuarine copepod identified in situ using DNA metabarcoding

Ann Holmes & Wim Kimmerer
Plankton trophic interactions play a crucial role in ecosystem processes. Diet analysis using high-throughput sequencing methods such as metabarcoding can provide new insight where traditional methods have been limited. We used 16S ribosomal RNA genemetabarcoding to identify phytoplankton fromthe guts of the copepod Pseudodiaptomus forbesi and in seston from the Cache Slough Complex, a tidal freshwater reach of the San Francisco Estuary. Cyanobacteria, assumed to have low nutritional value for copepods, were detected in all...

Data from: Host and habitat specialization of avian malaria in Africa

Claire Loiseau, Ryan J. Harrigan, Alexandre Robert, Rauri C. K. Bowie, Henri A. Thomassen, Thomas B. Smith & Ravinder N. M. Sehgal
Studies of both vertebrates and invertebrates have suggested that specialists, as compared to generalists, are likely to suffer more serious declines in response to environmental change. Less is known about the effects of environmental conditions on specialist vs. generalist parasites. Here, we study the evolutionary strategies of malaria parasites (Plasmodium spp.) among different bird host communities. We determined the parasite diversity and prevalence of avian malaria in three bird communities in the lowland forests in...

Data from: Deconstructing the landscape of fear in stable multi-species societies

A. E. Martínez, E. Parra, L. F. Collado & V. T. Vredenburg
Animal distributions are influenced by variation in predation risk in space, which has been described as the “landscape of fear.” Many studies suggest animals also reduce predation risk by eavesdropping on heterospecific alarm calls, allowing them to occupy otherwise risky habitats. One unexplored area of study is understanding how different species’ alarms vary in quality, and how this variation is distributed in the landscape. We tested this phenomenon in a unique system of avian mixed...

Data from: Links between blood parasites, blood chemistry, and the survival probability of nestling American crows

Andrea K. Townsend, Sarah S. Wheeler, David Freund, Ravinder N.M. Sehgal, Walter M. Boyce & Ravinder N. M. Sehgal
1. Many studies have used the avian haemosporidians (Leucocytozoon, Plasmodium, and Haemoproteus) to test hypotheses of host-parasite co-evolution, yet documented health and survival consequences of these blood parasites vary among studies and generalizations about their pathogenicity are debatable. In general, the negative effects of the haemosporidians are likely to be greatest during acute infections of young birds, yet most previous studies in wild passerines have examined chronic effects in adults. 2. Here, we evaluated responses...

Data from: Advancing mite phylogenomics: designing ultraconserved elements for Acari phylogeny

Matthew H. Van Dam, Michelle Trautwein, Greg Spicer & Lauren Esposito
Mites (Acari) are one of the most diverse groups of life on Earth, yet their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution,we design targeted ultraconserved genomic elements (UCEs) probes, intended for resolving the complex relationships between mite lineages and closely related arachnids. We then test our Acari UCE baits in-silico by...

Data from: Temporal scale-dependence of plant-pollinator networks

Benjamin Schwarz, Diego Vázquez, Paul CaraDonna, Tiffany Knight, Gita Benadi, Carsten Dormann, Benoit Gauzens, Elena Motivans, Julian Resasco, Nico Blüthgen, Laura Burkle, Qiang Fang, Christopher Kaiser-Bunbury, Ruben Alarcón, Justin Bain, Natacha Chacoff, Shuang-Quan Huang, Gretchen LeBuhn, Molly MacLeod, Theodora Petanidou, Claus Rasmussen, Michael Simanonok, Amibeth Thompson, Daniel Cariveau, Michael Roswell … & Jochen Fründ
The study of mutualistic interaction networks has led to valuable insights into ecological and evolutionary processes. However, our understanding of network structure may depend upon the temporal scale at which we sample and analyze network data. To date, we lack a comprehensive assessment of the temporal scale-dependence of network structure across a wide range of temporal scales and geographic locations. If network structure is temporally scale-dependent, networks constructed over different temporal scales may provide very...

Genetic Adaptation in New York City Rats

Arbel Harpak, Nandita Garud, Noah Rosenberg, Dmitri Petrov, Pleuni Pennings & Jason Munshi-South
Brown rats (Rattus norvegicus) thrive in urban environments by navigating the anthropocentric environment and taking advantage of human resources and by-products. From the human perspective, rats are a chronic problem that causes billions of dollars in damage to agriculture, health and infrastructure. Did genetic adaptation play a role in the spread of rats in cities? To approach this question, we collected whole-genome sequences from 29 brown rats from New York City (NYC) and scanned for...

Temporal and spatial variation in population structure among brooding sea stars in the genus Leptasterias

Laura Melroy & Sarah Cohen
Temporal genetic studies of low-dispersing organisms are rare. Marine invertebrates lacking a planktonic larval stage are expected to have lower dispersal, low gene flow, and a higher potential for local adaptation than organisms with planktonic dispersal. Leptasterias is a genus of brooding sea stars containing several cryptic species complexes. Population genetic methods were used to resolve patterns of fine-scale population structure in central California Leptasterias species using three loci from nuclear and mitochondrial genomes. Historic...

Snow modulates winter energy use and cold exposure across an elevation gradient in a montane ectotherm

Kevin Roberts, Nathan Rank, Elizabeth Dahlhoff, Jonathon Stillman & Caroline Williams
Snow insulates the soil from air temperature, decreasing winter cold stress and altering energy use for organisms that overwinter in the soil. As climate change alters snowpack and air temperatures, it is critical to account for the role of snow in modulating vulnerability to winter climate change. Along elevational gradients in snowy mountains, snow cover increases but air temperature decreases, and it is unknown how these opposing gradients impact performance and fitness of organisms overwintering...

Social group size influences pathogen transmission in salamanders

Andrew Zink
Individuals within animal societies are expected to mitigate the costs and enhance the benefits associated with group living. For example, sociality can facilitate the sharing of beneficial microbes among individuals, but can also increase transmission of pathogens, representing a major cost of group living. We examine the costs of sociality in the California slender salamander (Batrachoseps attenuatus), a terrestrial salamander which naturally forms close social aggregations. We investigate whether innate sociality (e.g., skin-to-skin contact) increases...

Data from: Plasticity in thermal tolerance has limited potential to buffer ectotherms from global warming

Alex R. Gunderson & Jonathon H. Stillman
Global warming is increasing the overheating risk for many organisms, though the potential for plasticity in thermal tolerance to mitigate this risk is largely unknown. In part, this shortcoming stems from a lack of knowledge about global and taxonomic patterns of variation in tolerance plasticity. To address this critical issue, we test leading hypotheses for broad-scale variation in ectotherm tolerance plasticity using a dataset that includes vertebrate and invertebrate taxa from terrestrial, freshwater and marine...

Data from: Using ricelands to provide temporary shorebird habitat during migration

Gregory H. Golet, Candace Low, Simon Avery, Katie Andrews, Christopher J. McColl, Rheyna Laney & Mark D. Reynolds
To help mitigate large wetland losses in California, The Nature Conservancy launched a dynamic conservation incentive program to create temporary wetland habitats in harvested and fallow rice fields for shorebirds migrating along the Pacific Flyway. Farmers were invited to participate in a reverse auction bidding process and winning bids were selected based on their cost and potential to provide high quality shorebird habitat. This was done in 2014 and 2015, for separate enrollment periods that...

Data from: Heterospecific eavesdropping in ant-following birds of the Neotropics is a learned behaviour

Henry S. Pollock, Ari E. Martinez, J.P. Kelley, Janeene M. Touchton, Corey E. Tarwater & J. Patrick Kelley
Animals eavesdrop on other species to obtain information about their environments. Heterospecific eavesdropping can yield tangible fitness benefits by providing valuable information about food resources and predator presence. The ability to eavesdrop may therefore be under strong selection, although extensive research on alarm-calling in avian mixed-species flocks has found only limited evidence that close association with another species could select for innate signal recognition. Nevertheless, very little is known about the evolution of eavesdropping behaviour...

Data from: Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host

Silas Ellison, Roland A. Knapp, Wesley Sparagon, Andrea Swei & Vance T. Vredenburg
The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects the skin of amphibians, and has caused severe declines and extinctions of amphibians globally. In this study, we investigate the interaction between Bd and the bacterial skin microbiome of the endangered Sierra Nevada yellow-legged frog, Rana sierrae, using both culture-dependent and culture-independent methods. Samples were collected from two populations of R. sierrae that likely underwent Bd epizootics in the past, but that continue to persist with Bd in...

Data from: Megaphylogeny resolves global patterns of mushroom evolution

Torda Varga, Krisztina Krizsán, Csenge Földi, Bálint Dima, Marisol Sánchez-García, Santiago Sánchez-Ramírez, Gergely J. Szöllősi, János G. Szarkándi, Viktor Papp, László Albert, William Andreopoulos, Claudio Angelini, Vladimír Antonín, Kerrie W. Barry, Neale L. Bougher, Peter Buchanan, Bart Buyck, Viktória Bense, Pam Catcheside, Mansi Chovatia, Jerry Cooper, Wolfgang Dämon, Dennis Desjardin, Péter Finy, József Geml … & László G. Nagy
Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfill diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree...

Molecular dynamics trajectories for ionic conductors in: Paradigms of frustration in superionic solid electrolytes

Brandon Wood, Joel Varley, Kyoung Kweon, Patrick Shea, Alex Hall, Andrew Grieder, Michael Ward, Vincent Aguirre, Dylan Ringling, Eduardo Ventura, Chimara Stancill & Nicole Adelstein
Superionic solid electrolytes have widespread use in energy devices, but the fundamental motivations for fast ion conduction are often elusive. Here, we draw upon atomistic simulations of a wide range of halide, oxide, sulfide, and closo-borate superionic conductors to illustrate some of the key features that enhance local cation mobility in these solids. We classify three types of frustration that create competition between different local atomic preferences, thereby flattening the diffusive energy landscape and enhancing...

Simulation trajectories from ab-initio molecular dynamics of 4x4x4 super cell of Li3OCl with 4 Li concentrations

Nicole Adelstein
Lithium-rich oxychloride antiperovskites are promising solid electrolytes for enabling next-generation batteries. Here, we report a comprehensive study varying Li+ concentrations in Li3OCl using ab-initio molecular dynamics simulations. The simulations accurately capture the complex interactions between Li+ vacancies (V'Li), the dominant mobile species in Li3OCl. The V'Li polarize and distort the host lattice, inducing additional non-vacancy mediated diffusion mechanisms and correlated diffusion events that reduce the activation energy barrier at concentrations as low as 1.5% V'Li....

Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress

Viridiana Avila-Magaña, Bishoy Kamel, Michael DeSalvo, Kelly Gómez-Campo, Susana Enríquez, Hiroaki Kitano, Rori Rohlfs, Roberto Iglesias-Prieto & Mónica Medina
As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities...

Data from: Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog

Roland Knapp, Maxwell Joseph, Thomas Smith, Ericka Hegeman, Vance Vredenburg, James Erdman, Daniel Boiano, Andrea Jani & Cheryl Briggs
The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity ("load") and in doing so alter frog-Bd dynamics and increase the probability of frog population...

Data from: Human-induced biotic invasions and changes in plankton interaction networks

Pavel Kratina, Ralph Mac Nally, James R. Thomson, Wim J. Kimmerer & Monika Winder
1.Pervasive and accelerating changes to ecosystems due to human activities remain major sources of uncertainty in predicting the structure and dynamics of ecological communities. Understanding which biotic interactions within natural multitrophic communities are threatened or augmented by invasions of non-native species in the context of other environmental pressures is needed for effective management. 2.We used multivariate autoregressive models with detailed time-series data from largely freshwater and brackish regions of the upper San Francisco Estuary to...

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  • San Francisco State University
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  • Pontifical Catholic University of Rio Grande do Sul
  • University of California, Santa Cruz