28 Works

Data from: Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus

Rachel M. Wright, Galina V. Aglyamova, Eli Meyer & Mikhail V. Matz
Background: Corals are capable of launching diverse immune defenses at the site of direct contact with pathogens, but the molecular mechanisms of this activity and the colony-wide effects of such stressors remain poorly understood. Here we compared gene expression profiles in eight healthy Acropora hyacinthus colonies against eight colonies exhibiting tissue loss commonly associated with white syndromes, all collected from a natural reef environment near Palau. Two types of tissues were sampled from diseased corals:...

Data from: Can observation skills of citizen scientists be estimated using species accumulation curves?

Steve Kelling, Alison Johnston, Wesley M. Hochachka, Marshall Iliff, Daniel Fink, Jeff Gerbracht, Carl Lagoze, Frank A. La Sorte, Travis Moore, Andrea Wiggins, Weng-Keen Wong, Chris Wood & Jun Yu
Volunteers are increasingly being recruited into citizen science projects to collect observations for scientific studies. An additional goal of these projects is to engage and educate these volunteers. Thus, there are few barriers to participation resulting in volunteer observers with varying ability to complete the project’s tasks. To improve the quality of a citizen science project’s outcomes it would be useful to account for inter-observer variation, and to assess the rarely tested presumption that participating...

Data from: Effects of pesticide mixtures on host-pathogen dynamics of the amphibian chytrid fungus

Julia C. Buck, Jessica Hua, , Trang D. Dang, Jenny Urbina, Randall J. Bendis, Aaron B. Stoler, Andrew R. Blaustein, Rick A. Relyea & William R. Brogan
Anthropogenic and natural stressors often interact to affect organisms. Amphibian populations are undergoing unprecedented declines and extinctions with pesticides and emerging infectious diseases implicated as causal factors. Although these factors often co-occur, their effects on amphibians are usually examined in isolation. We hypothesized that exposure of larval and metamorphic amphibians to ecologically relevant concentrations of pesticide mixtures would increase their post-metamorphic susceptibility to the fungus Batrachochytrium dendrobatidis (Bd), a pathogen that has contributed to amphibian...

Data from: Past tree influence and prescribed fire mediate biotic interactions and community reassembly in a grassland-restoration experiment

Charles B. Halpern, Joseph A. Antos, Donald McKenzie & Annette M. Olson
Woody plant encroachment of grasslands is occurring globally, with profound ecological consequences. Attempts to restore herbaceous dominance may fail if the woody state is resilient or if intervention leads to an alternate, undesirable state. Restoration outcomes often hinge on biotic interactions – particularly on priority effects that inhibit or promote community reassembly. Following experimental tree removal from conifer-invaded grasslands, we documented substantial variation in community reassembly associated with the changing abundance of the native clonal...

Data from: Recombinant DNA modification of gibberellin metabolism alters growth rate and biomass allocation in Populus

Haiwei Lu, Venkatesh Viswanath, Cathleen Ma, Elizabeth Etherington, Palitha Dharmawardhana, Olga Shevchenko, Steven H. Strauss, David W. Pearce, Stewart B. Rood & Victor Busov
Overexpression of genes that modify gibberellin (GA) metabolism and signaling have been previously shown to produce trees with improved biomass production but highly disturbed development. To examine if more subtle types of genetic modification of GA could improve growth rate and modify tree architecture, we transformed a model poplar genotype (Populus tremula × P. alba) with eight genes, including two cisgenes (intact copies of native genes), four intragenes (modified copies of native genes), and two...

Data from: Invasiveness of plant pathogens depends on the spatial scale of host distribution

Alexey Mikaberidze, Christopher C. Mundt & Sebastian Bonhoeffer
Plant diseases often cause serious yield losses in agriculture. A pathogen’s invasiveness can be quantified by the basic reproductive number, R0. Since pathogen transmission between host plants depends on the spatial separation between them, R0 is strongly influenced by the spatial scale of the host distribution.We present a proof of principle of a novel approach to estimate the basic reproductive number, R0, of plant pathogens as a function of the size of a field planted...

Data from: Penalized likelihood methods improve parameter estimates in occupancy models

Rebecca A. Hutchinson, Jonathon J. Valente, Sarah C. Emerson, Matthew G. Betts & Thomas G. Dietterich
1. Occupancy models are employed in species distribution modelling to account for imperfect detection during field surveys. While this approach is popular in the literature, problems can occur when estimating the model parameters. In particular, the maximum likelihood estimates can exhibit bias and large variance for data sets with small sample sizes, which can result in estimated occupancy probabilities near 0 and 1 (‘boundary estimates’). 2. In this paper, we explore strategies for estimating parameters...

Data from: Influence of sediment characteristics on the composition of soft-sediment intertidal communities in the northern Gulf of Mexico

Kyle E. Coblentz, Jessica R. Henkel, Bryan J. Sigel & Caz M. Taylor
Benthic infaunal communities are important components of coastal ecosystems. Understanding the relationships between the structure of these communities and characteristics of the habitat in which they live is becoming progressively more important as coastal systems face increasing stress from anthropogenic impacts and changes in climate. To examine how sediment characteristics and infaunal community composition were related along the northern Gulf of Mexico coast, we sampled intertidal infaunal communities at seven sites covering common habitat types...

Data from: A combined parasitological-molecular approach for non-invasive characterization of parasitic nematode communities in wild hosts

Sarah A. Budischak, Eric P. Hoberg, Art Abrams, Anna E. Jolles & Vanessa O. Ezenwa
Most hosts are concurrently or sequentially infected with multiple parasites; thus, fully understanding interactions between individual parasite species and their hosts depends on accurate characterization of the parasite community. For parasitic nematodes, noninvasive methods for obtaining quantitative, species-specific infection data in wildlife are often unreliable. Consequently, characterization of gastrointestinal nematode communities of wild hosts has largely relied on lethal sampling to isolate and enumerate adult worms directly from the tissues of dead hosts. The necessity...

Data from: Plant diversity and endemism in the California Floristic Province

Dylan O. Burge, James H. Thorne, Susan P. Harrison, Bart C. O'Brien, Jon P. Rebman, James R. Shevock, Edward R. Alverson, Linda K. Hardison, José Delgadillo-Rodríguez, Steven A. Junak, Thomas A. Oberbauer, Hugo Riemann, Sula E. Vanderplank & Teri Barry
The California Floristic Province (CFP) is an area of high biodiversity and endemism corresponding roughly to the portion of western North America having a Mediterranean-type climate. High levels of diversity and endemism in the CFP are attributed to the unique geo-climatic setting of the region. In recent years, much has been learned about the origins of plant diversity in western North America. This work, however, has been hindered by a focus on political rather than...

Data from: Successful recovery of nuclear protein-coding genes from small insects in museums using illumina sequencing

Kojun Kanda, James M. Pflug, John S. Sproul, Mark A. Dasenko & David R. Maddison
In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at...

Data from: De novo assembly and characterization of four anthozoan (phylum Cnidaria) transcriptomes

Sheila A. Kitchen, Camerron M. Crowder, Angela Z. Poole, Virginia M. Weis & Eli Meyer
Many nonmodel species exemplify important biological questions but lack the sequence resources required to study the genes and genomic regions underlying traits of interest. Reef-building corals are famously sensitive to rising seawater temperatures, motivating ongoing research into their stress responses and long-term prospects in a changing climate. A comprehensive understanding of these processes will require extending beyond the sequenced coral genome (Acropora digitifera) to encompass diverse coral species and related anthozoans. Toward that end, we...

Data from: A characterization of autumn nocturnal migration detected by weather surveillance radars in the northeastern US

Andrew Farnsworth, Benjamin Mark Van Doren, Wesley M. Hochachka, Daniel Sheldon, Kevin Winner, Jed Irvine, Jeffrey Geevarghese & Steve Kelling
Billions of birds migrate at night over North America each year. However, few studies have described the phenology of these movements, such as magnitudes, directions, and speeds, for more than one migration season and at regional scales. In this study, we characterize density, direction, and speed of nocturnally migrating birds using data from 13 weather surveillance radars in the autumns of 2010 and 2011 in the northeastern US. After screening radar data to remove precipitation,...

Data from: Prey state alters trait-mediated indirect interactions in rocky tide pools

Sarah A. Gravem & Steven G. Morgan
Several studies on trait-mediated indirect interactions (TMIIs) have shown that predators can initiate trophic cascades by altering prey behaviour. Although it is well recognized that individual prey state alters antipredator and foraging behaviour, few studies explore whether this state-dependent prey behaviour can alter the strength of the ensuing tritrophic cascade. Here, we link state-dependent individual behaviour to community processes by experimentally testing whether hunger level and body size of prey altered antipredator behaviour and thus...

Data from: Large wildlife removal drives immune defense increases in rodents

Hillary S. Young, Rodolfo Dirzo, Kristofer M. Helgen, Douglas J. McCauley, Charles L. Nunn, Paul Snyder, Kari E. Veblen, Serena Zhao & Vanessa O. Ezenwa
Anthropogenic disturbances involving land use change, climate disruption, pollution, and invasive species have been shown to impact immune function of wild animals. These immune changes have direct impacts on the fitness of impacted animals and, also, potentially indirect effects on other species and on ecological processes, notably involving the spread of infectious disease. Here, we investigate whether the selective loss of large wildlife can also drive changes in immune function of other consumer species. Using...

Data from: Phylogenetic placement of the unusual jumping spider Depreissia Lessert, and a new synapomorphy uniting Hisponinae and Salticinae (Araneae, Salticidae)

Wayne P. Maddison, David R. Maddison, Junxia Zhang & Tamás Szűts
The relationships of the unusual salticid spider Depreissia from central Africa and Borneo have been difficult to resolve, obscured by its highly modified ant-like body. Phylogenetic analysis of the gene 28S strongly supports its placement outside the major clade Salticinae and within the clade of cocalodines, spartaeines and lapsiines, with weaker support for a relationship with the cocalodines in particular. Excluding the genus from the Salticinae is supported also by the presence of a median...

Data from: Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)

Roswitha Schmickl, Aaron Liston, Vojtěch Zeisek, Kenneth Oberlander, Kevin Weitemier, Shannon C. K. Straub, Richard C. Cronn, Léanne L. Dreyer & Jan Suda
Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African...

Data from: Behavioural responses of Atlantic cod to sea temperature changes

Carla Freitas, Esben Moland Olsen, Even Moland, Lorenzo Ciannelli & Halvor Knutsen
Understanding responses of marine species to temperature variability is essential to predict impacts of future climate change in the oceans. Most ectotherms are expected to adjust their behavior to avoid extreme temperatures and minimize acute changes in body temperature. However, measuring such behavioral plasticity in the wild is challenging. Combining 4 years of telemetry-derived behavioral data on juvenile and adult (30–80 cm) Atlantic cod (Gadus morhua), and in situ ocean temperature measurements, we found a...

Data from: Carotenoids and amphibians: effects on life history and susceptibility to the infectious pathogen, Batrachochytrium dendrobatidis

Rickey D. Cothran, Stephanie S. Gervasi, Cindy Murray, Beverly J. French, Paul W. Bradley, Jenny Urbina, Andrew R. Blaustein & Rick A. Relyea
Carotenoids are considered beneficial nutrients because they provide increased immune capacity. Although carotenoid research has been conducted in many vertebrates, little research has been done in amphibians, a group that is experiencing global population declines from numerous causes, including disease. We raised two amphibian species through metamorphosis on three carotenoid diets to quantify the effects on life-history traits and post-metamorphic susceptibility to a fungal pathogen (Batrachochytrium dendrobatidis; Bd). Increased carotenoids had no effect on survival...

Data from: Swing-Leg Trajectory of Running Guinea Fowl Suggests Task-Level Priority of Force Regulation Rather than Disturbance Rejection

Yvonne Blum, Hamid R. Vejdani, Aleksandra V. Birn-Jeffery, Christian M. Hubicki, Jonathan W. Hurst & Monica A. Daley
To achieve robust and stable legged locomotion in uneven terrain, animals must effectively coordinate limb swing and stance phases, which involve distinct yet coupled dynamics. Recent theoretical studies have highlighted the critical influence of swing-leg trajectory on stability, disturbance rejection, leg loading and economy of walking and running. Yet, simulations suggest that not all these factors can be simultaneously optimized. A potential trade-off arises between the optimal swing-leg trajectory for disturbance rejection (to maintain steady...

Data from: Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America

John S. Sproul, Derek D. Houston, C. Riley Nelson, R. Paul Evans, Keith A. Crandall & Dennis K. Shiozawa
Background: Phylogeographic studies of aquatic insects provide valuable insights into mechanisms that shape the genetic structure of communities, yet studies that include broad geographic areas are uncommon for this group. We conducted a broad scale phylogeographic analysis of the least salmonfly Pteronarcella badia (Plecoptera) across western North America. We tested hypotheses related to mode of dispersal and the influence of historic climate oscillations on population genetic structure. In order to generate a larger mitochondrial data...

Data from: The complex net effect of reciprocal interactions and recruitment facilitation maintains an intertidal kelp community

Allison K. Barner, Sally D. Hacker, Bruce A. Menge & Karina J. Nielsen
1.Theoretical and empirical ecology has transitioned from a focus on the role of negative interactions in species coexistence to a more pluralistic view that acknowledges that coexistence in natural communities is more complex, and depends on species interactions that vary in strength, sign, and reciprocity, and such contexts as the environment and life history stage. 2. We used a whole-community approach to examine how species interactions contribute to the maintenance of a rocky intertidal macroalgal...

Data from: Temporal genetic variance and propagule-driven genetic structure characterize naturalized rainbow trout (Oncorhynchus mykiss) from a Patagonian lake impacted by trout farming

Javiera Nidia Benavente, Lisa Wishard Seeb, James Edward Seeb, Ivan Arismendi, Cristián Esteban Hernández, Gonzalo Gajardo, Ricardo Galleguillos, Maria Ignacia Cádiz, Selim Seman Musleh & Daniel Gomez-Uchida
Knowledge about the genetic underpinnings of invasions—a theme addressed by invasion genetics as a discipline—is still scarce amid well documented ecological impacts of non-native species on ecosystems of Patagonia in South America. One of the most invasive species in Patagonia’s freshwater systems and elsewhere is rainbow trout (Oncorhynchus mykiss). The species was introduced in Chile during the early twentieth century for stocking and promoting recreational fishing and, during the late twentieth century, for farming purposes...

Data from: Genomic determinants of coral heat tolerance across latitudes

Groves B. Dixon, Sarah W. Davies, Galina A. Aglyamova, Eli Meyer, Line K. Bay & Mikhail V. Matz
As global warming continues, reef-building corals could avoid local population declines through “genetic rescue” involving exchange of heat-tolerant genotypes across latitudes, but only if latitudinal variation in thermal tolerance is heritable. Here, we show an up–to–10-fold increase in odds of survival of coral larvae under heat stress when their parents come from a warmer lower-latitude location. Elevated thermal tolerance was associated with heritable differences in expression of oxidative, extracellular, transport, and mitochondrial functions that indicated...

Data from: Geographic patterns of genetic variation in three genomes of North American diploid strawberries with special reference to Fragaria vesca subsp. bracteata

Lauren Stanley, Nicole J. Forrester, Rajanikanth Govindarajulu, Aaron Liston & Tia-Lynn Ashman
Geographic patterns of genetic variation in wild species reflect the interplay of ecological and evolutionary processes. We assessed genetic variation in three genomes across four North American diploid strawberry taxa, with special emphasis on the gynodioecious Fragaria vesca subsp. bracteata (A.Heller) Staudt. Specifically, we sequenced one chloroplast (rpoC2) and two mitochondrial (atp8 and atp8-orf225) genes along with several nuclear microsatellite markers. In addition, we assessed indicators of breeding system (pollen viability and female frequency) for...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Oregon State University
  • University of Washington
  • University of Georgia
  • University of Pittsburgh
  • United States Department of Agriculture
  • The University of Texas at Austin
  • University of Michigan-Ann Arbor
  • University of British Columbia
  • University of California, Davis
  • Department of Agriculture