509 Works

Data from: Broad-scale trophic shift in the pelagic North Pacific revealed by an oceanic seabird

Peggy H. Ostrom, Anne E. Wiley, Helen F. James, Sam Rossman, William A. Walker, Elise F. Zipkin & Yoshito Chikaraishi
Human-induced ecological change in the open oceans appears to be accelerating. Fisheries, climate change and elevated nutrient inputs are variously blamed, at least in part, for altering oceanic ecosystems. Yet it is challenging to assess the extent of anthropogenic change in the open oceans, where historical records of ecological conditions are sparse, and the geographical scale is immense. We developed millennial-scale amino acid nitrogen isotope records preserved in ancient animal remains to understand changes in...

Fall Creek Reservoir Water Quality Dataset

Stephen Hamilton, Christina Murphy, Sherri Johnson & Amanda Pollock
Water chemistry measurements taken at or downstream of Fall Creek Reservoir, OR (43.9459714, -122.755765). Fall Creek is a tributary of the Middle Fork Willamette River, located approximately 20 miles SE of Eugene, Oregon, USA. Water chemistry measurements included water samples collected from the reservoir outflow (during autumn drawdown) and within Fall Creek Reservoir (during August). These water samples were analyzed to determine concentrations of dissolved organic carbon, suspended sediment, and nutrients. A sonde was used...

Data for: Silica Induction of Diverse Inflammatory Proteome in Lungs of Lupus-prone Mice Quelled by Dietary Docosahexaenoic Acid Supplementation

James Pestka, Lichchavi Rajasinghe & Abby Benninghoff
Repeated short-term intranasal instillation of lupus-prone mice with to crystalline silica (cSiO2) induces inflammatory gene expression and ectopic lymphoid neogenesis in the lung, leading to early onset of systemic autoimmunity and rapid progression to glomerulonephritis. These responses are suppressed by dietary supplementation with the ω-3 polyunsaturated fatty acid docosahexaenoic acid (DHA). Here, we tested the hypothesis that dietary DHA supplementation suppresses cSiO2-induced inflammatory proteins in bronchoalveolar alveolar lavage fluid (BALF) and plasma of lupus-prone mice....

Data from: Runaway sexual selection leads to good genes

Christopher H. Chandler, Charles Ofria & Ian Dworkin
Mate choice and sexual displays are widespread in nature, but their evolutionary benefits remain controversial. Theory predicts these traits can be favored by runaway sexual selection, in which preference and display reinforce one another due to genetic correlation; or by good genes benefits, in which mate choice is advantageous because extreme displays indicate a well-adapted genotype. However, these hypotheses are not mutually exclusive, and the adaptive benefits underlying mate choice can themselves evolve. In particular,...

Data from: Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway

Robert L. Last, Gaurav D. Moghe, Bryan J Leong, Steven M Hurney & A Daniel Jones
The diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome-localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenetics in non-model species. Our results reveal that hundreds of acylsugars...

Data from: Leaf development and demography explain photosynthetic seasonality in Amazon evergreen forests

Jin Wu, Loren P. Albert, Aline P. Lopes, Natalia Restrepo-Coupe, Matthew Hayek, Kenia T. Wiedemann, Kaiyu Guan, Scott C. Stark, Bradley Christoffersen, Neill Prohaska, Julia V. Tavares, Suelen Marostica, Hideki Kobayashi, Mauricio L. Ferreira, Kleber Silva Campos, Rodrigo Da Silva, Paulo M. Brando, Dennis G. Dye, Travis E. Huxman, Alfredo R. Huete, Bruce W. Nelson & Scott R. Saleska
In evergreen tropical forests, the extent, magnitude, and controls on photosynthetic seasonality are poorly resolved and inadequately represented in Earth system models. Combining camera observations with ecosystem carbon dioxide fluxes at forests across rainfall gradients in Amazônia, we show that aggregate canopy phenology, not seasonality of climate drivers, is the primary cause of photosynthetic seasonality in these forests. Specifically, synchronization of new leaf growth with dry season litterfall shifts canopy composition toward younger, more light-use...

Data from: Causes and consequences of genetic background effects illuminated by integrative genomic analysis

Christopher H. Chandler, Sudarshan Chari, David Tack & Ian Dworkin
The phenotypic consequences of individual mutations are modulated by the wild-type genetic background in which they occur. Although such background dependence is widely observed, we do not know whether general patterns across species and traits exist, nor about the mechanisms underlying it. We also lack knowledge on how mutations interact with genetic background to influence gene expression, and how this in turn mediates mutant phenotypes. Furthermore, how genetic background influences patterns of epistasis remains unclear....

Data from: Constraints on geographic variation in fiddler crabs (Ocypodidae: Uca) from the western Atlantic

Melanie J. Hopkins, Annat Haber & Carl L Thurman
A key question in evolutionary biology is how intraspecific variation biases the evolution of a population and its divergence from other populations. Such constraints potentially limit the extent to which populations respond to selection, but may endure long enough to have macroevolutionary consequences. Previous studies have focused on the association between covariation patterns and divergence among isolated populations. Few have focused on geographic variation among semi-connected populations, however, even though this may be indicative of...

Data from: A simple, cost-effective emitter for controlled release of fish pheromones: development, testing, and application to management of the invasive sea lamprey

C. Michael Wagner, James E. Hanson, Trevor D. Meckley, Nicholas S. Johnson & Jason D. Bals
Semiochemicals that elicit species-specific attraction or repulsion have proven useful in the management of terrestrial pests and hold considerable promise for control of nuisance aquatic species, particularly invasive fishes. Because aquatic ecosystems are typically large and open, use of a semiochemical to control a spatially dispersed invader will require the development of a cost-effective emitter that is easy to produce, environmentally benign, inexpensive, and controls the release of the semiochemical without altering its structure. We...

Data from: No release for the wicked: enemy release is dynamic and not associated with invasiveness

Elizabeth H. Schultheis, Andrea E. Berardi & Jennifer A. Lau
The enemy release hypothesis predicts that invasive species will receive less damage from enemies, compared to co-occurring native and noninvasive exotic species in their introduced range. However, release operating early in invasion could be lost over time and with increased range size as introduced species acquire new enemies. We used three years of data, from 61 plant species planted into common gardens, to determine whether (1) invasive, noninvasive exotic, and native species experience differential damage...

Data from: Nutritional control of body size through FoxO-Ultraspiracle mediated ecdysone biosynthesis

Takashi Koyama, Marisa A. Rodrigues, Alekos Athanasiadis, Alexander W. Shingleton & Christen K. Mirth
Despite their fundamental importance for body size regulation, the mechanisms that stop growth are poorly understood. In Drosophila melanogaster, growth ceases in response to a peak of the molting hormone ecdysone that coincides with a nutrition-dependent checkpoint, critical weight. Previous studies indicate that insulin/insulin-like growth factor signaling (IIS)/Target of Rapamycin (TOR) signaling in the prothoracic glands (PGs) regulates ecdysone biosynthesis and critical weight. Here we elucidate a mechanism through which this occurs. We show that...

Data from: A meta-analysis of non-consumptive predator effects in arthropods: the influence of organismal and environmental characteristics

Amanda L. Buchanan, Sara L. Hermann, Margaret Lund & Zsofia Szendrei
Non-consumptive effects (NCEs) – changes in prey behavior or physiology in response to predator threat – are common and can be as strong as consumptive effects. However, our knowledge of NCEs in arthropod systems is lacking. Factors related to study organism and environment have the potential to influence the occurrence and magnitude of NCEs in arthropod systems. While factors such as coevolutionary history of natural enemies and their prey, predator cue, predator or prey feeding...

Data from: Plant functional traits and environmental conditions shape community assembly and ecosystem functioning during restoration

Chad R. Zirbel, Tyler Basset, Emily Grman, Lars A. Brudvig & Tyler Bassett
Recovering biological diversity and ecosystem functioning are primary objectives of ecological restoration, yet these outcomes are often unpredictable. Assessments based on functional traits may help with interpreting variability in both community composition and ecosystem functioning because of their mechanistic and generalizable nature. This promise remains poorly realized, however, because tests linking environmental conditions, functional traits, and ecosystem functioning in restoration are rare. Here, we provide such a test through what is to our knowledge the...

Data from: Novel loci underlie natural variation in vitamin E levels in maize grain

Christine H. Diepenbrock, Catherine B. Kandianis, Alexander E. Lipka, Maria Magallanes-Lundback, Brieanne Vaillancourt, Elsa Góngora-Castillo, Jason G. Wallace, Jason Cepela, Alex Mesberg, Peter J. Bradbury, Daniel C. Ilut, Maria Mateos-Hernandez, John Hamilton, Brenda F. Owens, Tyler Tiede, Edward S. Buckler, Rocheford Torbert, C. Robin Buell, Michael A. Gore & Dean DellaPenna
Tocopherols, tocotrienols and plastochromanols (collectively termed tocochromanols) are lipid-soluble antioxidants synthesized by all plants. Their dietary intake, primarily from seed oils, provides vitamin E and other health benefits. Tocochromanol biosynthesis has been dissected in the dicot Arabidopsis thaliana, which has green, photosynthetic seeds, but our understanding of tocochromanol accumulation in major crops, whose seeds are non-photosynthetic, remains limited. To understand the genetic control of tocochromanols in grain, we conducted a joint linkage and genome-wide association...

Data from: Spectral diversity area relationships for assessing biodiversity in a wildland-agriculture matrix

Kyla Marie Dahlin
Species-area relationships have long been used to assess patterns of species diversity across scales. Here this concept is extended to spectral diversity using hyperspectral data collected by NASA's Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) over western Michigan. This mixture of mesic forest and agricultural lands offers two end-points on the local-scale diversity continuum – one set of well mixed forest patches and one set of highly homogeneous agricultural patches. Using the sum of the first three...

Data from: A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways

Dongyan Zhao, John P. Hamilton, Wajid Waheed Bhat, Sean R. Johnson, Grant T. Godden, Taliesin J. Kinser, Benoît Boachon, Natalia Dudareva, Douglas E. Soltis, Pamela S. Soltis, Bjoern Hamberger & C. Robin Buell
Background: Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired...

Data from: Genome-wide association and genomic prediction models of tocochromanols in fresh sweet corn kernels

Matheus Baseggio, Matthew Murray, Maria Magallanes-Lundback, Nicholas Kaczmar, James Chamness, Edward Buckler, Margaret Smith, Dean DellaPenna, William Tracy, Michael Gore, Margaret E. Smith, Michael A. Gore, William F. Tracy & Edward S. Buckler
Sweet corn (Zea mays L.), a highly consumed fresh vegetable in the United States, varies for tocochromanol (tocopherol and tocotrienol) levels, but makes limited contribution to daily intake of vitamin E and antioxidants. We performed a genome-wide association study of six tocochromanol compounds and 14 derivative traits across a sweet corn inbred line association panel to identify genes associated with natural variation for tocochromanols and vitamin E in fresh kernels. Concordant with prior studies in...

Data from: Gene discovery in Gelsemium highlights conserved gene clusters in monoterpene indole alkaloid biosynthesis

Jakob Franke, Jeongwoon Kim, John P. Hamilton, Dongyan Zhao, Gina M. Pham, Krystle Wiegert-Rininger, Emily Crisovan, Linsey Newton, Brieanne Vaillancourt, Evangelos Tatsis, C. Robin Buell & Sarah E. O'Connor
gel_v1_asm.fastaGenome assembly of Gelsemium sempervirens (version 1), containing 3,352 scaffold sequencescro_v2_asm.fastaGenome assembly of Catharanthus roseus (version 2), containing 2,090 scaffold sequencesgel_v1.gene_models.gff3Gene Model Annotation for Gelsemium sempervirens (version 1) in Generic Feature Format 3 (GFF3)gel_v1.transcripts.fastaGelsemium sempervirens (version 1) transcript sequencesgel_v1.proteins.fastaGelsemium sempervirens (version 1) protein sequencescro_v2.gene_models.gff3Gene Model Annotation for Catharanthus roseus (version 2) in Generic Feature Format 3 (GFF3)cro_v2.transcripts.fastaCatharanthus roseus (version 2) transcript sequencescro_v2.proteins.fastaCatharanthus roseus (version 2) protein sequencesREADME.txtREADME.txtREADME.txt

Data from: Tropical tree growth is correlated with soil phosphorus, potassium, and calcium, though not for legumes

Thomas W. Baribault, Richard K. Kobe & Andrew O. Finley
Tropical forest productivity is widely assumed to be limited by soil phosphorus (P), but biogeochemical processes that deplete P also could deplete base cations, suggesting multiple resource limitation. Limitation by several resources could arise from species and functional diversity, and variation among groups in resource requirements, including ecophysiological strategies that minimize P limitation. We hypothesized that tree growth is positively related to soil base cation and P availability and negatively related to local competition; Fabaceae...

Data from: Floral function: effects of traits on pollinators, male and female pollination success, and female fitness across three species of milkweeds (Asclepias)

Raffica J. La Rosa & Jeffrey K. Conner
PREMISE OF THE STUDY: Central questions in plant reproductive ecology are whether the functions of floral traits in hermaphrodites create conflict between sexes that could slow evolution, and whether individual floral traits function in pollinator attraction, efficiency, or both. We studied how floral traits affect pollinator visitation and efficiency, and how they affect male and female function and female fitness within and across three Asclepias species that differ in floral morphology. METHODS: Using separate multiple...

Data from: Stress hormones mediate predator-induced phenotypic plasticity in amphibian tadpoles

Jessica Middlemis Maher, Earl E. Werner & Robert J. Denver
Amphibian tadpoles display extensive anti-predator phenotypic plasticity, reducing locomotory activity and, with chronic predator exposure, developing relatively smaller trunks and larger tails. In many vertebrates, predator exposure alters activity of the neuroendocrine stress axis. We investigated predator-induced effects on stress hormone production and the mechanistic link to anti-predator defences in Rana sylvatica tadpoles. Whole-body corticosterone (CORT) content was positively correlated with predator biomass in natural ponds. Exposure to caged predators in mesocosms caused a reduction...

Data from: Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards

Travis Jay Hagey, Josef C. Uyeda, Kristen E. Crandell, Jorn A. Cheney, Kellar Autumn & Luke J. Harmon
Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics....

Data from: The influence of dispersal on the realized trajectory of a pond metacommunity

Patrick J. Hanly & Gary G. Mittelbach
Dispersal rates play a critical role in metacommunity dynamics, yet few studies have attempted to characterize dispersal rates for the majority of species in any natural community. Here we evaluate the relationship between the abundances of 179 plankton taxa in a pond metacommunity and their dispersal rates. We find the expected positive relationship between the regional abundances of phytoplankton, protozoa and metazoan zooplankton, which is suggestive of dispersal being a density-independent per capita rate for...

Data from: Species characteristics affect local extinctions

Meredith Ann Zettlemoyer, Duane D. McKenna & Jennifer A. Lau
Premise of the study. Human activities threaten thousands of species with extinction. However, it remains difficult to predict extinction risk for many vulnerable species. Species characteristics help predict responses to anthropogenic environmental change and may help predict likelihood of extinction. Phylogenetic signatures of extinction can also provide insights into patterns of species loss. Historical data on species losses can allow for testing phylogenetic patterns in extinctions and identifying traits that influence species vulnerability to local...

Data From - TE Density: a tool to investigate the biology of transposable elements

Scott Teresi & Patrick Edger
Background: Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to theirinherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE’s potential to impact phenotype is partially a factor of its location in the genome. Previous research has shown TEs’ ability to impact the expression of neighboring genes, however our understanding of this trend is hampered by...

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