387 Works

R/QTL datasets for fusiform rust resistance QTL mapping

Fikret Isik & Edwin Lauer
Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f. sp. fusiforme, is the most damaging disease affecting economically important pine species in the southeast United States. In this report, we detail the genomic localization and sequence-level discovery of candidate race-nonspecific broad-spectrum fusiform rust resistance genes in Pinus taeda L. Two full-sib families, each with ~1000 progeny, were challenged with a complex inoculum consisting of over 150 pathogen isolates. High-density linkage mapping revealed three...

National survey of college students' beliefs, attitudes, and behaviors related to hunting, fishing, and wildlife conservation

Lincoln Larson
This dataset contains responses from an online survey of diverse undergraduate students (ages 18-34 years) attending 22 different universities across 22 U.S. states (total n = 17,203). Survey questions focused on students' beliefs, attitudes, and behaviors related to hunting, fishing, and wildlife conservation. The survey was conducted from 2018-2020.

A greenhouse experiment partially supports inferences of ecogeographic isolation from niche models of Clarkia sister species

Kathleen Kay, Kaleb Goff & Cormac Martinez Del Rio
Premise: Ecogeographic isolation, or geographic isolation caused by ecological divergence, is thought to be of primary importance in speciation, yet is difficult to demonstrate and quantify. To determine whether distributions are limited by divergent adaptation or historical contingency, the gold standard is to reciprocally transplant taxa between their geographic ranges. Alternatively, ecogeographic isolation is inferred from species distribution models and niche divergence tests based on widely available environmental and occurrence data. Methods: We test for...

Compensatory growth and costs of molluscivory in Gambusia holbrooki

Brian Langerhans, Taylor Goins, Kenzi Stemp & Rüdiger Riesch
Some prey are exceptionally difficult to digest, and yet even non-specialized animals may consume them—why? Durophagy, the consumption of hard-shelled prey, is thought to require special adaptations for crushing or digesting the hard shells to avoid the many potential costs of this prey type. But many animals lacking specializations nevertheless include hard-bodied prey in their diets. We describe several non-mutually exclusive adaptive mechanisms that could explain such a pattern, and point to optimal foraging and...

Searching for deep-seated thrust faults on the moon

Matthew Collins
The lunar maria are large expanses of basalt that infill antecedent impact basins and show evidence for post-emplacement deformation. Landforms within many of these basins suggest a period of compressive tectonics, although the mechanism for their formation remains an open question. Previous work for Mare Crisium demonstrated that basin-circumferential wrinkle ridges, which typically demarcate the inner edge of an annulus of elevated terrain, are the result of deep-seated thrust faults that preferentially form along the...

Genomic population structure of striped bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River

Nathalie LeBlanc, Benjamin Gahagan, Samuel Andrews, Trevor Avery, Gregory Puncher, Benjamin Reading, Colin Buhariwalla, R Allen Curry, Andrew Whitely & Scott Pavey
Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish species that supports fisheries throughout North America and is native to the North American Atlantic Coast. Due to long coastal migrations that span multiple jurisdictions, a detailed understanding of population genomics is required to untangle demographic patterns, understand local adaptation, and characterize population movements. This study used 1256 single nucleotide polymorphism (SNP) loci to investigate genetic structure of 477 Striped Bass sampled from 15 locations...

Data from: Bee phenology is predicted by climatic variation and functional traits

Michael Stemkovski, Will Pearse, Sean Griffin, Gabriella Pardee, Jason Gibbs, Terry Griswold, John Neff, Ryan Oram, Molly RightMyer, Cory Sheffield, Karen Wright, Brian Inouye, David Inouye & Rebecca Irwin
Climate change is shifting the environmental cues that determine the phenology of interacting species. Plant-pollinator systems may be susceptible to temporal mismatch if bees and flowering plants differ in their phenological responses to warming temperatures. While the cues that trigger flowering are well-understood, little is known about what determines bee phenology. Using Generalized Additive Models, we analyzed time-series data representing 67 bee species collected over nine years in the Colorado Rocky Mountains to perform the...

Outdoor activity participation improves adolescents’ mental health and well-being during the COVID-19 pandemic

Steven Jackson, Kathryn Stevenson, Lincoln Larson, Nils Peterson & Erin Seekamp
The COVID-19 pandemic is reshaping human interactions with the natural environment, generating profound consequences for health and well-being. To assess the effects of COVID-19 on the outdoor recreation participation and well-being of adolescents we conducted a nationally representative survey of youth ages 10-18 across the United States (n = 624) using a Qualtrics XM panel between April 30 and June 15, 2020. Survey questions focused on frequency of participation in several types of outdoor activities...

Drought legacy affects microbial community trait distributions related to moisture along a savannah grassland precipitation gradient

Ainara Leizeaga, Lettice C. Hicks, Lokeshwaran Manoharan, Christine V. Hawkes & Johannes Rousk
Ecosystem models commonly use stable-state assumptions to predict responses of soil microbial functions to environmental change. However, past climatic conditions can shape microbial functional responses resulting in a “legacy effect”. For instance, exposure to drier conditions in the field may shape how soil microbial communities respond to subsequent drought and drying and rewetting events. We investigated microbial tolerance to low moisture levels (“resistance”) and ability to recover after a drying and rewetting (DRW) perturbation (“resilience”)...

Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby

Keith Weninger, Pengyu Hao, Sharonda J. LeBlanc, Brandon C. Case, Timothy C. Elston, Manju M. Hingorani & Dorothy A. Erie
DNA mismatch repair (MMR), the guardian of the genome, commences when MutS identifies a mismatch and recruits MutL to nick the error-containing strand, allowing excision and DNA resynthesis. Dominant MMR models posit that after mismatch recognition, ATP converts MutS to a hydrolysis-independent, diffusive mobile clamp that no longer recognizes the mismatch. Little is known about the postrecognition MutS mobile clamp and its interactions with MutL. Two disparate frameworks have been proposed: One in which MutS–MutL...

Data for: Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems

Thomas Jacobsen, Gloria Yi, Hadel Al Asafen, Ashley Jermusyk, Chase Beisel & Gregory Reeves
Advancements in the field of synthetic biology have been possible due to the development of genetic tools that are able to regulate gene expression. However, the current toolbox of gene regulatory tools for eukaryotic systems have been outpaced by those developed for simple, single-celled systems. Here, we engineered a set of gene regulatory tools by combining self-cleaving ribozymes with various upstream competing sequences that were designed to disrupt ribozyme self-cleavage. As a proof-of-concept, we were...

Large losses of ammonium-nitrogen from a rice ecosystem under elevated CO2

Lei Cheng, Chenchao Xu, Kaihang Zhang, Wanying Zhu, Jing Xiao, Chen Zhu, Naifang Zhang, Fangjian Yu, Shuyao Li, Chunwu Zhu, Qichao Tu, Xin Chen, Jianguo Zhu, Shuijin Hu, Roger T Koide & Mary K Firestone
Inputs of nitrogen into terrestrial ecosystems, mainly via the use of ammonium-based fertilizers in agroecosystems, are enormous, but its fate under elevated atmospheric carbon dioxide (CO2) is not well understood. We have taken advantage of a 15-year free air CO2 enrichment study to investigate the influence of elevated CO2 on the transformation of ammonium-nitrogen in a rice ecosystem in which ammonium is usually assumed to be stable under anaerobic conditions. We demonstrate that elevated CO2...

Data for: Predation risk and the evolution of a vertebrate stress response: parallel evolution of stress reactivity and sexual dimorphism

Jerker Vinterstare, Gustaf MO Ekelund Ugge, Kaj Hulthén, Alexander Hegg, Christer Brönmark, P Anders Nilsson, U Ronja Zellmer, Marcus Lee, Varpu Pärssinen, Yongcui Sha, Caroline Björnerås, Huan Zhang, Raphael Gollnisch, Simon David Herzog, Lars-Anders Hansson, Martin Škerlep, Nan Hu, Emma Johansson & R Brian Langerhans
Predation risk is often invoked to explain variation in stress responses. Yet, the answers to several key questions remain elusive, including: 1) how predation risk influences the evolution of stress phenotypes, 2) the relative importance of environmental versus genetic factors in stress reactivity, and 3) sexual dimorphism in stress physiology. To address these questions, we explored variation in stress reactivity (ventilation frequency) in a post-Pleistocene radiation of live-bearing fish, where Bahamas mosquitofish (Gambusia hubbsi) inhabit...

Data from: Plant host traits mediated by foliar fungal symbionts and secondary metabolites

Christine Hawkes & Moriah Sandy
Fungal symbionts living inside plant leaves (“endophytes”) can vary from beneficial to parasitic, but the mechanisms by which the fungi affect the plant host phenotype remain poorly understood. Chemical interactions are likely the proximal mechanism of interaction between foliar endophytes and the plant, as individual fungal strains are often exploited for their diverse secondary metabolite production. Here, we go beyond single strains to examine commonalities in how 16 fungal endophytes shift plant phenotypic traits such...

Growth and photosynthesis or red maples subjected to drought in North Carolina

Steven Frank
These data were collected from 27 April 2017 through 4 Septmber 2017. Data are measurements of plant physiology collected using a LI-COR LI-6400XT Portable Photosynthesis System. Methods detailed in: Lahr, E.C., Backe, K.M. & Frank, S.D. Intraspecific variation in morphology, physiology, and ecology of wildtype relative to horticultural varieties of red maple (Acer rubrum). Trees 34, 603–614 (2020).

Data from: Wing patterning gene redefines the mimetic history of Heliconius butterflies

Heather M. Hines, Brian A. Counterman, Riccardo Papa, Priscila Albuquerque De Moura, Marcio Z. Cardoso, Mauricio Linares, James Mallet, Robert D. Reed, Chris D. Jiggins, Marcus R. Kronforst, W. Owen McMillan, R. D. Reed, J. Mallet, W. O. McMillan, M. R. Kronforst, H. M. Hines, B. A. Counterman, M. Linares, M. Z. Cardoso & C. D. Jiggins
The mimetic butterflies Heliconius erato and H. melpomene have undergone parallel radiations to form a near-identical patchwork of over 20 different wing pattern races across the Neotropics. Previous molecular phylogenetic work on these radiations has suggested that similar but geographically disjunct color patterns arose multiple times independently in each species. The neutral markers used in these studies, however, can move freely across color pattern boundaries and therefore might not represent the history of the adaptive...

Data from: Evidence that Egfr contributes to cryptic genetic variation for photoreceptor determination in natural populations of Drosophila melanogaster

Ian Dworkin, Arnar Palsson, Kelli Birdsall & Greg Gibson
One objective of quantitative genetics is to identify the nucleotide variants within genes that contribute to phenotypic variation and susceptibility [1]. In an evolutionary context, this means characterizing the molecular polymorphisms that modify the penetrance and expressivity of perturbed traits. A survey of association between 267 SNPs in almost 11 kb of the D. melanogaster Egfr and the degree of eye roughening due to a gain-of-function EgfrE1 allele crossed into 210 isogenic wild-type lines provides...

Data from: Best practices for justifying fossil calibrations

James F. Parham, Philip C. J. Donoghue, Christopher J. Bell, Tyler D. Calway, Jason J. Head, Patricia A. Holroyd, Jun G. Inoue, Randall B. Irmis, Walter G. Joyce, Daniel T. Ksepka, José S. L. Patané, Nathan D. Smith, James E. Tarver, Marcel Van Tuinen, Ziheng Yang, Kenneth D. Angielczyk, Jenny M. Greenwood, Christy A. Hipsley, Jacobs Louis, Peter J. Makovicky, Johannes Müller, Krister T. Smith, Jessica M. Theodor, Rachel C. M. Warnock, Michael J. Benton … & Louis Jacobs
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule; with replacement rates established (calibrated) using inaccurate paleontological age estimates...

Data from: Loss of sexual recombination and segregation is associated with increased diversification in evening primroses

Marc T. J. Johnson, Richard Gareth FitzJohn, Stacey D. Smith, Mark D. Rausher & Sarah P. Otto
The loss of sexual recombination and segregation in asexual organisms has been portrayed as an irreversible process that commits asexually-reproducing lineages to reduced diversification. We test this hypothesis by estimating rates of speciation, extinction, and transition between sexuality and functional asexuality in the evening primroses. Specifically, we estimate these rates using the recently developed BiSSE (Binary State Speciation and Extinction) phylogenetic comparative method, which employs maximum likelihood and Bayesian techniques. We infer that net diversification...

Data from: Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster

Greg Gibson, Rebecca Riley-Berger, Larry Harshman, Artyom Kopp, Scott Vacha, Sergey Nuzhdin & Marta Wayne
Assessment of the degree to which gene expression is additive and heritable has important implications for understanding the maintenance of variation, adaptation, phenotypic divergence, and the mapping of genotype onto phenotype. We used whole-genome transcript profiling using Agilent long-oligonucleotide microarrays representing 12,017 genes to demonstrate that gene transcription is pervasively nonadditive in Drosophila melanogaster. Comparison of adults of two isogenic lines and their reciprocal F1 hybrids revealed 5820 genes as significantly different between at least...

Data from: Ecological effects on metabolic scaling amphipod responses to fish predators in freshwater springs

Douglas S. Glazier, Eric M. Butler, Sara A. Lombardi, Travis J. Deptola, Andrew J. Reese & Erin V. Satterthwaite
Metabolic rate is commonly thought to scale with body mass to the 3/4-power as a result of universal body-design constraints. However, recent comparative work has shown that the metabolic scaling slope may vary significantly among species and higher taxa, apparently in response to different lifestyles and ecological conditions, though the precise mechanisms involved are not well understood. To better understand these under-appreciated ecological effects and their causes, it is important to control for extraneous phylogenetic...

Data from: Gene expression profiles associated with the transition to parasitism in Ancylostoma caninum larvae

Jennifer M. Moser, Tori Freitas, Prema Arasu & Greg Gibson
Ancylostoma caninum is a common canine parasite responsible for anemia and death in infected dogs. Gene expression profiling was used to investigate molecular differences between two different forms of the third larval stage (L3s): infective free-living larvae and in vitro serum-stimulated larvae that mimic the initial stages of parasitism of a host. We developed an A. caninum cDNA microarray consisting of 4191 EST clones, and used it to identify a set of 113 genes that...

Data from: Phenotypic plasticity in sexual communication signal of a noctuid moth

Astrid Groot, Alice Classen, Heike Staudacher, Coby Schal & David Heckel
Variability within sex pheromone signalling systems is generally believed to be low because of strong stabilizing selection; yet the noctuid moth Heliothis subflexa (Hs) shows significant intraspecific variation. One possible explanation is that females may alter their sex pheromone blend depending on prevailing olfactory cues in the habitat, which we termed the "experience hypothesis". This could be adaptive if Hs females experiencing the pheromone of another species, Heliothis virescens (Hv), responded to reduce the frequency...

Data from: Comparing the genetic architecture and potential response to selection of native and invasive populations of reed canary grass

Brittny Calsbeek, Manisha Patel, Sebastien Lavergne & Jane Molofsky
Evolutionary processes such as migration, genetic drift, and natural selection are thought to play a prominent role in species invasions into novel environments. However, few empirical studies have explored the mechanistic basis of invasion in an evolutionary framework. One promising tool for inferring evolutionarily important changes in introduced populations is the genetic variance-covariance matrix (G matrix). G matrix comparisons allow for the inference of changes in the genetic architecture of introduced populations relative to their...

Data from: Mixture modeling of transcript abundance classes in natural populations

Wen-Ping Hsieh, Gisele Passador-Gurgel, Eric A. Stone & Greg Gibson
BACKGROUND: Populations diverge in genotype and phenotype under the influence of such evolutionary processes as genetic drift, mutation accumulation, and natural selection. Because genotype maps onto phenotype by way of transcription, it is of interest to evaluate how these evolutionary factors influence the structure of variation at the level of transcription. Here, we explore the distributions of cis-acting and trans-acting factors and their relative contributions to expression of transcripts that exhibit two or more classes...

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