18 Works

Data from: Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands environmental gradient

Miranda M. Gray, Paul St. Amand, Nora M. Bello, Mary Knapp, Karen A. Garrett, Theodore J. Morgan, Sara G. Baer, Brian R. Maricle, Eduard D. Akhunov, Loretta C. Johnson & Matthew B. Galliart
Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study the nature of population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation-by-distance (IBD)...

Data from: Emergence timing and fitness consequences of variation in seed oil composition in Arabidopsis thaliana

Sandra E. Pelc & C. Randal Linder
Early seedling emergence can increase plant fitness under competition. Seed oil composition (the types and relative amounts of fatty acids in the oils) may play an important role in determining emergence timing and early growth rate in oilseeds. Saturated fatty acids provide more energy per carbon atom than unsaturated fatty acids but have substantially higher melting points (when chain length is held constant). This characteristic forms the basis of an adaptive hypothesis that lower melting...

Data from: Hallauer's Tusón: a decade of selection for tropical- to-temperate phenological adaptation in maize

Juliana E. C. Teixeira, Teclemariam Weldekidan, Natalia De Leon, Sherry Flint-Garcia, James B. Holland, Nick Lauter, Seth C. Murray, Wenwei Xu, David A. Hessel, Adrienne E. Kleintop, James A. Hawk, Arnel R. Hallauer & Randall J. Wisser
Crop species exhibit an astounding capacity for environmental adaptation, but genetic bottlenecks resulting from intense selection for adaptation and productivity can lead to a genetically vulnerable crop. Improving the genetic resiliency of temperate maize depends upon the use of tropical germplasm, which harbors a rich source of natural allelic diversity. Here, the adaptation process was studied in a tropical maize population subjected to 10 recurrent generations of directional selection for early flowering in a single...

Data from: Weather-driven dynamics in a dual-migrant system: moths and bats

Jennifer J. Krauel, John K. Westbrook & Gary F. McCracken
Animal migrations generate large spatial and temporal fluctuations in biomass that provide a resource base for many predator-prey interactions. These interactions are often driven by continent-scale weather patterns and are difficult to study. Few studies have included migratory animals on more than a single trophic level or for periods spanning multiple entire seasons. We tracked migrations of three species of agricultural pest noctuid moths over the 2010-2012 autumn seasons as the moths traveled past a...

Data from: Predator community structure and trophic linkage strength to a focal prey

Jonathan G. Lundgren & Janet K. Fergen
Predator abundance and community structure can increase or decrease the suppression of lower trophic levels, although studies of these interactions under field conditions are relatively few. We investigated how the frequency of consumption (measured using PCR-based gut analysis) is affected by predator abundance, community diversity and evenness under realistic conditions. Soil arthropod communities in sixteen maize fields were measured (number of predators, diversity [Shannon H], and evenness [J]) and predator guts were searched for DNA...

Data from: SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation

Chao Li, Geoff Waldbieser, Brian Bosworth, Benjamin H. Beck, Wilawan Thongda & Eric Peatman
Blue catfish, Ictalurus furcatus, are valued in the United States as a trophy fishery for their capacity to reach large sizes, sometimes exceeding 45 kg. Additionally, blue catfish × channel catfish (I. punctatus) hybrid food fish production has recently increased the demand for blue catfish broodstock. However, there has been little study of the genetic impacts and interaction of farmed, introduced and stocked populations of blue catfish. We utilized genotyping-by-sequencing (GBS) to capture and genotype...

Data from: Global invasion history of the Tropical Fire Ant: a stowaway on the first global trade routes

Dietrich Gotzek, Heather Axen, Andrew Suarez, Sara Helms Cahan, D. DeWayne Shoemaker, Andrew V. Suarez & Heather J. Axen
Biological invasions are largely thought to be contemporary, having recently increased sharply in the wake of globalization. However, human commerce had already become global by the mid-16th century when the Spanish connected the New World with Europe and Asia via their Manila galleon and West Indies trade routes. We use genetic data to trace the global invasion of one of the world's most widespread and invasive pest ants, the Tropical Fire Ant, Solenopsis geminata. Our...

Data from: Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)

Eli Meyer, Michael J. Aspinwall, David B. Lowry, Juan Diego Palacio-Mejía, Tierney L. Logan, Philip A. Fay & Thomas E. Juenger
Background: In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel...

Data from: Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

Weidong Chen, Renuka N. Attanayake, Vidhura Tennekoon, Dennis A. Johnson, Lyndon D. Porter, Luis Del Río-Mendoza & Daohong Jiang
The occurrence and frequency of outcrossing in homothallic fungal species in nature is an unresolved question. Here we report detection of frequent outcrossing in the homothallic fungus Sclerotinia sclerotiorum. In using multilocus linkage disequilibrium (LD) to infer recombination among microsatellite alleles, high mutation rates confound the estimates of recombination. To distinguish high mutation rates from recombination to infer outcrossing, 8 population samples comprising 268 S. sclerotiorum isolates from widely distributed agricultural fields were genotyped for...

Data from: Conserved genetic regions across angiosperms as tools to develop single copy nuclear markers in gymnosperms: an example using cycads

Dayana E. Salas-Leiva, Alan W. Meerow, Javier Francisco-Ortega, Michael Calonje, M. Patrick Griffith, Dennis W. Stevenson & Kyoko Nakamura
Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: 1) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and, 2) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single Copy genes (APVO SSC) against the EST Zamia databases in Genbank. From the first strategy, 30 loci were selected, and from...

Data from: Complementarity of statistical treatments to reconstruct worldwide routes of invasion: the case of the Asian ladybird Harmonia axyridis

Eric Lombaert, Thomas Guillemaud, Jonathan Lundgren, Robert Koch, Benoît Facon, Audrey Grez, Antoon Loomans, Thibaut Malausa, Oldrich Nedved, Emma Rhule, Arnstein Staverlokk, Tove Steenberg & Arnaud Estoup
Inferences about introduction histories of invasive species remain challenging because of the stochastic demographic processes involved. Approximate Bayesian computation (ABC) can help to overcome these problems, but such method requires a prior understanding of population structure over the study area, necessitating the use of alternative methods and an intense sampling design. In this study, we made inferences about the worldwide invasion history of the ladybird Harmonia axyridis by various population genetics statistical methods, using a...

Data from: Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches

Martin P. Schilling, Paul G. Wolf, Aaron M. Duffy, Hardeep S. Rai, Carol A. Rowe, Bryce A. Richardson & Karen E. Mock
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in...

Data from: Interactive effects of a non-native invasive grass Microstegium vimineum and herbivore exclusion on experimental tree regeneration under differing forest management

Daniel J. Johnson, S. Luke Flory, Angela Shelton, Cynthia Huebner & Keith Clay
1. Invasive plants, herbivores and site management history can play crucial roles in determining plant community composition. The net effects of invasive species on plant communities are well known, but we have a poor understanding of the relative contributions of direct competitive effects of invasive species and their interactions with herbivores and management practices. Understanding interactions among plant invasions, herbivores and management history is critical for predicting and managing long-term ecological effects of invasions on...

Data from: Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle

Jared Egan Decker, Stephanie D. McKay, Megan M. Rolf, JaeWoo Kim, Antonio Molina Alcalá, Tad S. Sonstegard, Olivier Hanotte, Anders Götherström, Christopher M. Seabury, Lisa Praharani, Masroor Ellahi Babar, Luciana Correia De Almieda Regitano, Mehmet Ali Yildiz, Michael P. Heaton, Wan-Sheng Liu, Chu-Zhao Lei, James M. Reecy, Muhammad Saif-Ur-Rehman, Robert D. Schnabel & Jeremy F. Taylor
The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns...

Data from: Leaf litter nutrient uptake in an intermittent blackwater river: influence of tree species and associated biotic and abiotic drivers

Andrew S. Mehring, Kevin A. Kuehn, Aaron Thompson, Catherine M. Pringle, Amy D. Rosemond, Matthew R. First, R Richard Lowrance & George Vellidis
1. Organic matter may sequester nutrients as it decomposes, increasing in total N and P mass via multiple uptake pathways. During leaf litter decomposition, microbial biomass and accumulated inorganic materials immobilize and retain nutrients, and therefore, both biotic and abiotic drivers may influence detrital nutrient content. We examined the relative importance of these types of nutrient immobilization and compared patterns of nutrient retention in recalcitrant and labile leaf litter. 2. Leaf packs of water oak...

Data from: Distance, flow, and PCR inhibition: eDNA dynamics in two headwater steams

Stephen F. Jane, Taylor M. Wilcox, Kevin S. McKelvey, Michael K. Young, Michael K. Schwartz, Winsor H. Lowe, Benjamin H. Letcher & Andrew R. Whiteley
Environmental DNA (eDNA) detection has emerged as a powerful tool for monitoring aquatic organisms, but much remains unknown about the dynamics of aquatic eDNA over a range of environmental conditions. DNA concentrations in streams and rivers will depend not only on the equilibrium between DNA entering the water and DNA leaving the system through degradation, but also on downstream transport. To improve understanding of the dynamics of eDNA concentration in lotic systems, we introduced caged...

Data from: The Genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos)

Jacqueline M. Doyle, Todd E. Katzner, Peter H. Bloom, Yanzhu Ji, Bhagya K. Wijayawardena & J. Andrew DeWoody
Biologists routinely use molecular markers to identify conservation units, to quantify genetic connectivity, to estimate population sizes, and to identify targets of selection. Many imperiled eagle populations require such efforts and would benefit from enhanced genomic resources. We sequenced, assembled, and annotated the first eagle genome using DNA from a male golden eagle (Aquila chrysaetos) captured in western North America. We constructed genomic libraries that were sequenced using Illumina technology and assembled the high-quality data...

Data from: How topography induces reproductive asynchrony and alters gypsy moth invasion dynamics

Jonathan A. Walter, Marcia S. Meixler, Thomas Mueller, William F. Fagan, Patrick C. Tobin & Kyle J. Haynes
1. Reproductive asynchrony, a temporal mismatch in reproductive maturation between an individual and potential mates, may contribute to mate-finding failure and Allee effects that influence the establishment and spread of invasive species. Variation in elevation is likely to promote variability in maturation times for species with temperature-dependent development, but it is not known how strongly this influences reproductive asynchrony or the population growth of invasive species. 2. We examined whether spatial variation in reproductive asynchrony,...

Registration Year

  • 2014
    18

Resource Types

  • Dataset
    18

Affiliations

  • United States Department of Agriculture
    18
  • The University of Texas at Austin
    2
  • University of Vermont
    2
  • Texas A&M University
    2
  • Iowa State University
    2
  • North West Agriculture and Forestry University
    1
  • University of Massachusetts Amherst
    1
  • University of Montana
    1
  • University of Veterinary and Animal Sciences
    1
  • Utah State University
    1