Data from: River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish communityTyler J. Pilger, Keith B. Gido, David L. Propst, James E. Whitney & Thomas F. Turner
Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species’ genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for...
Data from: Comparative transcriptomics support evolutionary convergence of diapause responses across InsectaGregory J. Ragland & Evan Keep
Diapause is a common phenotype that is broadly phylogenetically dispersed across Insecta and appears to have multiple evolutionary origins. Nevertheless, there are clear commonalities in diapause regulation across insect taxa. In the present study, we report a meta-analysis of diapause whole transcriptomic data sets from 11 different insect species that addresses three questions: (i) how similar are whole-transcriptome diapause responses across species within and across different diapause life-cycle stages; (ii) do the most closely-related species...
Data from: Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)Eddy J. Dowle, Ryan R. Bracewell, Michael E. Pfrender, Karen E. Mock, Barbara J. Bentz & Gregory J. Ragland
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and gene flow analyses revealed three distinct...
Data from: Combining high-throughput phenotyping and genomic information to increase prediction and selection accuracy in wheat breedingJared Crain, Suchismita Mondal, Jessica Rutkoski, Ravi P. Singh & Jesse Poland
Genomics and phenomics have promised to revolutionize the field of plant breeding. The integration of these two fields has just begun and is being driven through big data by advances in next-generation sequencing and developments of field-based high-throughput phenotyping (HTP) platforms. Each year the International Maize and Wheat Improvement Center (CIMMYT) evaluates tens-of-thousands of advanced lines for grain yield across multiple environments. To evaluate how CIMMYT may utilize dynamic HTP data for genomic selection (GS),...
The seasonal phenology of latitudinal movements is one of the key life-history traits of migratory birds. We used quantile regression to examine long-term changes in the timing of spring and autumn migration in 5 species of migratory passerine birds captured at a banding station in northern California, USA, over a 22 yr period from 1987 to 2008. Our 5 study species included 3 short-distance migrants, Pacific-slope Flycatcher (Empidonax difficilis), Orange-crowned Warbler (Oreothlypis celata), and Wilson's...
When field research is cost- or time-prohibitive, models can inform decision-makers regarding the impact of agricultural policy on production and the environment, but process-based models that simulate animal-plant-soil interaction and ecosystem services in grazing lands are rare. In the U.S.A., APEX (Agricultural Policy/Environmental eXtender) is a model commonly used to inform policy on cropland, but its ability to simulate grazinglands was less robust. Therefore, we enhanced the APEX model’s plant growth module to improve its...
Data from: Comparative transcriptome and lipidome analyses reveal molecular chilling responses in chilling-tolerant sorghumsSandeep R. Marla, Sunitha Shiva, Ruth Welti, Sanzhen Liu, John J. Burke & Geoffrey P. Morris
Chilling temperatures (0 to 15°C) are a major constraint for temperate cultivation of tropical-origin crops, including the cereal crop sorghum (Sorghum bicolor [L.] Moench). Northern Chinese sorghums have adapted to early-season chilling, but molecular mechanisms of chilling tolerance are unknown. We used RNA sequencing of seedlings to compare the chilling-responsive transcriptomes of a chilling-tolerant Chinese accession with a chilling-sensitive US reference line, and mass spectrometry to compare chilling-responsive lipidomes of four chilling-tolerant Chinese accessions with...
1. Location error occurs when the true location is different than the reported location. Because habitat characteristics at the true location may be different than those at the reported location, ignoring location error may lead to unreliable inference concerning species-habitat relationships. 2. We explain how a transformation known in the spatial statistics literature as a change of support (COS) can be used to correct for location errors when the true locations are points with unknown...
Data from: Centennial-scale reductions in nitrogen availability in temperate forests of the United StatesK. K. McLauchlan, L. M. Gerhart, J. J. Battles, J. M. Craine, A. J. Elmore, P. E. Higuera, M. C. Mack, B. E. McNeil, D. M. Nelson, N. Pederson & S. S. Perakis
Forests cover 30% of the terrestrial Earth surface and are a major component of the global carbon (C) cycle. Humans have doubled the amount of global reactive nitrogen (N), increasing deposition of N onto forests worldwide. However, other global changes—especially climate change and elevated atmospheric carbon dioxide concentrations—are increasing demand for N, the element limiting primary productivity in temperate forests, which could be reducing N availability. To determine the long-term, integrated effects of global changes...
Data from: Increased power to dissect adaptive traits in global sorghum diversity using a nested association mapping populationSophie Bouchet, Marcus O. Olatoye, Sandeep R. Marla, Ramasamy Perumal, Tesfaye Tesso, Jianming Yu, Mitch Tuinstra & Geoffrey P. Morris
Adaptation of domesticated species to diverse agroclimatic regions has led to abundant trait diversity. However, the resulting population structure and genetic heterogeneity confounds association mapping of adaptive traits. To address this challenge in sorghum [Sorghum bicolor (L.) Moench]—a widely adapted cereal crop—we developed a nested association mapping (NAM) population using 10 diverse global lines crossed with an elite reference line RTx430. We characterized the population of 2214 recombinant inbred lines at 90,000 SNPs using genotyping-by-sequencing....
Data from: Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in ricePaul Tanger, Stephen Klassen, Julius P. Mojica, John T. Lovell, Brook T. Moyers, Marietta Baraoidan, Maria Elizabeth B. Naredo, Kenneth L. McNally, Jesse Poland, Daniel R. Bush, Hei Leung, Jan E. Leach & John K. McKay
To ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. Here we demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with...
Circadian clocks have evolved independently in all three domains of life, suggesting that internal mechanisms of time-keeping are adaptive in contemporary populations. However, the performance consequences of either discrete or quantitative clock variation have rarely been tested in field settings. Clock sensitivity of diverse segregating lines to the environment remains uncharacterized as do the statistical genetic parameters that determine evolutionary potential. In field studies with Arabidopsis thaliana, we found that major perturbations to circadian cycle...
Data from: Antagonistic pleiotropy and mutation accumulation contribute to age-related decline in stress responseElizabeth Rose Everman & Theodore J. Morgan
As organisms age, the effectiveness of natural selection weakens, leading to age-related decline in fitness-related traits. The evolution of age-related changes associated with senescence is likely influenced by mutation accumulation (MA) and antagonistic pleiotropy (AP). MA predicts that age-related decline in fitness components is driven by age-specific sets of alleles, non-negative genetic correlations within trait across age, and an increase in the coefficient of genetic variance. AP predicts that age-related decline in a trait is...
Kansas State University13
Colorado State University3
University of California, Berkeley2
United States Department of Agriculture2
University of Maryland, College Park2
International Rice Research Institute2
University of Kansas1
University of Montana1
Utah State University1
The University of Texas at Austin1