103 Works

Data from: Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal

Jacques M. Faye, Fanna Maina, Zhenbin Hu, Daniel Fonceka, Ndiaga Cisse & Geoffrey P. Morris
Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum (Sorghum bicolor L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. To address this issue, we characterized a large panel of 421 georeferenced sorghum landrace accessions from Senegal and adjacent locations at 213,916 single‐nucleotide polymorphisms (SNPs)...

Data from: How big of an effect do small dams have? Using geomorphological footprints to quantify spatial impact of low-head dams and identify patterns of across-dam variation

Jane S. Fencl, Martha E. Mather, Katie H. Costigan & Melinda D. Daniels
Longitudinal connectivity is a fundamental characteristic of rivers that can be disrupted by natural and anthropogenic processes. Dams are significant disruptions to streams. Over 2,000,000 low-head dams (<7.6 m high) fragment United States rivers. Despite potential adverse impacts of these ubiquitous disturbances, the spatial impacts of low-head dams on geomorphology and ecology are largely untested. Progress for research and conservation is impaired by not knowing the magnitude of low-head dam impacts. Based on the geomorphic...

Combining epidemiological and ecological methods to quantify social effects on E. coli transmission

Trevor Farthing, Daniel Dawson, Michael Sanderson, Hannah Seger & Cristina Lanzas
Enteric microparasites like Escherichia coli utilize multiple transmission pathways to propagate within and between host populations. Characterizing the relative transmission risk attributable to host social relationships, and direct physical contact between individuals is paramount for understanding how microparasites like E. coli spread within affected communities and estimating colonization rates. To measure these effects, we carried out commensal E. coli transmission experiments in two cattle (Bos taurus) herds, wherein all individuals were equipped with real-time location...

A 3D Adult Zebrafish Brain Atlas (AZBA) for the Digital Age

Justin W. Kenney, Patrick E. Steadman, Olivia Young, Meng Ting Shi, Maris Polanco, Saba Dubaishi, Kristopher Covert, Thomas Mueller & Paul W. Frankland
Zebrafish have made significant contributions to our understanding of the vertebrate brain and the neural basis of behavior, earning a place as one of the most widely used model organisms in neuroscience. Their appeal arises from the marriage of low cost, early life transparency, and ease of genetic manipulation with a behavioral repertoire that becomes more sophisticated as animals transition from larvae to adults. To further enhance the use of adult zebrafish, we created the...

Ecological consequences of large herbivore exclusion in an African savanna: 12 years of data from the UHURU experiment

Jesse Alston, Courtney Reed, Leo Khasoha, Bianca Brown, Gilbert Busienei, Nathaniel Carlson, Tyler Coverdale, Megan Dudenhoeffer, Marissa Dyck, John Ekeno, Abdikadir Hassan, Rhianna Hohbein, Rhiannon Jakopak, Buas Kimiti, Samson Kurukura, Peter Lokeny, Allison Louthan, Simon Musila, Paul Musili, Tosca Tindall, Sarah Weiner, Tyler Kartzinel, Todd Palmer, Robert Pringle & Jacob Goheen
Diverse communities of large mammalian herbivores (LMH), once widespread, are now rare. LMH exert strong direct and indirect effects on community structure and ecosystem functions, and measuring these effects is important for testing ecological theory and for understanding past, current, and future environmental change. This in turn requires long-term experimental manipulations, owing to the slow and often nonlinear responses of populations and assemblages to LMH removal. Moreover, the effects of particular species or body-size classes...

Data from: A field-based analysis of genetic improvement for grain yield in winter wheat cultivars developed in the us central plains from 1992 to 2014

Jesse A. Poland, Trevor W. Rife & Robert A. Graybosch
rpn_wheat_phenotypesThis file includes height, yield, and heading date phenotypic data for the entries evaluated in this study. Everest and TAM 112 were the two check cultivars used in the experimental design. Additional entries are identified in the line_num column by the designation assigned upon entry into the Regional Performance Nursery. Experimental names, when available, are included in the line_name column.

Data from: Increased power to dissect adaptive traits in global sorghum diversity using a nested association mapping population

Sophie 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....

Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium)

Jared Crain, Steve Larson, Kevin Dorn, Traci Hagedorn, Lee DeHaan & Jesse Poland
In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum intermedium), polycrossing is often used to generate novel recombinants through each cycle of selection, but it cannot track pollen-parent pedigrees and it is unknown how self-incompatibility (SI) genes may limit the number of unique crosses obtained. This study investigated the potential of using next-generation sequencing to assign paternity and identify putative SI loci in IWG. Using a reference population of 380 individuals made from controlled crosses...

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

Bridging the flux gap: sap flow measurements reveal species-specific patterns of water-use in a tallgrass prairie

Kimberly O'Keefe, David Bell, Katherine McCulloh & Jesse Nippert
Predicting the hydrological consequences following changes in grassland vegetation type (i.e., woody encroachment) requires an understanding of water flux dynamics at high spatiotemporal resolution for predominant species within grassland communities. However, grassland fluxes are typically measured at the leaf or landscape scale, which inhibits our ability to predict how individual species contribute to changing ecosystem fluxes. We used external heat balance sap flow sensors and a hierarchical Bayesian state-space modeling approach to bridge this “flux-gap”...

Data from: Fire, grazing, and climate shape plant-grasshopper interactions in a tallgrass prairie

Ellen A.R. Welti, Fan Qiu, Hannah M. Tetreault, Mark Ungerer, John Blair, Anthony Joern & Ellen A. R. Welti
1. Species interactions are integral to ecological community function and the structure of species interactions has repercussions for the consequences of species extinctions. Few studies have examined the role of environmental factors in controlling species interaction networks across time. 2. We examined variation in plant-grasshopper network structural properties in response to three major grassland drivers: periodic fire, ungulate grazing and climate. 3. We sequenced a plant barcoding gene from extracted grasshopper gut contents to characterize...

Data from: Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice

Paul 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...

Data from: Circadian rhythms vary over the growing season and correlate with fitness components

Matthew J. Rubin, Marcus T. Brock, Amanda M. Davis, Zachary M. German, Mary Knapp, Stephen M. Welch, Stacey L. Harmer, Julin N. Maloof, Seth J. Davis & Cynthia Weinig
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: Genomic signatures of adaptation to a precipitation gradient in Nigerian sorghum

Marcus O. Olatoye, Zhenbin Hu, Fanna Maina & Geoffrey P. Morris
Evolution of plants under climatic gradients may lead to clinal adaptation. Understanding the genomic basis of clinal adaptation in crops species could facilitate breeding for climate resilience. We investigated signatures of clinal adaptation in the cereal crop sorghum (Sorghum bicolor L. [Moench]) to the precipitation gradient in West Africa using a panel (n = 607) of sorghum accessions from diverse agroclimatic zones of Nigeria. Significant correlations were observed between common-garden phenotypes of three putative climate-adaptive...

Data from: Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

Scott P. Egan, Gregory J. Ragland, Lauren Assour, Thomas H. Q. Powell, Glen R. Hood, Scott Emrich, Patrik Nosil, Jeffrey L. Feder & Thomas H.Q. Powell
Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple...

Data from: Harvesting effects on wild bee communities in bioenergy grasslands depend on nesting guild

Brian J. Spiesman, Ashley Bennett, Rufus Isaacs & Claudio Gratton
Conversion of annual crops to native perennial grasslands for bioenergy production may help conserve wild bees by enhancing nest and food resources. However, bee response to the disturbance of biomass harvesting may depend on their nesting location, thus their vulnerability to nest destruction, and the response of the forb community on which they forage. Moreover, because bees have long foraging ranges, effects of local harvesting may depend on the amount of natural habitat in the...

Data from: Antagonistic pleiotropy and mutation accumulation contribute to age-related decline in stress response

Elizabeth 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...

Data from: Ovary development and cold tolerance of the invasive pest Drosophila suzukii (Matsumura) in the central plains of Kansas, United States

Elizabeth R. Everman, Philip J. Freda, Mariah Brown, Adam J. Schieferecke, Gregory J. Ragland & Theodore J. Morgan
Environmental challenges presented by temperature variation can be overcome through phenotypic plasticity in small invasive ectotherms. We tested the effect of thermal exposure to 21, 18, and 11°C throughout the whole life cycle of individuals, thermal exposure of adults reared at 25°C to 15 and 11°C for a 21-d period, and long (14:10 hr) and short (10:14 hr) photoperiod on ovary size and development in Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) cultured from a recently established...

Data from: Effects of grasshoppers on prairies: herbivore composition matters more than richness in three grassland ecosystems

Angela N. Laws, Chelse M. Prather, David H. Branson & Steven C. Pennings
1. Understanding how biodiversity affects ecosystem processes is a key question in ecology. Previous research has found that increasing plant diversity often enhances many ecosystem processes, but less is known about the role of consumer diversity to ecosystem processes, especially in terrestrial ecosystems. Furthermore, we do not know how general biodiversity responses are among ecosystem types. 2. We examined the role of insect herbivore (Orthoptera) diversity on plant production using parallel field experiments in three...

Data from: An integrated genotyping-by-sequencing polymorphism map for over 10,000 sorghum genotypes

Zhenbin Hu, Marcus O. Olatoye, Sandeep Marla & Geoffrey P. Morris
SNPs_imp.recode.vcfImputed SNP dataset for over 10,000 sorghum accessions.Original_chr1.recode.vcf.gzOriginal SNP which not merged, not imputed on chromosome 1.original_chr1.recode.vcf.gzOriginal_chr2.recode.vcfOriginal SNP which not merged, not imputed on chromosome 2original_chr2.recode.vcf.gzOriginal_chr3.recode.vcfOriginal SNP which not merged, not imputed on chromosome 3.original_chr3.recode.vcf.gzoriginal_chr4.recode.vcfOriginal SNP which not merged, not imputed on chromosome 4.Original_chr5.recode.vcfOriginal SNP which not merged, not imputed on chromosome 5.original_chr5.recode.vcf.gzOriginal_chr6.recode.vcfOriginal SNP which not merged, not imputed on chromosome 6.original_chr6.recode.vcf.gzOriginal_chr7.recode.vcfOriginal SNP which not merged, not imputed on chromosome 7.original_chr7.recode.vcf.gzOriginal_chr8.recode.vcfOriginal SNP which not merged,...

A genomics resource for genetics, physiology, and breeding of West African sorghum

Jacques Faye, Fanna Maina, Eyanawa Akata, Bassirou Sine, Cyril Diatta, Aissata Mamadou, Sandeep Marla, Sophie Bouchet, Niaba Teme, Jean-Francois Rami, Daniel Fonceka, Ndiaga Cisse & Geoffrey Morris
Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolor L. Moench) in West Africa has diversified across a mosaic of cultures and end-uses, and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping-by-sequencing was used to...

Data from: Social interactions do not drive territory aggregation in a grassland songbird

Sarah Winnicki, Alice Boyle, Emily Williams & Steffanie Munguia
Understanding the drivers of animal distributions is a fundamental goal of ecology and informs habitat management. The costs and benefits of colonial aggregations in animals are well established, but the factors leading to aggregation in territorial animals remain unclear. Territorial animals might aggregate to facilitate social behavior such as (1) group defense from predators and/or parasites, (2) cooperative care of offspring, (3) extra-pair mating, and/or (4) mitigating costs of extra-pair mating through kin selection. Using...

Data from: Patterns and drivers of intraspecific variation in avian life history along elevational gradients: a meta-analysis

W. Alice Boyle, Brett K. Sandercock & Kathy Martin
Elevational gradients provide powerful natural systems for testing hypotheses regarding the role of environmental variation in the evolution of life-history strategies. Case studies have revealed shifts towards slower life histories in organisms living at high elevations yet no synthetic analyses exist of elevational variation in life-history traits for major vertebrate clades. We examined (i) how life-history traits change with elevation in paired populations of bird species worldwide, and (ii) which biotic and abiotic factors drive...

Data from: Convergence of soil nitrogen isotopes across global climate gradients

Joseph M. Craine, Andrew J. Elmore, Lixin Wang, Laurent Augusto, W. Troy Baisden, E. N. J. Brookshire, Michael D. Cramer, Niles J. Hasselquist, Erik A. Hobbie, Ansgar Kahmen, Keisuke Koba, J. Marty Kranabetter, Michelle C. Mack, Erika Marin-Spiotta, Jordan R. Mayor, Kendra K. McLauchlan, Anders Michelsen, Gabriela B. Nardoto, Rafael S. Oliveira, Steven S. Perakis, Pablo L. Peri, Carlos A. Quesada, Andreas Richter, Louis A. Schipper, Bryan A. Stevenson … & Bernd Zeller
Quantifying global patterns of terrestrial nitrogen (N) cycling is central to predicting future patterns of primary productivity, carbon sequestration, nutrient fluxes to aquatic systems, and climate forcing. With limited direct measures of soil N cycling at the global scale, syntheses of the 15N:14N ratio of soil organic matter across climate gradients provide key insights into understanding global patterns of N cycling. In synthesizing data from over 6000 soil samples, we show strong global relationships among...

Data from: Stage-specific genotype-by-environment interactions for cold and heat hardiness in Drosophila melanogaster.

Philip J. Freda, Zainab M. Ali, Nicholas Heter, Gregory J. Ragland & Theodore J. Morgan
Environments often vary across a life cycle, imposing fluctuating natural selection across development. Such fluctuating selection can drive evolutionary responses specific to distinct life-history stages. However, selection and genetic variation, phenotypic plasticity, and their interaction (GxE), as well as genetic correlation across development dictate stage-specific evolution. Thus, quantifying genetic covariance of fitness-related traits and plasticity across development is vital to determine whether stage-specific adaptation occurs in nature. Additionally, the interaction of genetic variation and environmental...

Registration Year

  • 2022
    1
  • 2021
    15
  • 2020
    17
  • 2019
    8
  • 2018
    11
  • 2017
    13
  • 2016
    11
  • 2015
    15
  • 2014
    8
  • 2013
    3

Resource Types

  • Dataset
    103

Affiliations

  • Kansas State University
    103
  • University of Florida
    7
  • The Land Institute
    5
  • University of Kansas
    4
  • United States Department of Agriculture
    4
  • Southern Illinois University Carbondale
    4
  • University of Notre Dame
    3
  • Fort Hays State University
    3
  • University of Georgia
    3
  • University of Wyoming
    3