115 Works

Data from: Extremophile Poeciliidae: multivariate insights into the complexity of speciation along replicated ecological gradients

Rüdiger Riesch, Michael Tobler, Hannes Lerp, Jonas Jourdan, Tess Doumas, Patrik Nosil, R. Brian Langerhans & Martin Plath
Background: Replicate population pairs that diverge in response to similar selective regimes allow for an investigation of (a) whether phenotypic traits diverge in a similar and predictable fashion, (b) whether there is gradual variation in phenotypic divergence reflecting variation in the strength of natural selection among populations, (c) whether the extent of this divergence is correlated between multiple character suites (i.e., concerted evolution), and (d) whether gradual variation in phenotypic divergence predicts the degree of...

Data from: Ecological mismatches are moderated by local conditions in two populations of a long-distance migratory bird

Nathan Senner, Maria Stager, Brett K. Sandercock & Nathan R. Senner
Ecological mismatches between reproductive events and seasonal resource peaks are frequently proposed to be a key driver of population dynamics resulting from global climate change. Many local populations are experiencing reduced reproductive success as a consequence of mismatches, but few mismatches have led to species-level population declines. To better understand this apparent paradox, we investigated the breeding phenology and chick survival of two disjunct populations of Hudsonian godwits Limosa haemastica breeding at Churchill, Manitoba and...

Data from: Environmental heterogeneity generates opposite gene-by-environment interactions for two fitness-related traits within a population

Zachary Wyatt Culumber, Molly Schumer, Scott Monks & Michael Tobler
Theory predicts that environmental heterogeneity offers a potential solution to the maintenance of genetic variation within populations, but empirical evidence remains sparse. The livebearing fish Xiphophorus variatus exhibits polymorphism at a single locus, with different alleles resulting in up to five distinct melanistic “tailspot” patterns within populations. We investigated the effects of heterogeneity in two ubiquitous environmental variables (temperature and food availability) on two fitness-related traits (upper thermal limits and body condition) in two different...

Data from: Diversification of R2R3-MYB transcription factors in the tomato family Solanaceae

Daniel J. Gates, Susan R. Strickler, Lukas A. Mueller, Bradley J. S. C. Olson & Stacey D. Smith
MYB transcription factors play an important role in regulating key plant developmental processes involving defense, cell shape, pigmentation, and root formation. Within this gene family, sequences containing an R2R3 MYB domain are the most abundant type and exhibit a wide diversity of functions. In this study, we identify 559 R2R3 MYB genes using whole genome data from four species of Solanaceae and reconstruct their evolutionary relationships. We compare the Solanaceae R2R3 MYBs to the well-characterized...

Data from: Centennial-scale reductions in nitrogen availability in temperate forests of the United States

K. 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: Bias correction of bounded location errors in presence-only data

Trevor J. Hefley, Brian M. Brost & Mevin B. Hooten
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...

Functional consequences of phenotypic variation between locally adapted populations: swimming performance and ventilation in extremophile fish

Michael Tobler, Lenin Arias-Rodriguez & Henry Camarillo
Natural selection drives the evolution of traits to optimize organismal performance, but optimization of one aspect of performance can often influence other aspects of performance. Here, we asked how phenotypic variation between locally adapted fish populations affects locomotion and ventilation, testing for functional trade-offs and trait-performance correlations. Specifically, we investigated two populations of livebearing fish (Poecilia mexicana) that inhabit distinct habitat types (hydrogen-sulfide-rich springs and adjacent nonsulfidic streams). For each individual, we quantified different metrics...

Pathogen genetic control of transcriptome variation in the Arabidopsis thaliana – Botrytis cinerea pathosystem

Nicole Soltis, Celine Caseys, Wei Zhang, Jason Corwin, Susanna Atwell & Daniel Kliebenstein
In plant-pathogen relations, disease symptoms arise from the interaction of the host and pathogen genomes. Host-pathogen functional gene interactions are well described while little is known about how the pathogen genetic variation modulates both organisms’ transcriptomes. To model and generate hypotheses on a generalist pathogen control of gene expression regulation, we used the Botrytis cinerea - Arabidopsis thaliana pathosystem and the genetic diversity of a collection of 96 B. cinerea isolates. We performed expression-based genome-wide...

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 on universities offering undergraduate degrees that train students for soil science careers at universities in the USA and its territories

Eric C. Brevik, Holly Dolliver, Susan Edinger-Marshall, Danny Itkin, Jodi Johnson-Maynard, Garrett Liles, Monday Mbila, Colby Moorberg, Yaniria Sanchez-De Leon, Joshua J. Steffan, April Ulery & Karen Vaughan
Several soil science education studies over the last 15 years have focused on the number of students enrolled in soil science programs. However, no studies have quantitatively addressed the number of undergraduate soil science preparatory programs that exist in the United States, which means we do not have solid data concerning whether overall program numbers are declining, rising, or holding steady. This also means we do not have complete data on the same trends for...

The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements

S. Evan Staton, Bradley H. Bakken, Benjamin K. Blackman, Mark A. Chapman, Nolan C. Kane, Shunxue Tang, Mark C. Ungerer, Steven J. Knapp, Loren H. Rieseberg & John M. Burke
Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence...

Assembly of Aegilops comosa chromosomes

Mahmoud Said, Kateřina Holušová, András Farkas, László Ivanizs, Eszter Gaál, Petr Cápal, Michael Abrouk, Mihaela Martis-Thiele, Balázs Kalapos, Jan Bartoš, Bernd Friebe, Jaroslav Doležel & István Molnár
We sequenced and assembled seven chromosomes of Aegilops comosa. The assembly with Meraculous resulted in ~ 50k - 186k scaffolds per chromosome with N50 size 6.4kb - 20.2kb. The scaffold sequences were used for development of molecular markers specific for cDNAs sequences mapped on Ae. comosa chromosomes Pairwise alignment of wheat cDNA-sequences and the chromosomal scaffolds of Ae. comosa identified candidate sequences. In order to analyze the structure and homeology of Aegilops chromosomes, forty-three mapped...

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...

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...

Limited legacy effects of extreme multi-year drought on carbon and nitrogen cycling in a mesic grassland

Leena Vilonen, John Blair, Pankaj Trivedi, Lydia Zeglin & Melinda Smith
The intensification of drought throughout the US Great Plains has the potential to have large impacts on grassland functioning, as has been shown with dramatic losses of plant productivity annually. Yet, we have a poor understanding of how grassland functioning responds after drought ends. This study examined how belowground nutrient cycling responds after drought and whether legacy effects persist post-drought. We assessed the two-year recovery of nutrient cycling processes following a four-year experimental drought in...

Data from: Genome-environment associations in sorghum landraces predict adaptive traits

Jesse R. Lasky, Hari D. Upadhyaya, Punna Ramu, Santosh Deshpande, C. Tom Hash, Jason Bonnette, Thomas E. Juenger, Katie Hyma, Charlotte Acharya, Sharon E. Mitchell, Edward S. Buckler, Zachary Brenton, Stephen Kresovich & Geoffrey P. Morris
Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil...

Data from: Population genetics and origin of the native North American agricultural weed waterhemp (Amaranthus tuberculatus)

Katherine E. Waselkov & Kenneth M. Olsen
Premise of the study: The evolution of invasiveness has been extensively studied in natural ecosystems; however, far less is known about the evolution of agricultural invasiveness, despite the major economic impact of weeds on crop productivity. Examining the population structure of recently arisen weeds can provide insights into evolutionary avenues to invasion of agroecosystems. Weeds that originate from wild plants are the most common yet least frequently studied type of agricultural invasive. Here we address...

Data from: Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem

Allison M. Veach, James C. Stegen, Shawn P. Brown, Walter K. Dodds & Ari Jumpponen
Biofilms represent a metabolically active and structurally complex component of freshwater ecosystems. Ephemeral prairie streams are hydrologically harsh and prone to frequent perturbation. Elucidating both functional and structural community changes over time within prairie streams provides a general understanding of microbial responses to environmental disturbance. We examined microbial succession of biofilm communities at three sites in a third-order stream at Konza Prairie over a 2- to 64-day period. Microbial abundance (bacterial abundance, chlorophyll a concentrations)...

Data from: Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates

Eddy J. Dowle, Xavier Pochon, Jonathan C. Banks, Karen Shearer & Susanna A. Wood
Recent studies have advocated biomonitoring using DNA techniques. In this study, two high-throughput sequencing (HTS)-based methods were evaluated: amplicon metabarcoding of the cytochrome C oxidase subunit I (COI) mitochondrial gene and gene enrichment using MYbaits (targeting nine different genes including COI). The gene-enrichment method does not require PCR amplification and thus avoids biases associated with universal primers. Macroinvertebrate samples were collected from 12 New Zealand rivers. Macroinvertebrates were morphologically identified and enumerated, and their biomass...

Data from: Long-term changes in the seasonal timing of landbird migration on the Pacific Flyway

Gina G. Barton & Brett K. Sandercock
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...

Data from: Process-based simulation of prairie growth

Cody J. Zilverberg, Jimmy Williams, Curtis Jones, Keith Harmoney, Jay Angerer, Loretta J. Metz & William Fox
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: 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: Comparative transcriptome and lipidome analyses reveal molecular chilling responses in chilling-tolerant sorghums

Sandeep 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...

Data from: Combining high-throughput phenotyping and genomic information to increase prediction and selection accuracy in wheat breeding

Jared 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),...

Data from: Genomic analysis and prediction within a US public collaborative winter wheat regional testing nursery

Trevor W. Rife, Robert A. Graybosch & Jesse A. Poland
The development of inexpensive, whole-genome profiling enables a transition to allele-based breeding using genomic prediction models. These models consider alleles shared between lines to predict phenotypes and select new lines based on estimated breeding values. This approach can leverage highly-unbalanced datasets common to breeding programs. The Southern Regional Performance Nursery (SRPN) is a public nursery established by the USDA-ARS in 1931 to characterize performance and quality of near-release wheat varieties from breeding programs in the...

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