258 Works

Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution

Michael Hardigan, Mitchell Feldmann, Anne Lorant, Kevin Bird, Steven Knapp, Patrick Edger, Glenn Cole, Charlotte Acharya & Randi Famula
Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a...

Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods

Kimberly Ballare, Nathaniel Pope, Antonio Castilla, Sarah Cusser, Richard Metz & Shalene Jha
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next-generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we...

Phenotypic divergence among threespine stickleback that differ in nuptial coloration

Clara Jenck, Whitley Lehto, Brian Ketterman, Lukas Sloan, Aaron Sexton & Robin Tinghitella
By studying systems in their earliest stages of differentiation, we can learn about the evolutionary forces acting within and among populations and how those forces could contribute to reproductive isolation. Such an understanding would help us better discern and predict how selection leads to the maintenance of multiple morphs within a species, rather than speciation. The postglacial adaptive radiation of the threespine stickleback (Gasterosteus aculeatus) is one of the best-studied cases of evolutionary diversification and...

Novel plant-microbe interactions: rapid evolution of a legume-rhizobium mutualism in restored prairies

Susan Magnoli & Jennifer Lau
1. When plants colonize new habitats, the novel interactions they form with new mutualists or enemies can immediately affect plant performance. These novel interactions also may provoke rapid evolutionary responses and can be ideal scenarios for investigating how species interactions influence plant evolution. 2. To explore how mutualists influence the evolution of colonizing plant populations, we capitalized on an experiment in which two former agricultural fields were seeded with identical prairie seed mixes in 2010....

Data from: Agricultural land-use history and restoration impact soil microbial biodiversity

Nash Turley, Lars Brudvig, Lukas Bell-Dereske & Sarah Evans
Human land uses, such as agriculture, can leave long-lasting legacies as ecosystems recover. As a consequence, active restoration may be necessary to overcome land-use legacies; however, few studies have evaluated the joint effects of agricultural history and restoration on ecological communities. Those that have studied this joint effect have largely focused on plants and ignored other communities, such as soil microbes. We conducted a large-scale experiment to understand how agricultural history and restoration tree thinning...


Aniruddha Belsare
MIOvCWD is a spatially-explicit, agent-based model designed to simulate the spread of chronic wasting disease (CWD) in Michigan’s white-tailed deer populations. CWD is an emerging prion disease of North American cervids (white-tailed deer Odocoileus virginianus, mule deer Odocoileus hemionus, and elk Cervus elaphus) that is being actively managed by wildlife agencies in most states and provinces in North America, including Michigan. MIOvCWD incorporates features like deer population structure, social organization and behavior that are particularly...

Data from: Trait-environment interactions affect plant establishment success during restoration

Chad Zirbel & Lars Brudvig
Establishment and persistence are central to community assembly and are determined by how traits interact with the environment to determine performance ('trait-environment interactions'). Community assembly studies have rarely considered such trait-environment interactions, however, which can lead to incorrect inferences about how traits affect assembly. We evaluated how functional traits, environmental conditions, and trait-environment interactions structure plant establishment, as a measure of performance. Within 12 prairie restorations created by sowing 70 species, we quantified environmental conditions...

MIOvPOP Version 1.1.0

Aniruddha Belsare
An ABM simulating white-tailed deer population dynamics for selected Michigan counties. The model yields pre-harvest and post-harvest realistic population snapshots that can be used to initialize the surveillance model (MIOvPOPsurveillance) and the CWD transmission dynamics model (MIOvCWD) respectively.

Lasting signature of planting year weather on restored grasslands

Anna Groves, Jonathan Bauer & Lars Brudvig
Ecological restoration — the rebuilding of damaged or destroyed ecosystems — is a critical component of conservation efforts, but is hindered by inconsistent, unpredictable outcomes. We investigated a source of this variation that is anecdotally suggested by practitioners, but for which empirical evidence is rare: the weather conditions during the first growing season after planting. The idea of whether natural communities face long-term consequences from conditions even many years in the past, called historical contingency,...

Automated analysis of scanning electron microscopic images for assessment of hair surface damage

Fanny Chu, Deon Anex, A. Daniel Jones & Bradley Hart
Mechanical damage of hair can serve as an indicator of health status and its assessment relies on the measurement of morphological features via microscopic analysis, yet few studies have categorized the extent of damage sustained, and instead, have depended on qualitative profiling based on the presence or absence of specific features. We describe the development and application of a novel quantitative measure for scoring hair surface damage in scanning electron microscopic (SEM) images without predefined...

Identifying hidden biocomplexity and genomic diversity in Chinook salmon, an imperiled species with a history of anthropogenic influence

Mariah Meek, Molly R. Stephens, Alisha Goodbla, Bernie P May & Melinda R. Baerwald
Biocomplexity is an important mechanism for population resilience in changing environments. However, we are just beginning to understand how to identify biocomplexity so that species management efforts promote resilience and stability. Genomic techniques are emerging as an important method for identifying biocomplexity. Central Valley (CV) Chinook salmon are an example of a species at risk of extinction if better methods for identifying and protecting biocomplexity are not employed. To address this knowledge gap, we employed...

Developmental dieldrin exposure alters DNA methylation at genes related to dopaminergic neuron development and Parkinson’s disease in mouse midbrain

Joseph Kochmanski, Sarah E. VanOeveren, Joseph R Patterson & Alison I. Bernstein
Human and animal studies have shown that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson’s disease (PD). Despite previous work showing a link between developmental dieldrin exposure and increased neuronal susceptibility to MPTP toxicity in male C57BL/6 mice, the mechanism mediating this effect has not been identified. Here, we tested the hypothesis that developmental exposure to dieldrin increases neuronal susceptibility via genome-wide changes in DNA methylation. Starting at 8 weeks...

Population Genomics 'Beta vulgaris'

Paul Galewski
Population Genomic data sets from several papers descibing genetic diversity of beet crop types. 1) Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences (BMC Genomics paper )

Fusarium virguliforme transcriptional plasticity is revealed by host colonization of corn vs. soybean

Amy Baetsen-Young, Jennifer Wai, Robert VanDuren & Brad Day
We exploited the broad host range of Fusarium virguliforme to identify differential fungal responses leading to either an endophytic or a pathogenic lifestyle during colonization of corn (Zea mays) and soybean (Glycine max), respectively. To provide a foundation to survey the transcriptomic landscape, we produced an improved de novo genome assembly and annotation of F. virguliforme using PacBio sequencing. Next, we conducted a high-resolution time course of F. virguliforme colonization and infection of both soybean,...

Reciprocal cybrids reveal how organellar genomes affect plant phenotypes

Tom Theeuwen, Pádraic Flood, Korbinian Schneeberger, Paul Keizer, Willem Kruijer, Edouard Severing, Evangelos Kouklas, Jos Hageman, Raúl Wijfjes, Vanessa Calvo-Baltanas, Frank Becker, Sabine Schnabel, Leo Willems, Wilco Ligterink, Jeroen Van Arkel, Roland Mumm, José Gualberto, Linda Savage, David Kramer, Joost Keurentjes, Fred Van Eeuwijk, Maarten Koornneef, Jeremy Harbinson, Mark Aarts & Erik Wijnker
Assessing the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear derived variation (the nucleotype). Haploid inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids). We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1859 phenotypes under stable and fluctuating conditions....

Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn

Matheus Baseggio, Matthew Murray, Maria Magallanes-Lundback, Nicholas Kaczmar, James Chamness, Edward Buckler, Margaret Smith, Dean DellaPenna, William Tracy & Michael Gore
Sweet corn (Zea mays L.) is highly consumed in the United States, but does not make major contributions to the daily intake of carotenoids (provitamin A carotenoids, lutein and zeaxanthin) that would help in the prevention of health complications. A genome-wide association study of seven kernel carotenoids and twelve derivative traits was conducted in a sweet corn inbred line association panel ranging from light to dark yellow in endosperm color to elucidate the genetic basis...

Data from: Impacts of climate variability and adaptation strategies on crop yields and soil organic carbon in the US Midwest

Lin Liu & Bruno Basso
Climate change is likely to increase the frequency of drought and more extreme precipitation events. The objectives of this study were i) to assess the impact of extended drought followed by heavy precipitation events on yield and soil organic carbon (SOC) under historical and future climate, and ii) to evaluate the effectiveness of climate adaptation strategies (no-tillage and new cultivars) in mitigating impacts of increased frequencies of extreme events and warming. We used the validated...

Beneficial microbes ameliorate abiotic and biotic sources of stress on plants

Maren Friesen, Stephanie Porter, Roxanne Bantay, Colleen Friel, Kristi Gdanetz, Bethany Moore, Prateek Shetty, Eleanor Siler & Maren Friesen
1. Global climate change and shifting land-use are increasing plant stress due to abiotic factors such as drought, heat, salinity and cold, as well as via the intensification of biotic stressors such as herbivores and pathogens. The ability of plants to tolerate such stresses is modulated by the bacteria and fungi that live on or inside of plant tissues and comprise the plant microbiome. However, the impacts of diverse classes of beneficial microbes and the...

Maintaining historic disturbance regimes increases species’ resilience to catastrophic hurricanes

Erica H Henry, Martha O Burford Reiskind, Aerin Land & Nick M Haddad
As habitat loss and fragmentation, urbanization, and global climate change accelerate, conservation of rare ecosystems increasingly relies on human intervention. However, any conservation strategy is vulnerable to unpredictable, catastrophic events. Whether active management increases or decreases a system’s resilience to these events remains unknown. Following Hurricane Irma’s landfall in our habitat restoration study sites, we found that rare ecosystems with active, human-imposed management suffered less damage in a hurricane’s path than unmanaged systems. At the...

Data from: Complementary strengths of spatially-explicit and multi-species distribution models

Nina Lany, Phoebe Zarnetske, Andrew Finley & Deborah McCullough
Species distribution models (SDMs) project the outcome of community assembly processes - dispersal, the abiotic environment, and biotic interactions - onto geographic space. Recent advances in SDMs account for these processes by simultaneously modeling the species that comprise a community in a multivariate statistical framework or by incorporating residual spatial autocorrelation in SDMs. However, the effects of combining both multivariate and spatially-explicit model structures on the ecological inferences and the predictive abilities of a model...

Rapid and predictable evolution of admixed populations between two Drosophila species pairs

Daniel Matute, Aaron Comeault, Eric Earley, Antonio Serrato-Capuchina, David Peede, Anaïs Monroy-Eklund, Wen Huang, Corbin Jones, Trudy Mackay & Jerry Coyne
The consequences of hybridization are varied, ranging from the origin of new lineages, introgression of some genes between species, to the extinction of one of the hybridizing species. We generated replicate admixed populations between two pairs of sister species of Drosophila: D. simulans and D. mauritiana; and D. yakuba and D. santomea. Each pair consisted of a continental species and an island endemic. The admixed populations were maintained by random mating in discrete generations for...

Recent evolutionary history predicts population but not ecosystem level patterns

Sarah Fitzpatrick, Madison Miller & John Kronenberger
In the face of rapid anthropogenic environmental change, it is increasingly important to understand how ecological and evolutionary interactions affect the persistence of natural populations. Augmented gene flow has emerged as a potentially effective management strategy to counteract negative consequences of genetic drift and inbreeding depression in small and isolated populations. However, questions remain about the long-term impacts of augmented gene flow and whether changes in individual and population fitness are reflected in ecosystem structure,...

Long-term evapotranspiration rates for rainfed corn vs. perennial bioenergy crops in a mesic landscape

Michael Abraha, Jiquan Chen, Stephen K. Hamilton & G. Philip Robertson
Hydrologic implications of the conversion of agricultural or conservation lands for annual vs. perennial bioenergy crop production are scarce. We converted three 22 year-old Conservation Reserve Program (CRP) grasslands and three 50+ year-old conventionally tilled corn-soybean rotation agricultural (AGR) lands to no-till corn, switchgrass (Panicum virgatum L.) or restored prairie. A seventh site was maintained in the preexisting CRP grassland dominated by smooth brome grass (Bromus inermis L.). We measured evapotranspiration (ET) using the eddy...

At what spatial scale(s) do mammals respond to urbanization?

Remington Moll
Spatial scale is fundamental in understanding species-landscape relationships because species’ responses to landscape characteristics typically vary across scales. Nonetheless, such scales are often unidentified or unreliably predicted by theory. Many landscapes worldwide are urbanizing, yet the spatial scaling of species’ responses to urbanization is poorly understood. We investigated the spatial scaling of urbanization effects on a community of 15 mammal species using ~ 60,000 wildlife detections collected from a constellation of 207 camera traps across...

Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical-temperate congener pair

Carina Baskett, Lucy Schroeder, Marjorie Weber & Douglas Schemske
The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination...

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