59 Works

Data from: Climate-mediated hybrid zone movement revealed with genomics, museum collection and simulation modeling

Sean F. Ryan, Jillian M. Deines, J. Mark Scriber, Michael E. Pfrender, Stuart E. Jones, Scott J. Emrich & Jessica J. Hellmann
Climate-mediated changes in hybridization will dramatically alter the genetic diversity, adaptive capacity and evolutionary trajectory of interbreeding species. Our ability to predict the consequences of such changes will be key to future conservation and management decisions. Here we tested through simulations how recent warming (over a 32-year period) is affecting the geographic extent of a climate-mediated developmental threshold implicated in maintaining a butterfly hybrid zone (Papilio glaucus and Papilio canadensis; Lepidoptera: Papilionidae). These simulations predict...

Data from: Brassicales phylogeny inferred from 72 plastid genes: a reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses

Patrick P. Edger, Jocelyn C. Hall, Alex Harkess, Michelle Tang, Jill Coombs, Setareh Mohammadin, M. Eric Schranz, Zhiyong Xiong, James Leebens-Mack, Blake C. Meyers, Kenneth J. Systma, Marcus A. Koch, Ihsan A. Al-Shehbaz, J. Chris Pires & Kenneth J. Sytsma
PREMISE OF THE STUDY - Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family‐level phylogeny estimated using the plastid genome. METHODS - We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp...

Data from: Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species

Brendan N. Reid, Jamie M. Kass, Seth Wollney, Evelyn L. Jensen, Michael A. Russello, Ella M. Viola, Jenna Pantophlet, John B. Iverson, Marcus Z. Peery, Christopher J. Raxworthy & Eugenia Naro-Maciel
In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and...

Data from: Individual-level trait variation and negative density dependence affects growth in tropical tree seedlings

Maria Natalia Umana, Elise F. Zipkin, Caicai Zhang, Min Cao, Luxiang Lin & Nathan G. Swenson
1. Individual-level interactions with neighbours and their surrounding environments are key factors influencing performance that ultimately shape and maintain diversity in tropical plant communities. Theory predicts that the strength of these interactions depends on the similarity among neighbours, the turnover in composition caused by individuals that enter as new recruits and individuals that die, and fitting to local conditions. Despite considerable phenotypic variation among individuals and high community dynamics, these three factors have rarely been...

Data from: Host cues mediate growth and establishment of oak mistletoe (Phoradendron leucarpum, Viscaceae), an aerial parasitic plant.

Christopher P. Randle, Brandi C. Cannon, Amber L. Faust, Angela K. Hawkins, Sarah E. Cabrera, Stephen Lee, Amy A. Perez, Michelle L. Lewis, James Sopas, Timothy J. Verastegui, Justin K. Williams & Sara E. Cabrera
The oak mistletoe (Phoradendron leucarpum, Viscaceae) is well-documented to exhibit preference for a few potential host species in a given locality, even when many potential host species are present. In trying to explain this distribution, we examined the mechanisms by which mistletoe seedlings recognize potentially suitable hosts in the Piney Woods ecoregion of east Texas. An initial survey of patterns of infection on the campus of Sam Houston State University revealed that water oak (Quercus...

Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes

Genevieve M. Hoopes, John P. Hamilton, Joshua C. Wood, Eddi Esteban, Asher Pasha, Brieanne Vaillancourt, Nicholas J. Provart & C. Robin Buell
Maize(Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide.The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long‐read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA‐sequencing datasets from 79 tissues and five...

Data from: Prediction of cooking time for soaked and unsoaked dry beans (Phaseolus vulgaris L.) using hyperspectral imaging technology

Fernando A. Mendoza, Jason A. Wiesinger, Renfu Lu, Susan Nchimbi-Msolla, Phillip N. Miklas, James D. Kelly & Karen A. Cichy
The cooking time of dry beans varies widely by genotype and is also influenced by the growing environment, storage conditions and cooking method. Thus, high throughput phenotyping methods to assess cooking time would be useful to breeders interested in developing cultivars with desired cooking time. The objective of this study was to evaluate the performance of hyperspectral imaging technology for predicting dry bean cooking time. Fourteen dry bean (Phaseolus vulgaris L.) genotypes with a wide...

Data from: Landscape heterogeneity is key to forecasting outcomes of plant reintroduction

T. Trevor Caughlin, Ellen I. Damschen, Nick M. Haddad, Douglas J. Levey, Christopher Warneke & Lars A. Brudvig
Conservation and restoration projects often involve starting new populations by introducing individuals into portions of their native or projected range. Such efforts can help meet many related goals, including habitat creation, ecosystem service provisioning, assisted migration, and the reintroduction of imperiled species following local extirpation. The outcomes of reintroduction efforts, however, are highly variable, with results ranging from local extinction to dramatic population growth; reasons for this variation remain unclear. Here, we ask whether population...

Data from: Eco-evolutionary rescue promotes host-pathogen coexistence

Graziella V. DiRenzo, Elise F. Zipkin, Evan H. Campbell Grant, J. Andrew Royle, Ana V. Longo, Kelly R. Zamudio & Karen R. Lips
Emerging infectious pathogens are responsible for some of the most severe host mass-mortality events in wild populations. Yet, effective pathogen control strategies are notoriously difficult to identify, in part because quantifying and forecasting pathogen spread and disease dynamics is challenging. Following an outbreak, hosts must cope with the presence of the pathogen, leading to host-pathogen coexistence or extirpation. Despite decades of research, little is known about host-pathogen coexistence post-outbreak when low host abundances and cryptic...

Data from: Evaluating consumptive and nonconsumptive predator effects on prey density using field times series data

, Scott D. Peacor, David B. Bunnell, Henry A. Vanderploeg, Steve A. Pothoven, Ashley K. Elgin, James R. Bence, Jing Jiao, Edward L. Ionides, D.B. Bunnell, J.A. Marino, E.L. Ionides, S.A. Pothoven, A.K. Elgin, H.A. Vanderploeg, S.D. Peacor & J.R. Bence
Determining the degree to which predation affects prey abundance in natural communities constitutes a key goal of ecological research. Predators can affect prey through both consumptive effects (CEs) and nonconsumptive effects (NCEs), although the contributions of each mechanism to the density of prey populations remain largely hypothetical in most systems. Common statistical methods applied to time series data cannot elucidate the mechanisms responsible for hypothesized predator effects on prey density (e.g., differentiate CEs from NCEs),...

Data from: A whole methylome study of ethanol exposure in brain and blood: an exploration of the utility of peripheral blood as proxy tissue for brain in alcohol methylation studies

Shaunna L. Clark, Blair N. Costin, Robin F. Chan, Alexander W. Johnson, Linying Xie, Jessica L. Jurmain, Gaurav Kumar, Andrey A. Shabalin, Ashutosh K. Pandey, Karolina A. Aberg, Michael F. Miles & Edwin Van Den Oord
Background: Recent reviews have highlighted the potential use of blood‐based methylation biomarkers as diagnostic and prognostic tools of current and future alcohol use and addiction. Due to the substantial overlap that often exists between methylation patterns across different tissues, including blood and brain, blood‐based methylation may track methylation changes in brain; however, little work has explored the overlap in alcohol‐related methylation in these tissues. Methods: To study the effects of alcohol on the brain methylome...

Data from: Organic matter loading by hippopotami causes subsidy overload resulting in downstream hypoxia and fish kills

Christopher L. Dutton, Amanda L. Subalusky, Stephen K. Hamilton, Emma J. Rosi & David M. Post
Organic matter and nutrient loading into aquatic ecosystems affects ecosystem structure and function and can result in eutrophication and hypoxia. Hypoxia is usually attributed to anthropogenic pollution and is rarely documented in unpolluted systems, particularly in rivers. Here we show that organic matter loading from hippopotami causes the repeated occurrence of hypoxia in the Mara River, East Africa. We documented 49 high flow events over three years that caused dissolved oxygen decreases, including 13 events...

Data from: Space use by 4 strains of laying hens to perch, wing flap, dust bathe, stand and lie down

Elizabeth R. Riddle, Ahmed B. A. Ali, Dana L. M. Campbell & Janice M. Siegford
The laying hen industry is implementing aviary systems intended to improve welfare by providing hens with more space and resources to perform species-specific behaviors. To date, limited research has examined spatial requirements of various strains of laying hens for performing key behaviors and none has been conducted within an alternative housing system. This study investigated the amount of space used by 4 strains of laying hens (Hy-Line Brown [HB], Bovans Brown [BB], DeKalb White [DW],...

Data from: Tropical bird species have less variable body sizes

Quentin D. Read, Benjamin Baiser, John M. Grady, Phoebe L. Zarnetske, Sydne Record & Jonathan Belmaker
Ecologists have often predicted that species’ niche breadths should decline toward the equator. Dan Janzen arrived at this prediction based on climatic constraints, while Robert MacArthur argued that a latitudinal gradient in resource specialization drives the pattern. This idea has some support when it comes to thermal niches, but has rarely been explored for other niche dimensions. Body size is linked to niche dimensions related to diet, competition, and environmental tolerance in vertebrates. We identified...

Data from: Field-scale experiments reveal persistent yield gaps in low-input and organic cropping systems

Alexandra N. Kravchenko, Sieglinde S. Snapp & G. Philip Robertson
Knowledge of production-system performance is largely based on observations at the experimental plot scale. Although yield gaps between plot-scale and field-scale research are widely acknowledged, their extent and persistence have not been experimentally examined in a systematic manner. At a site in southwest Michigan, we conducted a 6-y experiment to test the accuracy with which plot-scale crop-yield results can inform field-scale conclusions. We compared conventional versus alternative, that is, reduced-input and biologically based–organic, management practices...

Data from: The evolution of floral signals in relation to range overlap in a clade of California Jewelflowers (Streptanthus s.l.)

Marjorie G. Weber, N. Ivalu Cacho, Martin J. Q. Phan, Caprice Disbrow, Santiago R. Ramirez & Sharon Y. Strauss
Because of their function as reproductive signals in plants, floral traits experience distinct selective pressures related to their role in speciation, reinforcement, and prolonged coexistence with close relatives. However, few studies have investigated whether population-level processes translate into detectable signatures at the macroevolutionary scale. Here, we ask whether patterns of floral trait evolution and range overlap across a clade of California Jewelflowers reflect processes hypothesized to shape floral signal differentiation at the population level. We...

Data from: Evolution of increased Medicaco polymorpha size during invasion does not result in increased competitive ability

Zoe L. Getman-Pickering, Casey P. TerHorst, Susan M. Magnoli & Jennifer A. Lau
Species invading new habitats experience novel selection pressures that can lead to rapid evolution, which may contribute to invasion success and/or increased impact on native community members. Many studies have hypothesized that plants in the introduced range will be larger than those in the native range, leading to increases in competitive ability. There is mixed support for evolution of larger sizes in the introduced range, but few studies have explicitly tested whether evolutionary changes result...

Data from: Local interactions and self-organized spatial patterns stabilize microbial cross-feeding against cheaters

Simon Maccracken Stump, Evan Curtis Johnson & Christopher A. Klausmeier
Mutualisms are ubiquitous, but models predict they should be susceptible to cheating. Resolving this paradox has become relevant to synthetic ecology: cooperative cross-feeding, a nutrient exchange mutualism, has been proposed to stabilize microbial consortia. Previous attempts to understand how cross-feeders remain robust to non-producing cheaters have relied on complex behavior (e.g., cheater punishment) or group selection. Using a stochastic spatial model, we demonstrate two novel mechanisms that can allow cross-feeders to outcompete cheaters, rather than...

Data from: Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter

Mark Eric Benbow, Philip S. Barton, Michael D. Ulyshen, James C. Beasley, Travis L. DeVault, Michael S. Strickland, Jeffery K. Tomberlin, Heather R. Jordan & Jennifer L. Pechal
Decomposition contributes to global ecosystem function by contributing to nutrient recycling, energy flow and limiting biomass accumulation. The decomposer organisms influencing this process form diverse, complex, and highly dynamic communities that often specialize on different plant or animal resources. Despite performing the same net role, there is a need to conceptually synthesize information on the structure and function of decomposer communities across the spectrum of dead plant and animal resources. A lack of synthesis has...

Data from: Early accumulation of active fraction soil carbon in newly established cellulosic biofuel systems

Christine D. Sprunger & G. Philip Robertson
We examined relative changes in soil C pools shortly after the establishment of six perennial and two annual bioenergy cropping systems that differed in diversity (monoculture vs. polyculture). Perennial systems included two monocultures (switchgrass, Panicum virgatum; and miscanthus, Miscanthus × giganteus) and four polycultures including hybrid poplar (Populus sp.) + herbaceous understory; mixed native grasses, successional vegetation, and restored prairie. Two annual systems included no-till continuous corn (Zea mays) and rotational corn (corn-soybean (Glycine max)-canola...

Data from: Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

Rohan Maddamsetti & Richard E. Lenski
Few experimental studies have examined the role that sexual recombination plays in bacterial evolution, including the effects of horizontal gene transfer on genome structure. To address this limitation, we analyzed genomes from an experiment in which Escherichia coli K-12 Hfr (high frequency recombination) donors were periodically introduced into 12 evolving populations of E. coli B and allowed to conjugate repeatedly over the course of 1000 generations. Previous analyses of the evolved strains from this experiment...

Data from: Legacy effects of land use on soil nitrous oxide emissions in annual crop and perennial grassland ecosystems

Michael Abraha, Ilya Gelfand, Stephen K. Hamilton, Jiquan Chen & G. Philip Robertson
Land use conversions into and out of agriculture may influence soil-atmosphere greenhouse gas fluxes for many years. We tested the legacy effects of land use on cumulative soil nitrous oxide (N2O) fluxes for five years following conversion of 22 year-old Conservation Reserve Program (CRP) grasslands and conventionally tilled agricultural fields (AGR) to continuous no-till corn, switchgrass, and restored prairie. An unconverted CRP field served as a reference. We assessed the labile soil C pool of...

Data from: Trans-species predictors of tree leaf mass

Garret T. Dettmann, Dave W. MacFarlane & David W. MacFarlane
Tree leaf mass is a small, highly variable, but critical, component of forest ecosystems. Estimating leaf mass on standing trees with models is challenging because leaf mass varies both within and between tree species and at different locations and points in time. Typically, models for estimating tree leaf mass are species-specific, empirical models that predict intra-specific variation from stem diameter at breast height (DBH). Such models are highly limited in their application because there are...

Data from: Plant community responses to long-term fertilization: changes in functional group abundance drive changes in species richness

Timothy L. Dickson & Katherine L. Gross
Declines in species richness due to fertilization are typically rapid and associated with increases in aboveground production. However, in a long-term experiment examining the impacts of fertilization in an early successional community, we found it took 14 years for plant species richness to significantly decline in fertilized plots, despite fertilization causing a rapid increase in aboveground production. To determine what accounted for this lag in the species richness response, we examined several potential mechanisms. We...

Data from: Weed evolution: genetic differentiation among wild, weedy, and crop radish

Amanda Charbonneau, David Tack, Allison Lale, Josh Goldston, Mackenzie Caple, Emma Conner, Oz Barazani, Jotham Ziffer-Berger, Ian Dworkin & Jeffrey K. Conner
Approximately 200 weed species are responsible for more than 90% of crop losses and these comprise less than one percent of all named plant species, suggesting that there are only a few evolutionary routes that lead to weediness. Agricultural weeds can evolve along three main paths: they can be escaped crops, wild species, or crop-wild hybrids. We tested these three hypotheses in weedy radish, a weed of small grains and an emerging model for investigating...

Registration Year

  • 2018
    59

Resource Types

  • Dataset
    59

Affiliations

  • Michigan State University
    59
  • University of Wisconsin-Madison
    10
  • Cornell University
    5
  • University of Michigan-Ann Arbor
    3
  • University of Notre Dame
    3
  • University of Vermont
    3
  • United States Department of Agriculture
    3
  • University of Florida
    3
  • Great Lakes Science Center
    3
  • California State University, Northridge
    2