54 Works

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Nicholas Fountain-Jones, Nicholas Clark, Amy Kinsley, Michelle Carstensen, James Forester, Johnson Timothy, Elizabeth Miller, Seth Moore, Tiffany Wolf & Meggan Craft
Microbial communities are increasingly recognised as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free-living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison to other factors such as host characteristics or spatial proximity of hosts. Here we ask how gut microbial communities are structured...

Data from: Species Selection Regime and Phylogenetic Tree Shape

George Verboom, Florian Boucher, David Ackerly, Lara Wootton & William Freyman
Species selection, the effect of heritable traits in generating between-lineage diversification rate differences, provides a valuable conceptual framework for understanding the relationship between traits, diversification and phylogenetic tree shape. An important challenge, however, is that the nature of real diversification landscapes – curves or surfaces which describe the propensity of species-level lineages to diversify as a function of one or more traits – remains poorly understood. Here we present a novel, time-stratified extension of the...

How much do rare and crop-pollinating bees overlap in identity and flower preferences?

Molly MacLeod, James Reilly, Daniel Cariveau, Mark Genung, Michael Roswell, Jason Gibbs & Rachael Winfree
1. The biodiversity-centered approach to conservation prioritizes rare species, whereas the ecosystem services approach prioritizes species that provide services to people. The two approaches align when rare species provide ecosystem services, or when both groups of species benefit from the same management action. We use data on bee pollinators and the plant species they forage on to determine if there are rare species among the most important crop pollinators, and the extent to which plant...

Data from: The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives

Riccardo Aversano, Felice Contaldi, Maria Raffaella Ercolano, Valentina Grosso, Massimo Iorizzo, Filippo Tatino, Luciano Xumerle, Alessandra Dal Molin, Carla Avanzato, Alberto Ferrarini, Massimo Delledonne, Walter Sanseverino, Riccardo Aiese Cigliano, Salvador Capella-Gutierrez, Toni Gabaldón, Luigi Frusciante, James M. Bradeen & Domenico Carputo
Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data...

Data from: Global patterns in fine root decomposition: climate, chemistry, mycorrhizal association, and woodiness

Craig R. See, Michael Luke McCormack, Sarah E. Hobbie, Habacuc Flores-Moreno, Whendee L. Silver & Peter G. Kennedy
Fine root decomposition constitutes a critical yet poorly understood flux of carbon and nutrients in terrestrial ecosystems. Here, we present the first large‐scale synthesis of species trait effects on the early stages of fine root decomposition at both global and local scales. Based on decomposition rates for 279 plant species across 105 studies and 176 sites, we found that mycorrhizal association and woodiness are the best categorical traits for predicting rates of fine root decomposition....

Data from: Past tree influence and prescribed fire exert strong controls on reassembly of mountain grasslands after tree removal

Charles B. Halpern, Joseph A. Antos, Shan Kothari & Annette M. Olson
Woody-plant encroachment represents a global threat to grasslands. Although the causes and consequences of this regime shift have received substantial attention, the processes that constrain reassembly of the grassland state remain poorly understood. We experimentally tested two potentially important controls on reassembly—the past influence of trees and the effects of fire—in conifer-invaded grasslands (mountain meadows) of western Oregon. Previously, we had reconstructed the history of tree invasion at fine spatial and temporal resolution. Using small...

APAL \"Sensitivity to changes in dynamic affordances for walking on land and at sea\" Data Sets

Hannah Walter, Ruixuan Li, Nicolette Peterson, Thomas Stoffregen & Jeffrey Wagman

Cloquet Forestry Center arboretum larch individual tree diameter and height 2016

Benjamin Koenig & Kyle Gill
During August 2 through September 20, 2016 Kyle Gill, University of Minnesota Cloquet Forestry Center (CFC) Manager and Research Coordinator, led an effort to sample individual tree size on 139 larch trees of six different genetic and geographic sources found in the CFC arboretum; genetic or geographic source available upon request.

Individual-Based-Model used in \"Population context matters: predicting effects of metabolic stress mediated by food availability and predation with an agent- and energy budget-based model\"

Maxime Vaugeois, Valery E Forbes, Paul A Venturelli, Chiara Accolla & Stephanie L Hummel
This is the programming software code of the model developed to investigate the population-level impacts of a hypothetical, sublethal stressor that can affect an individual’s metabolism (growth, reproduction, maintenance, or assimilation) in systems in which population size is controlled by different combinations of food availability and predation pressure. The life cycle of fathead minnow (Pimephales promelas) is describe through their metabolism, using the Dynamic Energy Budget theory (DEB) and we represent the populations through an...

SAM Filtering Pipeline (SFP): Algorithm for the determination of integration sites from next generation sequencing data

Sofie A O'Brien & Wei-Shou Hu
The locus at which a vector harboring a product transgene integrates into the genome can have a profound effect on the transgene’s transcript level and the stability of the resulting cell line. In order to identify integration site(s) of a transfected vector from next generation genome sequencing data, the SAM filtering pipeline (SFP) was created. It is best suited for targeted sequence data, such as that from sequence capture of probed vector regions. However, it...

Data from: Feline immunodeficiency virus in puma: estimation of force of infection reveals insights into transmission

Jennifer Reynolds, Scott Carver, Mark Cunningham, Ken Logan, Winston Vickers, Kevin Crooks, Sue VandeWoude & Meggan Craft
Determining parameters that govern pathogen transmission (such as the force of infection, FOI), and pathogen impacts on morbidity and mortality, is exceptionally challenging for wildlife. Vital parameters can vary, for example across host populations, between sexes and within an individual's lifetime. Feline immunodeficiency virus (FIV) is a lentivirus affecting domestic and wild cat species, forming species-specific viral--host associations. FIV infection is common in populations of puma (Puma concolor), yet uncertainty remains over transmission parameters and...

Data from: Resistance of soil biota and plant growth to disturbance increases with plant diversity

Jonathan Bennett, Alexander Koch, Jennifer Forsythe, Nancy Johnson, David Tilman & John Klironomos
Plant diversity is critical to the functioning of ecosystems, potentially mediated in part by interactions with soil biota. Here, we characterized multiple groups of soil biota across a plant diversity gradient in a long-term experiment. We then subjected soil samples taken along this gradient to drought, freezing, and a mechanical disturbance to test how plant diversity affects the responses of soil biota and growth of a focal plant to these disturbances. High plant diversity resulted...

Invasive species and biotic homogenization in temperate aquatic plant communities

Ranjan Muthukrishnan & Daniel Larkin
Aim: Biotic homogenization (BH), a reduction in the distinctness of species composition between geographically separated ecological communities in a region, is an important but underappreciated potential consequence of biological invasions. While BH theory has always considered invasions, it has generally been in a relatively narrow context, i.e., that the cosmopolitan nature of invasive species increases BH because of their shared presence across many locations. We sought to evaluate this component of BH as well as...

Data from: Nitrogen addition reduced ecosystem stability regardless of its impacts on plant diversity

Jushan Liu, Xiaofei Li, Quanhui Ma, Xiang Zhang, Ying Chen, Forest Isbell & Deli Wang
1. Global environmental changes are altering ecosystem stability, sometimes by altering biodiversity. For example, by driving grassland plant species loss, nitrogen (N) addition can reduce ecosystem stability. In other cases, however, N addition may alter productivity and ecosystem stability, by increasing the dominance of particularly productive or stable species. 2. We examined how N addition affected plant diversity, productivity, and the temporal stability of productivity in an 8-year grassland experiment. We found that N addition...

Data from: Meiotic drive shapes rates of karyotype evolution in mammals

Heath Blackmon, Joshua Justison, Itay Mayrose & Emma E. Goldberg
Chromosome number is perhaps the most basic characteristic of a genome, yet generalizations that can explain the evolution of this trait across large clades have remained elusive. Using karyotype data from over 1,000 mammals, we developed and applied a phylogenetic model of chromosome evolution that links chromosome number changes with karyotype morphology. Using our model, we infer that rates of chromosome number evolution are significantly lower in species with karyotypes that consist of either all...

Data from: Soil organic carbon stability in forests: distinct effects of tree species identity and traits

Gerrit Angst, Kevin E. Mueller, David M. Eissenstat, Susan Trumbore, Katherine H. Freeman, Sarah E. Hobbie, Jon Chorover, Jacek Oleksyn, Peter B. Reich & Carsten W. Mueller
Rising atmospheric CO2 concentrations have increased interest in the potential for forest ecosystems and soils to act as carbon (C) sinks. While soil organic C contents often vary with tree species identity, little is known about if, and how, tree species influence the stability of C in soil. Using a 40‐year‐old common garden experiment with replicated plots of eleven temperate tree species, we investigated relationships between soil organic matter (SOM) stability in mineral soils and...

Data from: Geographic variation in thermal sensitivity of early life traits in a widespread reptile

Brooke L. Bodensteiner, Daniel A. Warner, John B. Iverson, Carrie L. Milne-Zelman, Timothy S. Mitchell, Jeanine M. Refsnider & Fredric J. Janzen
Taxa with large geographic distributions generally encompass diverse macroclimatic conditions, potentially requiring local adaptation and/or phenotypic plasticity to match their phenotypes to differing environments. These eco-evolutionary processes are of particular interest in organisms with traits that are directly affected by temperature, such as embryonic development in oviparous ectotherms. Here we examine the spatial distribution of fitness-related early-life phenotypes across the range of a widespread vertebrate, the painted turtle (Chrysemys picta). We quantified embryonic and hatchling...

Data from: Adult nutritional stress decreases oviposition choosiness and fecundity in female butterflies

Sarah Jaumann & Emilie C. Snell-Rood
Despite the benefits of careful decision-making, not all animals are choosy. One explanation is that choosiness can cost time and energy and thus depend on nutrition. However, it is not clear how allocation to choosiness versus other components of life history shifts in the face of nutritional stress. We tested two hypotheses about the effects of nutritional stress on choosiness and other life history traits: 1) poor nutrition leads to compensatory shifts in life history...

Data from: Meta-analytic and economic approaches for evaluation of pesticide impact on Sclerotinia stem rot control and soybean yield in the North Central U.S.

Jaime F. Willbur, Paul Mitchell, Mamadou L. Fall, Adam M. Byrne, Scott Chapman, Crystal M. Floyd, Carl A. Bradley, Keith Ames, Martin I. Chilvers, Nathan Kleczewski, Dean Malvick, Brian Mueller, Daren Mueller, Mehdi Kabbage, Shawn P. Conley & Damon Smith
As complete host resistance in soybean has not been achieved, Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum continues to be of major economic concern for farmers. Thus, chemical control remains a prevalent disease management strategy. Pesticide evaluations were conducted in Illinois, Iowa, Michigan, Minnesota, New Jersey, and Wisconsin from 2009 to 2016, for a total of 25 site-years (n = 2057 plot-level data points). These studies were used in network meta-analyses to evaluate the...

Data from: Natural and sexual selection on cuticular hydrocarbons: a quantitative genetic analysis

Jacob D. Berson, Marlene Zuk & Leigh W. Simmons
While the reproductive benefits of sexual displays have been widely studied, we have relatively limited evidence of the fitness costs associated with most display traits. Insect cuticular hydrocarbon (CHC) profiles are sexually selected traits that also protect against desiccation. These two functions are thought to oppose each other, with investment in particular compounds believed to increase attractiveness at the expense of compounds that protect against water-loss. We investigated this potential trade-off in a quantitative genetic...

Water quality and coral reef monitoring along the southeast Florida coast.

Christopher D. Sinigalliano, Ian C. Enochs, S. Jack (Speridon Jack) Stamates, Paul R. Jones, Charles M. Featherstone, Gidley, Stephanie M. Rosales, Lewis J. Gramer, Chris Staley & Thomas P. Carsey
NOAA Technical Report OAR AOML 47

Delta Basin-2 Wave Experiments (2018-2019)

Nicholas J Rodgers & Chris Paola
These experiments were conducted in St. Anthony Fall Laboratory (SAFL) Delta Basin. This is a fixed based basin (5 m wide x 5 m long x 0.5 m deep) that is fed sediment and water from an input source to create model deltas. Sea-level adjustment via relative sea-level rise is available in this facility and was used for these experiments along with a floating wave generator. This facility is able to collect data via an...

VCF file of SNP data of 556 isolates of the wheat leaf rust fungus, Puccinia triticina from 11 world-wide regions

James Kolmer
This a file of ca. 6500 SNPs of 556 isolates of the wheat leaf rust fungus, Puccina triticina from 11 worldwide regions that were mapped to the reference genome. This data was used to examine the population structure of Puccinia triticina on a worldwide basis, and to examine the evolutionary relationship between collections from a wheat progenitor, collections from durum wheat, and collections from common wheat. Groups of isolates that were highly related were found...

Data from: Patterns of nitrogen-fixing tree abundance in forests across Asia and America

Duncan N. L. Menge, Ryan A. Chisholm, Stuart J. Davies, Kamariah Abu Salim, David Allen, Mauricio Alvarez, Norm Bourg, Warren Y. Brockelman, Sarayudh Bunyavejchewin, Nathalie Butt, Min Cao, Wirong Chanthorn, Wei-Chun Chao, Keith Clay, Richard Condit, Susan Cordell, João Batista Da Silva, H. S. Dattaraja, Ana Cristina Segalin De Andrade, Alexandre A. Oliveira, Jan Den Ouden, Michael Drescher, Christine Fletcher, Christian P. Giardina, C. V. Savitri Gunatilleke … & Tak Fung
Symbiotic nitrogen (N)‐fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N‐fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N‐fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America...

Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide

Daryl R Trumbo, Patricia E Salerno, Kenneth Logan, Mat Alldredge, Roderick B Gagne, Christopher P Kozakiewicz, Simona Kraberger, Nick Fountain-Jones, Meggan E Craft, Scott Carver, Holly B Ernest, Kevin Crooks, Sue VandeWoude & W. Chris Funk
Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 130 pumas on the...

Registration Year

  • 2019

Resource Types

  • Dataset
  • Software
  • Text


  • University of Minnesota
  • Utah State University
  • University of Florida
  • Commonwealth Scientific and Industrial Research Organisation
  • University of Kansas
  • Columbia University
  • University of Notre Dame
  • Duke University
  • University of Georgia
  • Oregon State University