49 Works

Data from: Controlled comparison of species- and community-level models across novel climates and communities

Kaitlin Clare Maguire, Diego Nieto-Lugilde, Jessica Blois, Matthew Fitzpatrick, John Williams, Simon Ferrier & David Lorenz
Species distribution models (SDMs) assume species exist in isolation and do not influence one another's distributions, thus potentially limiting their ability to predict biodiversity patterns. Community-level models (CLMs) capitalize on species co-occurrences to fit shared environmental responses of species and communities, and therefore may result in more robust and transferable models. Here, we conduct a controlled comparison of five paired SDMs and CLMs across changing climates, using palaeoclimatic simulations and fossil-pollen records of eastern North...

Data from: Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States

Samuel M. Simkin, Edith B. Allen, William D. Bowman, Christopher M. Clark, Jayne Belnap, Matthew L. Brooks, Brian S. Cade, Scott L. Collins, Linda H. Geiser, Frank S. Gilliam, Sarah E. Jovan, Linda H. Pardo, Bethany K. Schulz, Carly J. Stevens, Katharine N. Suding, Heather L. Throop & Donald M. Waller
Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may be contingent on these environmental factors. We assessed the effect of N deposition on herbaceous richness for 15,136 forest, woodland, shrubland, and grassland sites across the continental United...

Data from: Shape analysis of moss (Bryophyta) sporophytes: insights into land plant evolution

Jeffrey P. Rose, Ricardo Kriebel & Kenneth J. Sytsma
PREMISE OF THE STUDY: The alternation of generations life cycle represents a key feature of land-plant evolution and has resulted in a diverse array of sporophyte forms and modifications in all groups of land plants. We test the hypothesis that evolution of sporangium (capsule) shape of the mosses—the second most diverse land-plant lineage—has been driven by differing physiological demands of life in diverse habitats. This study provides an important conceptual framework for analyzing the evolution...

Data from: Genetic effects of landscape, habitat preference, and demography on three co-occurring turtle species

Brendan N. Reid, David J. Mladenoff & M. Zachariah Peery
Expanding the scope of landscape genetics beyond the level of single species can help to reveal how species traits influence responses to environmental change. Multispecies studies are particularly valuable in highly threatened taxa, such as turtles, in which the impacts of anthropogenic change are strongly influenced by interspecific differences in life-history strategies, habitat preferences, and mobility. We sampled approximately 1500 individuals of three co-occurring turtle species across a gradient of habitat change (including varying loss...

Data from: Factors related to building loss due to wildfires in the conterminous United States

Patricia M. Alexandre, Susan I. Stewart, Nicholas S. Keuler, Murray K. Clayton, Miranda H. Mockrin, Avi Bar-Massada, Alexandra D. Syphard & Volker C. Radeloff
Wildfire is globally an important ecological disturbance affecting biochemical cycles, and vegetation composition, but also puts people and their homes at risk. Suppressing wildfires has detrimental ecological effects and can promote larger and more intense wildfires when fuels accumulate, which increases the threat to buildings in the Wildland Urban Interface (WUI). Yet, when wildfires occur, typically only a small proportion of the buildings within the fire perimeter are lost, and the question is what determines...

Data from: Colour change on different body regions provides thermal and signalling advantages in bearded dragon lizards

Kathleeen R. Smith, Viviana Cadena, John A. Endler, Warren P. Porter, Michael R. Kearney, Devi Stuart-Fox & Kathleen R. Smith
Many terrestrial ectotherms are capable of rapid colour change, yet it is unclear how these animals accommodate the multiple functions of colour, particularly camouflage, communication and thermoregulation, especially when functions require very different colours. Thermal benefits of colour change depend on an animal's absorptance of solar energy in both UV–visible (300–700 nm) and near-infrared (NIR; 700–2600 nm) wavelengths, yet colour research has focused almost exclusively on the former. Here, we show that wild-caught bearded dragon...

Data from: Seed transmission of soybean vein necrosis virus: the first Tospovirus implicated in seed transmission

Carol Groves, Thomas German, Ranjit Dasgupta, Daren Mueller & Damon L. Smith
Soybean vein necrosis virus (SVNV; genus Tospovirus; Family Bunyaviridae) is a negative-sense single-stranded RNA virus that has been detected across the United States and in Ontario, Canada. In 2013, a seed lot of a commercial soybean variety (Glycine max) with a high percentage of discolored, deformed and undersized seed was obtained. A random sample of this seed was planted in a growth room under standard conditions. Germination was greater than 90% and the resulting seedlings...

Data from: Rapid identification of major histocompatibility complex class I haplotypes using deep sequencing in an endangered Old World monkey

Noah D. Simons, Maria Jose Ruiz-Lopez, Colin A. Chapman, Tony L. Goldberg, Julie A. Karl, Roger W. Wiseman, Patrick S. Bohn, David H. O'Connor & Nelson Ting
Immunogenetic data from wild primate populations have been difficult to obtain, due to logistic and methodological constraints. We applied a well-characterized deep sequencing method for MHC I typing, developed for macaques, to a population of wild red colobus to assess the feasibility of identifying MHC I-A/B haplotypes. Ten individuals produced sufficient data from blood and tissue samples to assign haplotypes. Eighty-two sequences were classified as red colobus MHC I alleles distributed across six MHC I...

Data from: Evaluation of downscaled, gridded climate data for the conterminous United States

Ruben Behnke, Stephen Vavrus, Andrew Allstadt, Thomas Albright, Wayne E. Thogmartin & Volker C. Radeloff
Weather and climate affect many ecological processes, making spatially continuous yet fine-resolution weather data desirable for ecological research and predictions. Numerous downscaled weather data sets exist, but little attempt has been made to evaluate them systematically. Here we address this shortcoming by focusing on four major questions: (1) How accurate are downscaled, gridded climate data sets in terms of temperature and precipitation estimates? (2) Are there significant regional differences in accuracy among data sets? (3)...

Data from: Finding the right coverage: The impact of coverage and sequence quality on SNP genotyping error rates

Emily D. Fountain, Jonathan N. Pauli, Brendan N. Reid, Per J. Palsboll & M. Zachariah Peery
Restriction-enzyme-based sequencing methods enable the genotyping of thousands of single nucleotide polymorphism (SNP) loci in non-model organisms. However, in contrast to traditional genetic markers, genotyping error rates in SNPs derived from restriction-enzyme-based methods remain largely unknown. Here, we estimated genotyping error rates in SNPs genotyped with double digest RAD sequencing from Mendelian incompatibilities in known mother-offspring dyads of Hoffman's two-toed sloth (Choloepus hoffmanni) across a range of coverage and sequence quality criteria, for both reference-aligned...

Data from: A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales

Michael R. McKain, Haibao Tang, Joel R. McNeal, Saravanaraj Ayyampalayam, Jerrold I. Davis, Claude W. DePamphilis, Thomas J. Givnish, J. Chris Pires, Dennis Wm. Stevenson & Jim H. Leebens-Mack
Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intra-genomic syntenic blocks. Three such whole genome duplication (WGD) events, designated as rho (ρ), sigma (σ), and tau (τ), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein coding sequences. The timing of...

Data from: Ecosystem interactions underlie the spread of avian influenza A viruses with pandemic potential

Justin Bahl, Truc T. Pham, Nichola J. Hill, Islam T. M. Hussein, Eric J. Ma, Bernard C. Easterday, Rebecca A. Halpin, Timothy B. Stockwell, David E. Wentworth, Ghazi Kayali, Scott Krauss, Stacey Schultz-Cherry, Robert G. Webster, Richard J. Webby, Michael D. Swartz, Gavin J. D. Smith & Jonathan A. Runstadler
Despite evidence for avian influenza A virus (AIV) transmission between wild and domestic ecosystems, the roles of bird migration and poultry trade in the spread of viruses remain enigmatic. In this study we integrate ecosystem interactions into a phylogeographic model to assess the contribution of wild and domestic hosts to AIV distribution and persistence. Analysis of globally sampled AIV datasets shows frequent two-way transmission between wild and domestic ecosystems. In general, viral flow from domestic...

Data from: Social behaviours and networks of vervet monkeys are influenced by gastrointestinal parasites

Colin A. Chapman, Sagan Friant, Kathleen Godfrey, Cynthia Liu, Dipto Sarkar, Valérie A. M. Schoof, Raja Sengupta, Dennis Twinomugisha, Kim Valenta, Tony L. Goldberg & Dipto Sakar
Substantial research has shown that while some parasite infections can be fatal to hosts, most infections are sub-clinical and non-lethal. Such sub-clinical infections can nonetheless have negative consequences for the long-term fitness of the host such as reducing juvenile growth and the host’s ability to compete for food and mates. With such effects, infected individuals are expected to exhibit behavioural changes. Here we use a parasite removal experiment to quantify how gastrointestinal parasite infections affect...

Data from: The Mouse Universal Genotyping Array: from substrains to subspecies

Andrew P. Morgan, Chen-Ping Fu, Chia-Yu Kao, Catherine E. Welsh, John P. Didion, Liran Yadgary, Leeanna Hyacinth, Martin T. Ferris, Timothy A. Bell, Darla R. Miller, Paola Giusti-Rodriguez, Randal J. Nonneman, Kevin D. Cook, Jason K. Whitmire, Lisa E. Gralinski, Mark Keller, Alan D. Attie, Gary A. Churchill, Petko Petkov, Patrick F. Sullivan, Jennifer R. Brennan, Leonard McMillan & Fernando Pardo-Manuel De Villena
Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In...

Data from: Colonization and demographic expansion of freshwater fauna across the Hawaiian Archipelago

Fernando Alda, Roderick B. Gagne, Ryan P. Walter, J. Derek Hogan, Kristine N. Moody, Frida Zink, Peter B. McIntyre, James F. Gilliam & Michael J. Blum
It is widely accepted that insular terrestrial biodiversity progresses with island age because colonization and diversification proceed over time. Here we assess whether this principle extends to oceanic island streams. We examined range-wide mtDNA sequence variation in four stream-dwelling species across the Hawaiian archipelago to characterize the relationship between colonization and demographic expansion, and to determine whether either factor reflects island age. We found that colonization and demographic expansion are not related and that neither...

Data from: Deterministic and stochastic processes lead to divergence in plant communities 25 years after the 1988 Yellowstone fires

William H. Romme, Timothy G. Whitby, Daniel B. Tinker & Monica G. Turner
Young, recently burned forests are increasingly widespread throughout western North America, but forest development after large wildfires is not fully understood, especially regarding effects of variable burn severity, environmental heterogeneity, and changes in drivers over time. We followed development of subalpine forests after the 1988 Yellowstone fires by periodically re-sampling permanent plots established soon after the fires. We asked two questions about patterns and processes over the past 25 years: (1) Are plant species richness...

Data from: Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum

Michael A. Hardigan, Emily Crisovan, John P. Hamilton, Jeongwoon Kim, Parker Laimbeer, Courtney P. Leisner, Norma C. Manrique-Carpintero, Linsey Newton, Gina M. Pham, Brieanne Vaillancourt, Xueming Yang, Zixian Zeng, David S. Douches, Jiming Jiang, Richard E. Veilleux & C. Robin Buell
Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species, and...

Data from: Divergence and isolation of cryptic sympatric taxa within the annual legume Amphicarpaea bracteata

Rebecca Y. Kartzinel, Daniel Spalink, Donald M. Waller & Thomas J. Givnish
The amphicarpic annual legume Amphicarpaea bracteata is unusual in producing aerial and subterranean cleistogamous flowers that always self-fertilize and, less commonly, aerial chasmogamous flowers that outcross. Although both morphologic and genetic variants are known in this highly selfing species, debate continues over whether this variation is continuous, reflecting the segregation of standing genetic variation, or discontinuous, reflecting distinct taxa that rarely intercross. We characterized SNP variation in 128 individuals in southern Wisconsin to assess within-...

Data from: Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

Carlos I. Arbizu, Shelby L. Ellison, Douglas Senalik, Philipp W. Simon & David M. Spooner
Background: The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing...

Data from: Puma predation subsidizes an obligate scavenger in the high Andes

Paula L. Perrig, Emiliano Donadio, Arthur D. Middleton & Jonathan N. Pauli
The ungulate–carnivore–vulture complex is a key trophic module of many terrestrial ecosystems, but one that is globally under threat. Few have explored cross-species dependencies in this module, and the degree to which vultures rely on trophic facilitation by apex carnivores is rarely known and almost never quantified. We investigated the importance of puma Puma concolor predation on its native camelid prey, vicuñas Vicugna vicugna and guanacos Lama guanicoe, in food provisioning for Andean condors Vultur...

Data from: Distinctive fungal communities in an obligate African ant-plant mutualism

Christopher C.M. Baker, Dino J. Martins, Julianne N. Pelaez, Johan P.J. Billen, Anne Pringle, Megan E. Frederickson, Naomi E. Pierce, Christopher C. M. Baker & Johan P. J. Billen
Three ant species nest obligately in the swollen-thorn domatia of the African ant-plant Vachellia (Acacia) drepanolobium, a model system for the study of ant-defence mutualisms and species coexistence. Here we report on the characteristic fungal communities generated by these ant species in their domatia. First, we describe behavioural differences between the ant species when presented with a cultured fungal isolate in the laboratory. Second, we use DNA metabarcoding to show that each ant species has...

Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Candice N. Hirsch, Cory D. Hirsch, Alex B. Brohammer, Megan J. Bowman, Ilya Soifer, Omer Barad, Doron Sehm-Tov, Kobi Baruch, Fei Lu, Alvaro G. Hernandez, Christopher J. Fields, Chris L. Wright, Klaus Koehler, Nathan M. Springer, Edward S. Buckler, C. Robin Buell, Natalia De Leon, Shawn M. Kaeppler, Kevin Childs & Mark A. Mikel
Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder...

Data from: Life history evolution and cellular mechanisms associated with increased size in high-altitude Drosophila

Justin B. Lack, Amir Yassin, Quentin D. Sprengelmeyer, Evan J. Johanning, Jean R. David & John E. Pool
Understanding the physiological and genetic basis of growth and body size variation has wide-ranging implications, from cancer and metabolic disease to the genetics of complex traits. We examined the evolution of body and wing size in high-altitude Drosophila melanogaster from Ethiopia, flies with larger size than any previously known population. Specifically, we sought to identify life history characteristics and cellular mechanisms that may have facilitated size evolution. We found that the large-bodied Ethiopian flies laid...

Data from: Downscaled and debiased climate simulations for North America from 21,000 years ago to 2100AD

David J. Lorenz, Diego Nieto-Lugilde, Jessica L. Blois, Matthew C. Fitzpatrick & John W. Williams
Increasingly, ecological modellers are integrating paleodata with future projections to understand climate-driven biodiversity dynamics from the past through the current century. Climate simulations from earth system models are necessary to this effort, but must be debiased and downscaled before they can be used by ecological models. Downscaling methods and observational baselines vary among researchers, which produces confounding biases among downscaled climate simulations. We present unified datasets of debiased and downscaled climate simulations for North America...

Registration Year

  • 2016

Resource Types

  • Dataset


  • University of Wisconsin-Madison
  • University of Wyoming
  • University of California, Merced
  • Columbia University
  • Duke University
  • University of Groningen
  • University of North Carolina
  • University of Minnesota
  • McGill University
  • Indiana University Bloomington