23 Works

Data from: Climate modifies response of non-native and native species richness to nutrient enrichment

Habacuc Flores-Moreno, Peter B. Reich, Eric M. Lind, Lauren L. Sullivan, Eric W. Seabloom, Laura Yahdjian, Andrew S. MacDougall, Lara G. Reichmann, Juan Alberti, Selene Báez, Jonathan D. Bakker, Marc W. Cadotte, Maria C. Caldeira, Enrique J. Chaneton, Carla M. D'Antonio, Philip A. Fay, Jennifer Firn, Nicole Hagenah, W. Stanley Harpole, Oscar Iribarne, Kevin P. Kirkman, Johannes M. H. Knops, Kimberly J. La Pierre, Ramesh Laungani, Andrew D. B. Leakey … & Elizabeth T. Borer
Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of...

Data from: Don’t put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array

Shawn P. Brown, Astrid Ferrer, James W. Dalling & Katy D. Heath
With the increasing democratization of high-throughout sequencing (HTS) technologies, along with the concomitant increase in sequence yield per dollar, many researchers are exploring HTS for microbial community ecology. Many elements of experimental design can drastically affect the final observed community structure, notably the choice of primers for amplification prior to sequencing. Some targeted microbes can fail to amplify due to primer-targeted sequence divergence and be omitted from obtained sequences, leading to differences among primer pairs...

DEM of the Great Unconformity, USA cratonic platform

Stephen Marshak, Stefanie Domrois, Curtis Abert & Timothy Larson
These show the topography and relief of the Precambrian surface of the Cratonic Platform of the United States.

Data from: Intensifying drought eliminates the expected benefits of elevated carbon dioxide for soybean

Sharon B. Gray, Orla Dermody, Stephanie P. Klein, Anna M. Locke, Justin M. McGrath, Rachel E. Paul, David M. Rosenthal, Ursula M. Ruiz-Vera, Matthew H. Siebers, Reid Strellner, Elizabeth A. Ainsworth, Carl J. Bernacchi, Stephen P. Long, Donald R. Ort & Andrew D. B. Leakey
Stimulation of C3 crop yield by rising concentrations of atmospheric carbon dioxide ([CO2]) is widely expected to counteract crop losses that are due to greater drought this century. But these expectations come from sparse field trials that have been biased towards mesic growth conditions. This eight-year study used precipitation manipulation and year-to-year variation in weather conditions at a unique open-air field facility to show that the stimulation of soybean yield by elevated [CO2] diminished to...

Data from: Habitat, predators, and hosts regulate disease in Daphnia through direct and indirect pathways

Alexander T. Strauss, Marta S. Shocket, David J. Civitello, Jessica L. Hite, Rachel M. Penczykowski, Meghan A. Duffy, Carla E. Cáceres & Spencer R. Hall
Community ecology can link habitat to disease via interactions among habitat, focal hosts, other hosts, their parasites, and predators. However, complicated food web interactions (i.e., trophic interactions among predators, and their impacts on host density and diversity) often obscure the important pathways regulating disease. Here, we disentangle community drivers in a case study of planktonic disease, using a two-step approach. In step one, we tested univariate field patterns linking community interactions to two disease metrics....

Data from: Herbivorous dinosaur jaw disparity and its relationship to extrinsic evolutionary drivers

Jamie A. MacLaren, Philip S. L. Anderson, Paul Barrett & Emily J. Rayfield
Morphological responses of nonmammalian herbivores to external ecological drivers have not been quantified over extended timescales. Herbivorous nonavian dinosaurs are an ideal group to test for such responses, because they dominated terrestrial ecosystems for more than 155 Myr and included the largest herbivores that ever existed. The radiation of dinosaurs was punctuated by several ecologically important events, including extinctions at the Triassic/Jurassic (Tr/J) and Jurassic/Cretaceous (J/K) boundaries, the decline of cycadophytes, and the origin of...

Data from: Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice

Julie M. Allen, J. Gordon Burleigh, Jessica E. Light & David L. Reed
Phylogenetic trees can reveal the origins of endosymbiotic lineages of bacteria and detect patterns of co-evolution with their hosts. Although taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships are based on few available bacterial sequences. Here we examined how different sampling strategies of Gammaproteobacteria sequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using...

Data from: The first organ-based ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions

Christian S. Wirkner, Torben Göpel, Jens Runge, Jonas Keiler, Bastian-Jesper Klussmann-Fricke, Katarina Huckstorf, Stephan Scholz, István Mikó, Matthew J. Yoder & Stefan Richter
Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the “linguistic problem of morphology”, concerns the usage of terminology and also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use...

Data from: Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus)

Collin P. Jaeger, Melvin R. Duvall, Bradley J. Swanson, Christopher A. Phillips, Michael J. Dreslik, Sarah J. Baker & Richard B. King
Genetic diversity is fundamental to maintaining the long-term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment...

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: Phylogenomics from whole genome sequences using aTRAM

Julie M. Allen, Bret Boyd, Nam-Phuong Nguyen, Pranjal Vachaspati, Tandy Warnow, Daisie I. Huang, Patrick G. S. Grady, Kayce C. Bell, Quentin C.B. Cronk, Lawrence Mugisha, Barry R. Pittendrigh, M. Soledad Leonardi, David L. Reed & Kevin P. Johnson
Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (<1000 Mbp) it is feasible to sequence the...

New York City Hourly Traffic Estimates (2010-2013)

Brian Donovan, Alec Mori, Nimit Agrawal, Yalan Meng, Jong Lee & Daniel Work
This dataset contains hourly traffic estimates (speeds) for individual links of the New York City road network for the years 2010-2013, estimated from New York City Taxis.

Phylogenetic Analysis of the NRPS AmbE Condensation Domains for the L-2-amino-4-methoxy-trans-3-butenoic acid (AMB) Biosynthetic Pathway in Pseudomonas aeruginosa

Heidi Imker
This dataset contains the protein sequences and trees used to compare Non-Ribosomal Peptide Synthetase (NRPS) condensation domains in the AMB gene cluster and was used to create figure S1 in Rojas et al. 2015. Instead of having to collect representative sequences independently, this set of condensation domain sequences may serve as a quick reference set for coarse classification of condensation domains.

HIPPI Dataset

Nam-phuong Nguyen, Mike Nute, Siavash Mirarab & Tandy Warnow
This archive contains all the alignments and trees used in the HIPPI paper [1]. The pfam.tar archive contains the PFAM families used to build the HMMs and BLAST databases. The file structure is: ./X/Y/initial.fasttree ./X/Y/initial.fasta where X is a Pfam family, Y is the cross-fold set (0, 1, 2, or 3). Inside the folder are two files, initial.fasta which is the Pfam reference alignment with 1/4 of the seed alignment removed and initial.fasttree, the FastTree-2...

Data from: \"Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia\"

Lindsay V. Clark, Elena Dzyubenko, Nikolay Dzyubenko, Larisa Bagmet, Andrey Sabitov, Pavel Chebukin, Douglas A. Johnson, Jens Bonderup Kjeldsen, Karen Koefoed Petersen, Uffe Jørgensen, Ji Hye Yoo, Kweon Heo, Chang Yeon Yu, Hua Zhao, Xiaoli Jin, Junhua Peng, Toshihiko Yamada & Erik J. Sacks
Datasets and R scripts relating to the manuscript "Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia" published in Annals of Botany, 10.1093/aob/mcw137. Field data, including collection locations, physical and ecological information for each location, and plant phenotypes relating to biomass are included. Genetic data in this repository include single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq), as well as plastid microsatellites. A file is...

Data from: Laboratory rearing of Anopheles arabiensis: impact on genetic variability and implications for Sterile Insect Technique (SIT) based mosquito control in northern Sudan

Rasha Siddig Azrag, Kamal M. Ibrahim, Colin Malcolm, Elamin El Rayah & Badria El-Sayed
Background: Mosquito colony populations often show significant changes in their population genetic make-up compared to the field populations that were used as founding source. Most of the changes that have been reported are indicators of depletion in the overall genetic diversity of the colony populations. The Sterile Insect Techniques programme of mosquito control that is underway in Northern Sudan uses sterilized males produced from a laboratory-maintained colony population. The genetic diversity of an advanced generation...

Data from: Intrasexual competition underlies sexual selection on male breeding coloration in the orangethroat darter, Etheostoma spectabile

Muchu Zhou & Rebecca C. Fuller
Elaborate, sexually dimorphic traits are widely thought to evolve under sexual selection through female preference, male–male competition, or both. The orangethroat darter (Etheostoma spectabile) is a sexually dichromatic fish in which females exhibit no preferences for male size or coloration. We tested whether these traits affect individual reproductive success in E. spectabile when multiple males are allowed to freely compete for a female. The quality and quantity of male coloration were associated with greater success...

Data from: Miocene flooding events of western Amazonia

Carlos Jaramillo, Ingrid Romero, Carlos D'Apolito, German Bayona, Edward Duarte, Stephen Louwye, Jaime Escobar, Javier Luque, Jorge D. Carrillo-Briceño, Vladimir Zapata, Andrés Mora, Stefan Schouten, Michael Zavada, Guy Harrington, John Ortiz & Frank P. Wesselingh
There is a considerable controversy about whether western Amazonia was ever covered by marine waters during the Miocene [23 to 5 Ma (million years ago)]. We investigated the possible occurrence of Miocene marine incursions in the Llanos and Amazonas/Solimões basins, using sedimentological and palynological data from two sediment cores taken in eastern Colombia and northwestern Brazil together with seismic information. We observed two distinct marine intervals in the Llanos Basin, an early Miocene that lasted...

Data from: Anthropogenic ecosystem disturbance and the recovery debt

David Moreno Mateos, Edward B. Barbier, Peter C. Jones, Holly P. Jones, James Aronson, Jose A. Lopez-Lopez, Michelle L. McCrackin, Paula Meli, Daniel Montoya & José Rey Benayas
Ecosystem recovery from anthropogenic disturbances, either without human intervention or assisted by ecological restoration, is increasingly occurring worldwide. As ecosystems progress through recovery, it is important to estimate any resulting deficit in biodiversity and functions. Here we use data from 3,035 sampling plots worldwide, to quantify the interim reduction of biodiversity and functions occurring during the recovery process (that is, the ‘recovery debt’). Compared with reference levels, recovering ecosystems run annual deficits of 46–51% for...

Data from: Intra-population genomics in a model mutualist: population structure and candidate symbiosis genes under selection in Medicago truncatula

Michael A. Grillo, Stephane De Mita, Patricia V. Burke, Kathryn L.S. Solórzano-Lowell & Katy Denise Heath
Bottom-up evolutionary approaches, including geographically-explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here we conduct a population genomic analysis in the model legume, Medicago truncatula, in order to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially-variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe. Results from STRUCTURE analysis identify 5 distinct genetic...

Data from: Elevated CO2 and temperature increase soil C losses from a soybean-maize ecosystem

Christopher K. Black, Sarah C. Davis, Tara W. Hudiburg, Carl J. Bernacchi & Evan H. DeLucia
Warming temperatures and increasing CO2 are likely to have large effects on the amount of carbon stored in soil, but predictions of these effects are poorly constrained. We elevated temperature (canopy: +2.8 °C; soil growing season: +1.8 °C; soil fallow: +2.3 °C) for 3 years within the 9th–11th years of an elevated CO2 (+200 ppm) experiment on a maize–soybean agroecosystem, measured respiration by roots and soil microbes, and then used a process-based ecosystem model (DayCent)...

Data from: Distinguishing migration events of different timing for wild boar in the Balkans

Panoraia Alexandri, Hendrik-Jan Megens, Richard P. M. A. Crooijmans, Martien A. M. Groenen, Daniel J. Goedbloed, Juan M. Herrero-Medrano, Lauretta A. Rund, Lawrence B. Schook, Evangelos Chatzinikos, Costas Triantaphyllidis, Alexandros Triantafyllidis, Laurence B. Schook & Alexander Triantafyllidis
Aim: We compared the power of different nuclear markers to investigate genetic structure of southern Balkan wild boar. We distinguished between historic events, such as isolation in different refugia during glacial periods, from recent demographic processes, such as naturally occurring expansions. Location: Southern Balkans/Greece. Methods: We sampled 555 wild boars from 20 different locations in southern Balkans/Greece. All individuals were analysed with 10 microsatellites and a subgroup of 91 with 49,508 single nucleotide polymorphisms (SNPs)....

Data from: Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation

Christopher J. Holmes, Jelena H. Pantel, Kimberly L. Schulz & Carla E. Cáceres
When newly created habitats are initially colonized by genotypes with rapid population growth rates, later arriving colonists may be prevented from establishing. Although these priority effects have been documented in multiple systems, their duration may be influenced by the diversity of the founding population. We conducted a large-scale field manipulation to investigate how initial clonal diversity influences temporal and landscape patterns of genetic structure in a developing metapopulation. Six genotypes of obligately asexual Daphnia pulex...

Registration Year

  • 2016
    23

Resource Types

  • Dataset
    23

Affiliations

  • University of Illinois at Urbana Champaign
    18
  • University of Illinois
    5
  • University of Minnesota
    2
  • University of Wisconsin-Madison
    2
  • French National Centre for Scientific Research
    2
  • Smithsonian Tropical Research Institute
    2
  • University of Bristol
    2
  • University of Illinois System
    2
  • Michigan State University
    2
  • Helmholtz Centre for Environmental Research
    1