27 Works

Data from: Spatiotemporal patterns of duck nest density and predation risk: a multi-scale analysis of 18 years and more than 10 000 nests

Kevin Ringelman, John M. Eadie, Joshua T. Ackerman, Andy Sih, Daniel L. Loughman, Gregory S. Yarris, Shaun L. Oldenburger, M. Robert McLandress, Kevin M. Ringelman & Andrew Sih
Many avian species are behaviorally-plastic in selecting nest sites, and may shift to new locations or habitats following an unsuccessful breeding attempt. If there is predictable spatial variation in predation risk, the process of many individuals using prior experience to adaptively change nest sites may scale up to create shifting patterns of nest density at a population level. We used 18 years of waterfowl nesting data to assess whether there were areas of consistently high...

Spatiotemporal patterns of male and female white-tailed deer on a hunted landscape

William Gulsby, Dylan Stewart, Stephen Ditchkoff & Bret Collier
Resource selection in sexually dimorphic ungulates is at least partially explained by sex-specific resource requirements and risk aversion strategies. Females generally spend more time in areas with less risk and abundant, high-quality forage due to their smaller body size. However, demographically variable responses to risk are context dependent, and few have concurrently quantified male and female behavior within areas with the same resource base. We captured 111 (54 males, 57 females) adult white-tailed deer (Odocoileus...

Additional file 2 of Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Additional file 2: Table S2. The average of the inter- specific nucleotide percentage of pairwise identities (mean ± standard deviation%) of each species to all the others at each locus; overall is the average value of all the means across all the species for each locus.

Data from: Model choice, missing data and taxon sampling impact phylogenomic inference of deep Basidiomycota relationships

Arun N. Prasanna, Daniel Gerber, Teeratas Kijpornyongpan, M. Catherine Aime, Vinson P. Doyle & Laszlo G. Nagy
Resolving deep divergences in the tree of life is challenging even for analyses of genome-scale phylogenetic datasets. Relationships between Basidiomycota subphyla, the rusts and allies (Pucciniomycotina), smuts and allies (Ustilaginomycotina) and mushroom-forming fungi and allies (Agaricomycotina) were found particularly recalcitrant both to traditional multigene and genome-scale phylogenetics. Here, we address basal Basidiomycota relationships using concatenated and gene-tree based analyses of various phylogenomic datasets to examine the contribution of several potential sources of bias. We evaluate...

Phylogenetic data for: High diversity of new and known Phytophthora species from phylogenetic Clade 10 in natural ecosystems of Asia, Europe and the Americas

Thomas Jung, Ivan Milenković, Tamara Corcobado, Tomáš Májek, Josef Janoušek, Tomáš Kudláček, Michal Tomšovský, Zoltán Nagy, Álvaro Durán, Marthin Tarigan, Eugenio Sanfuentes Von Stowasser, Raghuwinder Singh, Monique Ferreira, Joan Webber, Bruno Scanu, Nguyen Minh Chi, Pham Quang Thu, Muhammad Junaid, Ade Rosmana, Baharuddin Baharuddin, Tutik Kuswinanti, Nasri Nasri, Koji Kageyama, Ayaka Hieno, Hayato Masuya … & Marília Horta Jung
During extensive surveys of Phytophthora diversity, 14 new species were detected in natural ecosystems in Chile, Louisiana, Sweden, Ukraine, Vietnam and Indonesia. Multigene phylogeny based on the nuclear LSU, rpl10, ITS, ßtub, enl, hsp90, tef-1α, ras-ypt1 and tigA and the mitochondrial cox1, nadh1 and rps10 gene sequences demonstrated that they belong to phylogenetic Clade 10 which is structured into three subclades. Subclades 10a and 10b comprise soil- and waterborne species with nonpapillate sporangia and variable...

Additional file 5 of Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Additional file 5: Figure S3. The ML phylogenetic tree based on the 28S rRNA gene sequences with reference sequences from NCBI (Accession number: LN484108.1) and Forcipomyia pluvialis as the outgroup. Confidence values at branches are based on ultrafast bootstrap analysis with 10,000 bootstrap alignments.

Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Abstract Background Orbivirus-induced hemorrhagic diseases cause high mortality in wild and captive white-tailed deer in North America. The role of different Culicoides species in Orbivirus transmission outside of areas of intensive animal production has not been established. At our study location, bluetongue virus (BTV) RNA-positive female Culicoides debilipalpis pools have been detected annually since 2012 when BTV transmission was noted in a captive deer herd. Identifying specific larval habitats of suspected vectors at active transmission...

Additional file 4 of Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Additional file 4: Figure S2. The ML phylogenetic tree based on the sequences of the 18S rRNA gene (region 2) with reference sequences from NCBI (Accession number: U48380.1 and LN484108.1) and Dixella cornuta as the outgroup. Confidence values at branches are based on ultrafast bootstrap analysis with 10,000 bootstrap alignments.

Data from: Co-feeding intra- and interspecific transmission of an emerging insect-borne rickettsial pathogen

Lisa D. Brown, Rebecca C. Christofferson, Kaikhushroo H. Banajee, Fabio Del Piero, Lane D. Foil & Kevin R. Macaluso
Cat fleas (Ctenocephalides felis) are known as the primary vector and reservoir of Rickettsia felis, the causative agent of flea-borne spotted fever; however, field surveys regularly report molecular detection of this infectious agent from other blood-feeding arthropods. The presence of R. felis in additional arthropods may be the result of chance consumption of an infectious bloodmeal, but isolation of viable rickettsiae circulating in the blood of suspected vertebrate reservoirs has not been demonstrated. Successful transmission...

Data from: Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus)

Jean P. Elbers, Rachel W. Clostio & Sabrina S. Taylor
Levels of adaptive genetic variation influence how species deal with environmental and ecological change, but these levels are frequently inferred using neutral genetic markers. Major histocompatibility complex (MHC) genes play a key role in the adaptive branch of the immune system and have been used extensively to estimate levels of adaptive genetic variation. Parts of the peptide binding region, sites where MHC molecules directly interact with pathogen and self-proteins, were sequenced from a MHC class...

Additional file 6 of Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Additional file 6: Figure S4. The ML phylogenetic tree based on the COI gene sequences with reference sequences from NCBI (with Accession numbers) and Dasyhelea notata as the outgroup. Confidence values at branches are based on ultrafast bootstrap analysis with 10,000 bootstrap alignments.

Additional file 1 of Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Additional file 1: Table S1. a. The average of the intra- specific nucleotide percentage of pairwise identities (mean ± standard deviation [SD], in %) of each adult specimen to all the others within one species at each locus. n is the number of the specimens within each species; ‘overall’ is the average value of all the means across all the species for each locus. b The average of the inter- specific nucleotide percentage of pairwise...

Additional file 2 of Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Additional file 2: Table S2. The average of the inter- specific nucleotide percentage of pairwise identities (mean ± standard deviation%) of each species to all the others at each locus; overall is the average value of all the means across all the species for each locus.

Additional file 3 of Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Additional file 3: Figure S1. The ML phylogenetic tree based on the sequences of the 18S rRNA gene (region 1) with reference sequences from NCBI (Accession number: LN484108.1 and U48380.1) and Dasyhelea sp. as the outgroup. Confidence values at branches are based on ultrafast bootstrap analysis with 10,000 bootstrap alignments.

Additional file 4 of Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Additional file 4: Figure S2. The ML phylogenetic tree based on the sequences of the 18S rRNA gene (region 2) with reference sequences from NCBI (Accession number: U48380.1 and LN484108.1) and Dixella cornuta as the outgroup. Confidence values at branches are based on ultrafast bootstrap analysis with 10,000 bootstrap alignments.

Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

Jorge Duitama, Alexander Silva, Yamid Sanabria, Daniel Felipe Cruz, Constanza Quintero, Carolina Ballen, Mathias Lorieux, Brian Scheffler, Andrew Farmer, Edgar Torres, James Oard & Joe Tohme
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we...

Data from: Meta-analysis of yield response of foliar fungicide-treated hybrid corn in the United States and Ontario, Canada

Kiersten A. Wise, Damon L. Smith, Anna Freije, Daren S. Mueller, Yuba Kandel, Tom Allen, Carl A. Bradley, Emmanuel Byamukama, Martin Chilvers, Travis Faske, Andrew Friskop, Clayton Hollier, Tamra A. Jackson-Ziems, Heather Kelly, Bob Kemerait, Paul Price, Alison Robertson & Albert Tenuta
Background: Foliar fungicide applications to corn (Zea mays) occur at one or more application timings ranging from early vegetative growth stages to mid-reproductive stages. Previous studies indicated that fungicide applications are profitable under high disease pressure when applied during the tasseling to silking growth stages. Few comprehensive studies in corn have examined the impact of fungicide applications at an early vegetative growth stage (V6) compared to late application timings (VT) for yield response and return...

Louisiana mottled duck telemetry summer survival data 2018-2020 and water level data from Hurricane Laura surge

Kevin Ringelman, Elizabeth Bonczek, Joseph Marty, Ashley Booth & Alexandre Dopkin
Tropical cyclones are the most powerful storms on earth, causing catastrophic damage to human lives and infrastructure. Hurricanes also cause wildlife mortality when they make landfall, but the severity of these effects is difficult to quantify because data collection is either logistically impossible or deprioritized in the wake of human tragedy. On 27 August 2020, Hurricane Laura made landfall in southwestern Louisiana with maximum sustained winds of 241 kph (150 mph), making it one of...

Additional file 5 of Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Additional file 5: Figure S3. The ML phylogenetic tree based on the 28S rRNA gene sequences with reference sequences from NCBI (Accession number: LN484108.1) and Forcipomyia pluvialis as the outgroup. Confidence values at branches are based on ultrafast bootstrap analysis with 10,000 bootstrap alignments.

Additional file 3 of Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Additional file 3: Figure S1. The ML phylogenetic tree based on the sequences of the 18S rRNA gene (region 1) with reference sequences from NCBI (Accession number: LN484108.1 and U48380.1) and Dasyhelea sp. as the outgroup. Confidence values at branches are based on ultrafast bootstrap analysis with 10,000 bootstrap alignments.

Additional file 1 of Assigning Culicoides larvae to species using DNA barcoding of adult females and phylogenetic associations

Tao Jin, Claudia Husseneder & Lane Foil
Additional file 1: Table S1. a. The average of the intra- specific nucleotide percentage of pairwise identities (mean ± standard deviation [SD], in %) of each adult specimen to all the others within one species at each locus. n is the number of the specimens within each species; ‘overall’ is the average value of all the means across all the species for each locus. b The average of the inter- specific nucleotide percentage of pairwise...

Louisiana Historic Rice Yields from 1895 to 2019

P. Lynn Kennedy
This data set presents Louisiana rice yields in pounds per acre and kilograms per hectare from 1895 to 2019. This rice yield data is based on Louisiana rice statistics provided by the USDA National Agricultural Statistics Service (USDA-NASS, 2019) and Louisiana State University Agricultural Center (LSU AgCenter, 2019).

Data from: A generalized residual technique for analyzing complex movement models using earth mover's distance

Jonathan R. Potts, Marie Auger-Méthé, Karl Mokross & Mark A. Lewis
1. Complex systems of moving and interacting objects are ubiquitous in the natural and social sciences. Predicting their behavior often requires models that mimic these systems with sufficient accuracy, while accounting for their inherent stochasticity. Though tools exist to determine which of a set of candidate models is best relative to the others, there is currently no generic goodness-of-fit framework for testing how close the best model is to the real complex stochastic system. 2....

Data from: Light stabilizers added to the shell of coextruded wood-high density polyethylene composites to improve mechanical and anti-UV aging properties

Chaozheng Liu, Changtong Mei, Bing Xu, Weimin Chen, Cheng Yong, Ke Wang & Qinglin Wu
Weathering of wood-plastic composite (WPC) leads to discoloration and cracks, which greatly limits its outdoor application. In this study, light stabilizers (including UV-327, HS-944, and Nano-SiO2) were added to the shell of coextruded high-density polyethylene (HDPE) based WPC to improve its anti-ultraviolet (UV) aging property and simultaneously to maintain its good mechanical property. The obtained results showed that the UV-327 was the most effective light stabilizer on improving the mechanical and anti-UV aging properties of...

Early nest initiation and vegetation density enhance nest survival in Wild Turkeys

Allison C. Keever, Bret A. Collier, Michael J. Chamberlain & Bradley S. Keever
The theory of adaptive habitat selection suggests resource selection by animals should reflect underlying quality, such that individual selection confers an adaptive advantage via increased fitness. Using resource selection functions and nest survival models, we demonstrated that visual obstruction at the nest site was adaptively significant but timing of nest initiation had the greatest effect on nest survival for eastern wild turkeys (Meleagris gallopavo silvestris). Predation risk is a selective pressure, and if individuals can...

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