126 Works

Data from: Mountain Plover habitat selection and nest survival in relation to weather variability and spatial attributes of Black-tailed Prairie Dog disturbance

Courtney Duchardt, Jeffrey Beck & David Augustine
Habitat loss and altered disturbance regimes have led to declines in many species of grassland and sagebrush birds, including the imperiled Mountain Plover (Charadrius montanus). In certain parts of their range Mountain Plovers rely almost exclusively on Black-Tailed Prairie Dog (Cynomys ludovicianus) colonies as nesting habitat. Previous studies have examined Mountain Plover nest and brood survival on prairie dog colonies, but little is known about how colony size and shape influence these vital rates or...

A roadmap to durable BCTV resistance using long-read genome assembly of genetic stock KDH13

Paul Galewski & Imad Euyjal
PacBio Sequence data associated with genetic stock KDH13.Datasets include genome resources and annotated files associated with the manuscript "Long-read genome assembly of Double Haploid Sugar Beet KDH13 provides roadmap for durable genetic resistance to Beet Curly Top Virus". This includes genome assembly, ordered genome assembly, protein predictions, variant call format files for an F1 hybrid (KDH13xKDH19-17).

Data from: Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines

Jennifer Spindel, Hasina Begum, Deniz Akdemir, Parminder Virk, Bertrand Collard, Edilberto Redoña, Gary Atlin, Jean-Luc Jannink & Susan R. McCouch
Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363...

Data from: The genetic structure of Asian corn borer, Ostrinia furnacalis, populations in China: haplotype variance in Northern populations and potential impact on management of resistance to transgenic maize

Jing Li, Brad S. Coates, Kyung Seok Kim, Denis Bourguet, Sergine Ponsard, Kanglai He & Zhenying Wang
Asian corn borer, Ostrinia furnacalis (Guenée), is a severe pest that infests cultivated maize in the major production regions of China. Populations show genotype-by-environment variation in voltinism, such that populations with a single generation (univoltine) are fixed in Northern China where growing seasons are short. Low genetic differentiation was found among samples from 33 collection sites across China and one site from North Korea (n = 1,673) using variation at 6 nuclear microsatellite loci (ENA...

Data from: Genetic variation and evolution of secondary compounds in native and introduced populations of the invasive plant Melaleuca quinquenervia

Steven J. Franks, Gregory S. Wheeler & Charles J. Goodnight
We examined multivariate evolution of 20 leaf terpenoids in the invasive plant Melaleuca quinquenervia in a common garden experiment. While most compounds, including 1,8-Cineole and Viridiflorol, were reduced in home compared with invaded range genotypes, consistent with an evolutionary decrease in defense, one compound (E-Nerolidol) was greater in invaded than home range genotypes. Nerolidol was negatively genetically correlated with Cineole and Viridiflorol, and the increase in this compound in the new range may have been...

Data from: Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis)

Brittany S. Barker, Krikor Andonian, Sarah M. Swope, Doug G. Luster & Katrina M. Dlugosch
Identifying sources of genetic variation and reconstructing invasion routes for non-native introduced species is central to understanding the circumstances under which they may evolve increased invasiveness. In this study, we used genome-wide single nucleotide polymorphisms to study the colonization history of Centaurea solstitialis in its native range in Eurasia and invasions into the Americas. We leveraged this information to pinpoint key evolutionary shifts in plant size, a focal trait associated with invasiveness in this species....

Data from: Transcriptional markers of sub-optimal nutrition in developing Apis mellifera nurse workers

Vanessa Corby-Harris, Beryl M. Jones, Alexander Walton, Melissa R. Schwan & Kirk E. Anderson
Background: Honey bees (Apis mellifera) contribute substantially to the worldwide economy and ecosystem health as pollinators. Pollen is essential to the bee’s diet, providing protein, lipids, and micronutrients. The dramatic shifts in physiology, anatomy, and behavior that accompany normal worker development are highly plastic and recent work demonstrates that development, particularly the transition from nurse to foraging roles, is greatly impacted by diet. However, the role that diet plays in the developmental transition of newly...

Temporal nitrogen dynamics in intensively managed loblolly pine early stand development

Gabriel Ferreira, Benjamin Rau & Doug Aubrey
Forest production is strongly dependent on nutrient uptake; however, sustainable management of intensively managed plantations requires an improved understanding of this relationship when fertilization occurs frequently across short rotations. Here, we studied temporal nitrogen (N) concentration ([N]) and content (Nc) dynamics under different silvicultural practices (herbicide, fertilization, and planting density) throughout early loblolly pine (Pinus taeda) stand development (5 years). We describe relationships of [N] and Nc of different stand components (foliage, branches, stem, roots,...

GLOWCAD: A global database of woody tissue carbon concentrations/fractions

Mahendra Doraisami, Rosalyn Kish, Nicholas Paroshy, Grant Domke, Sean Thomas & Adam Martin
Woody tissue carbon (C) concentration is a key wood trait necessary for accurately estimating forest C stocks and fluxes, which also varies widely across species and biomes. However, coarse approximations of woody tissue C (e.g., 50%) remain commonplace in forest C estimation and reporting protocols, despite leading to substantial errors in forest C estimates. Here, we describe the Global Woody Tissue Carbon Concentration Database (GLOWCAD): a database containing 3,676 individual records of woody tissue C...

Integrating UCE phylogenomics with traditional taxonomy reveals a trove of New World Syscia species (Formicidae, Dorylinae)

Michael G. Branstetter & John T. Longino
The ant genus Syscia is part of the cryptic ant fauna inhabiting leaf litter and rotten wood in the Asian and American tropics. It is a distinct clade within the Dorylinae, the subfamily from which army ants arose. Prior to this work the genus comprised seven species, each known from a single or very few collections. Extensive collecting in Middle America revealed an unexpected and challenging diversity of morphological forms. Locally distinct forms could be...

Filtered SNP tables - Rangewide, Hamilton, Tejon, and Madera transects

Paul Gugger, Sorel Fitz-Gibbon, Ana Albarrán-Lara, Jessica Wright & Victoria Sork
Understanding how the environment shapes genetic variation provides critical insight about the evolution of local adaptation in natural populations. At multiple spatial scales and multiple geographic contexts within a single species, such information could address a number of fundamental questions about the scale of local adaptation and whether or not the same loci are involved at different spatial scales or geographic contexts. We used landscape genomic approaches from three local elevational transects and range-wide sampling...

Phylogenomics in the hard pines (Pinus subsection Ponderosae; Pinaceae) confirms paraphyly in Pinus ponderosa, and places Pinus jeffreyi with the California big cone pines

Ann Willyard, David S. Gernandt, Blake Cooper, Connor Douglas, Kristen Finch, Hassan Karemera, Erik Lindberg, Stephen K. Langer, Julia Lefler, Paula Marquardt, Dakota Pouncey & Frank Telewski
We sampled 130 individuals (2 to 25 per taxon) of subsections Ponderosae and Sabinianae. Nucleotide sequences were obtained by targeting 703 low copy nuclear genes. From the unenriched portion of the short reads, we assembled nearly complete plastome nucleotide sequences. We used 600 nuclear genes and the plastome sequences to create phylogenies and species trees that we compared to evaluate cytonuclear concordance and reticulation. We found that Pinus jeffreyi belongs with subsect. Sabinianae based on...

No net insect abundance and diversity declines across US Long Term Ecological Research sites

Michael Crossley, Amanda Meier, Emily Baldwin, Lauren Berry, Leah Crenshaw, Glen Hartman, Doris Lagos-Kutz, David Nichols, Krishna Patel, Sofia Varriano, Matthew Moran & William Snyder
Recent reports of dramatic declines in insect abundance suggest grave consequences for global ecosystems and human society. Most evidence comes from Europe, however, leaving uncertainty about insect population trends worldwide. We used > 5,300 time series for insects and other arthropods, collected over 4-36 years at monitoring sites representing 68 different natural and managed areas, to search for evidence of declines across the United States. Some taxa and sites showed decreases in abundance and diversity...

Data from: Breeding heat tolerant orchardgrass germplasm for summer persistence in high temperature stress environments of the southeastern United States

Eric Billman, Jesse Morrison & Brian Baldwin
This is digital research data corresponding to a published manuscript, Breeding heat tolerant orchardgrass germplasm for summer persistence in high temperature stress environments of the southeastern United States, in Crop Science, Volume 61, p. 1915 - 1925. Orchardgrass (Dactylis glomerata L.) could serve as a cool-season perennial in southeastern production systems, but often does not behave as a true perennial under high temperature stress conditions of the region. This work sought to develop heat-tolerant orchardgrass...

Vegetation characteristics and precipitation jointly influence grassland bird abundance beyond the effects of grazing management

Kristin Davis, David Augustine, Adrian Monroe & Cameron Aldridge
Grassland birds have experienced some of the steepest population declines of any guild of birds in North America. The shortgrass steppe contains some of North America’s most-intact grasslands, which makes the region particularly important for these species. Grassland birds differentially respond to variation in vegetation structure generated by spatiotemporally-varying disturbance like grazing management. However, understanding how species respond to characteristics beyond vegetation structure or grazing could better inform management for these species in the shortgrass...

Database of non-target invertebrates recorded in field experiments of genetically engineered Bt maize and corresponding non-Bt maize: data files

Michael Meissle, Steven Naranjo & Jörg Romeis
This database represents a comprehensive collection of experimental field data from all over the world on non-target invertebrates recorded in genetically engineered/modified Bt and non-Bt maize. The three data files deposited here are described by Meissle et al. (2022), BMC Research Notes, https://doi.org/10.1186/s13104-022-06021-3 . The database was created for a systematic review with the question if growing Bt maize changes abundance or ecological function of non-target animals compared to growing of non-GM maize, published by...

Variation in behavior drives multiscale responses to habitat conditions in timber rattlesnakes (Crotalus horridus)

Andrew Hoffman, Annalee Tutterow, Meaghan Gade, Bryce Adams & William Peterman
Variations in both the behavior of wildlife and the scale at which the environment most influences the space use of wild animals (i.e., scale of effect) are critical, but often overlooked in habitat selection modeling. Ecologists have proposed that biological responses happening over longer time frames are influenced by environmental variables at larger spatial scales, but this has rarely been empirically tested. Here, we hypothesized that long-term patterns of behavior (i.e., lasting multiple weeks to...

Data from: Discovery and exploitation of a natural ecological trap for a mosquito disease vector

Allison M. Gardner, Ephantus J. Muturi & Brian F. Allan
Ecological traps occur due to a mismatch between a habitat’s attractiveness and quality, wherein organisms show preference for low-quality habitats over other available high-quality habitats. Our previous research identified leaf litter from common blackberry (Rubus allegheniensis) as a natural ecological trap for an important vector for West Nile virus (Culex pipiens), attracting mosquitoes to oviposit in habitats deleterious to the survival of their larvae. Here we demonstrate that manipulation of leaf litter in stormwater catch...

Data from: Evolution of long centromeres in fire ants

Yu-Ching Huang, Chih-Chi Lee, Chia-Yi Kao, Ni-Chen Chang, Chung-Chi Lin, DeWayne Shoemaker & John Wang
Background: Centromeres are essential for accurate chromosome segregation, yet sequence conservation is low even among closely related species. Centromere drive predicts rapid turnover because some centromeric sequences may compete better than others during female meiosis. In addition to sequence composition, longer centromeres may have a transmission advantage. Results: We report the first observations of extremely long centromeres, covering on average 34 % of the chromosomes, in the red imported fire ant Solenopsis invicta. By comparison,...

Data from: Genetic variation in adaptive traits and seed transfer zones for Pseudoroegneria spicata (bluebunch wheatgrass) in the northwestern United States

John Bradley St. Clair, Francis F. Kilkenny, Richard C. Johnson, Nancy L. Shaw & George Weaver
A genecological approach was used to explore genetic variation in adaptive traits in Pseudoroegneria spicata, a key restoration grass, in the intermountain western United States. Common garden experiments were established at three contrasting sites with seedlings from two maternal parents from each of 114 populations along with five commercial releases commonly used in restoration. Traits associated with size, flowering phenology and leaf width varied considerably among populations and were moderately correlated to the climates of...

Data from: Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences

Romina Gazis, Stephen Rehner & Priscila Chaverri
The estimation of species diversity in fungal endophyte communities is based either on species counts or the assignment of operational taxonomic units (OTUs). Consequently, the application of different species recognition criteria affects not only diversity estimates but also the ecological hypotheses that arise from those observations. The main objective of the study was to examine how the choice and number of genetic markers and species delimitation criteria influences biodiversity estimates. Here, we compare approaches to...

Data from: Invasion of Hawaiian rainforests by an introduced amphibian predator and N2-fixing tree increases soil N2O emissions

Sharon J. Hall, David P. Huber & R. Flint Hughes
Invasions of introduced species have homogenized ecological communities worldwide, leading to losses of native species and the services they provide. Some of these invaders substantially alter nutrient cycling, which changes conditions for all other organisms, but less is known about the potential influence of these species on nitrogen (N) trace gas emissions that affect atmospheric processes. We used a natural experiment to explore whether the establishment of an introduced nitrogen (N) fixing tree (Falcataria moluccana)...

Data from: Elevated CO2 induces substantial and persistent declines in forage quality irrespective of warming in mixedgrass prairie

David J. Augustine, Dana M. Blumenthal, Tim L. Springer, Daniel R. LeCain, Stacey A. Gunter & Justin D. Derner
Increasing atmospheric [CO2] and temperature are expected to affect the productivity, species composition, biogeochemistry, and therefore the quantity and quality of forage available to herbivores in rangeland ecosystems. Both elevated CO2 (eCO2) and warming affect plant tissue chemistry through multiple direct and indirect pathways, such that the cumulative outcomes of these effects are difficult to predict. Here, we report on a 7-year study examining effects of CO2 enrichment (to 600 ppm) and infrared warming (+1.5°C...

Data from: A thorny issue: woody plant defence and growth in an East African savanna

Benjamin J. Wigley, Corli Coetsee, David J. Augustine, Jayashree Ratnam, Dawood Hattas & Mahesh Sankaran
1. Recent work suggests that savanna woody plant species separate into two different strategies based on their defences against herbivory; a low nutrient/high chemical defence strategy and a nutrition paired with mostly architectural defences strategy. The concept that chemical and structural defences can augment each other and do not necessarily trade-off has emanated from this work. In this study we examine woody plant defence strategies, how these respond to herbivore removal and how they affect...

Data from: Little white lies: pericarp color provides insights into the origins and evolution of Southeast Asian weedy rice

Yongxia Cui, Beng Kah Song, Lin-Feng Li, Ya-Ling Li, Zhongyun Huang, Ana L. Caicedo, Yulin Jia & Kenneth M. Olsen
Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here we examined variation in pericarp...

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