93 Works

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...

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...

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: 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...

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: 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: 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: 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...

An Evaluation of the Susceptibility of Goats to Larkspur Toxicosis

Kevin D. Welch, Clint A. Stonecipher, Dale R. Gardner, Benidict T. Green & Daniel Cook
Larkspurs (Delphinium spp.) are a major cause of cattle losses in western North America, whereas sheep have been shown to be resistant to larkspur toxicosis. Goats are often used as a small ruminant model to study poisonous plants, even though they can be more resistant to some poisonous plants. It is not known how susceptible goats are to the adverse effects of larkspurs. In this study, we evaluated the susceptibility of goats to larkspur toxicosis...

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,...

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...

Modelled average percentage yield loss due to ozone damage for four global staple crops (2010-2012)

K. Sharps, G. Mills, D. Simpson, H. Pleijel, M. Frei, K. Burkey, L. Emberson, J. Uddling, M. Broberg, Z. Feng, K. Kobayashi & M. Agrawal
Modelled average percentage yield loss due to ground-level ozone pollution (per 1 degree by 1 degree grid cell) are presented for the crops maize (Zea mays), rice (Oryza sativa), soybean (Glycine max) and wheat (Triticum aestivum) for the period 2010-2012. Data are on a global scale, based on the distribution of production for each crop, according to the Food and Agriculture Organisation’s (FAO) Global Agro-Ecological Zones (GAEZ) crop production data for the year 2000. Modelled...

Data from: Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis

Eric Lombaert, Thomas Guillemaud, Cathleen E. Thomas, Lori J. Lawson Handley, Jiahui Li, Su Wang, Hong Pang, Irina Goryacheva, Ilya A. Zakharov, Emmanuelle Jousselin, Remy L. Poland, Alain Migeon, Joop Van Lenteren, Patrick De Clercq, Nick Berkvens, Walker Jones & Arnaud Estoup
Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia...

Pitfall and refuge trap sampling Linn Co March 2018-June2019

Inga Reich, Casi Jessie, Seung-Joon Ahn, Man-Yeon Choi, Christopher Williams, Mike Gormally & Rory Mc Donnell
Numbers of carabid beetles, caterpillars, cranefly larvae and slugs collected from pitfall and refuge traps in ten Annual Ryegrass fields in Linn County, Oregon between March 23, 2018 and June 20, 2019. Given are details on sampling date, trap, size and sex (carabids only), weight (slugs only) and species (where possible). Provided are also the results of the molecular gut content analysis of the carabid beetles: Date of gut dissection and associated details on the...

Ms3 dominant genetic male sterility for wheat improvement with molecular breeding

Mary Guttieri
Genetic dominant male sterility (DMS) has not been widely used as a breeding tool in wheat (Triticum aestivum L.), although DMS-facilitated backcross, mass selection, half-sib selection, and S1 family recurrent selection strategies have been described, and Ms2-facilitated recurrent selection has been used in China. Our objective was to revisit these strategies using the tools of molecular breeding. Development of a mechanism for seedling identification of sterile progeny was a key component of designing practical DMS-facilitated...

Data from: Hemiptera phylogenomic resources: tree-based orthology prediction and conserved exon identification

Christopher Owen, David Stern, Sarah Hilton & Keith Crandall
High-throughput sequencing of transcriptomes and targeted genomic regions are advancing our knowledge of The Tree of Life. Building phylogenies with regions of the genome requires 1-to-1 ortholog resources of genes and non-coding loci. One organismal group that has received little attention in this area is the Hemiptera, the fifth largest insect order represented by approximately 103,590 named species. Here, we present a set of 3,872 Hemiptera 1-to-1 orthogroups based on tree-based orthology inference of 8...

Data from: Plant biomass, not plant economics traits, determines responses of soil CO2 efflux to precipitation in the C4 grass Panicum virgatum

Robert Heckman, Albina Khasanova, Nicholas Johnson, Sören Weber, Jason Bonnette, Mike Aspinwall, Lara Reichman, Thomas Juenger, Philip Fay & Christine Hawkes
1. Plant responses to major environmental drivers like precipitation can influence important aspects of carbon (C) cycling like soil CO2 efflux (JCO2). These responses may be predicted by two independent classes of drivers: plant size—larger plants respire more and produce a larger quantity of labile C, and plant economics—plants possessing more acquisitive plant economics strategies (i.e., high metabolic rate and tissue nutrient content) produce higher-quality tissue that respires rapidly and decomposes quickly. 2. At two...

Data from: The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish

Noah M. Reid, Dina A. Proestou, Bryan W. Clark, Wesley C. Warren, John K. Colbourne, Joseph R. Shaw, Sibel I. Karchner, Mark E. Hahn, Diane Nacci, Marjorie F. Oleksiak, Douglas L. Crawford & Andrew Whitehead
Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor–based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant...

Data from: Crop production in the USA is frequently limited by a lack of pollinators

James Reilly, Derek Artz, David Biddinger, Kyle Bobiwash, Natalie Boyle, Claire Brittain, Julia Brokaw, Josh Campbell, Jaret Daniels, Elizabeth Elle, Jamie Ellis, Shelby Fleischer, Jason Gibbs, Robert Gillespie, Knute Gundersen, Larry Gut, George Hoffman, Neelendra Joshi, Ola Lundin, Keith Mason, Carley McGrady, Steve Peterson, Theresa Pitts-Singer, Sujaya Rao, Nikki Rothwell … & Rachael Winfree
Most of the world’s crops depend on pollinators, so declines in both managed and wild bees raise concerns about food security. However, the degree to which insect pollination is actually limiting current crop production is poorly understood, as is the role of wild species (as opposed to managed honey bees) in pollinating crops, particularly in intensive production areas. We established a nation-wide study to assess the extent of pollinator limitation in seven crops at 131...

Evaluation of a microplate spectrophotometer for soil organic carbon determination in south central Idaho

Andrew Bierer, April Leytem, Christopher Rogers & Robert Dungan
Determination of soil organic carbon (SOC) is highly desirable for assessing fertility and carbon sequestration; however, numerous methods of determination warrant study of method agreement. Recently, a novel method was developed following dichromate oxidation using a microplate spectrophotometer. This novel method was compared with (i) total C by dry combustion - soil inorganic carbon (DCw/o pretreatment - Pcal); (ii) traditional Walkley-Black titration (WBTIT) and (iii) loss on ignition (LOI360°C) in calcareous soils of south central...

Datasets used to support the work presented in: Beringer, C.J., K.W. Goyne, R.N. Lerch, E.B. Webb, and D. Mengel. 2020: Clothianidin decomposition in Missouri wetland soils. J. Environ. Qual. JEQ-2020-05-0167-TR

C. J. Beringer, K. W. Goyne, Robert Lerch, E. B. Webb & D. Mengel
Neonicotinoid pesticides can persist in soils for extended time periods; however, they also have a high potential to contaminate ground and surface waters. Studies have reported negative effects associated with neonicotinoids and non-target taxa, including aquatic invertebrates, pollinating insect species, and insectivorous birds. This study evaluated factors associated with clothianidin (1-[(2-chloro-1,3-thiazol-5-yl) methyl]-3-methyl-2-nitroguanidine, CTN) degradation and sorption in Missouri wetland soils to assess the potential for wetland soils to mitigate potential environmental risks associated with neonicotinoids....

Data from: Arbuscular mycorrhizal fungi increase organic carbon decomposition under elevated CO2

Lei Cheng, Fitzgerald L. Booker, Cong Tu, Kent O. Burkey, Lishi Zhou, H. David Shew, Thomas W. Rufty & Shuijin Hu
The extent to which terrestrial ecosystems can sequester carbon to mitigate climate change is a matter of debate. The stimulation of arbuscular mycorrhizal fungi (AMF) by elevated atmospheric carbon dioxide (CO2) has been assumed to be a major mechanism facilitating soil carbon sequestration by increasing carbon inputs to soil and by protecting organic carbon from decomposition via aggregation. We present evidence from four independent microcosm and field experiments demonstrating that CO2 enhancement of AMF results...

Data from: Phenotypic integration in an extended phenotype: among‐individual variation in nest‐building traits of the alfalfa leafcutting bee (Megachile rotundata)

Raphaël Royauté, Elisabeth S. Wilson, Bryan R. Helm, Rachel E. Malinger, Jarrad Prasifka, Kendra J. Greenlee & Julia H. Bowsher
Structures such as nests and burrows are an essential component of many organisms’ life-cycle and requires a complex sequence of behaviors. Because behaviors can vary consistently among individuals and be correlated with one another, we hypothesized that these structures would 1) show evidence of among-individual variation, 2) be organized into distinct functional modules, and 3) show evidence of trade-offs among functional modules due to limits on energy budgets. We tested these hypotheses using the alfalfa...

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