1,105 Works

Data from: Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster

Greg Gibson, Rebecca Riley-Berger, Larry Harshman, Artyom Kopp, Scott Vacha, Sergey Nuzhdin & Marta Wayne
Assessment of the degree to which gene expression is additive and heritable has important implications for understanding the maintenance of variation, adaptation, phenotypic divergence, and the mapping of genotype onto phenotype. We used whole-genome transcript profiling using Agilent long-oligonucleotide microarrays representing 12,017 genes to demonstrate that gene transcription is pervasively nonadditive in Drosophila melanogaster. Comparison of adults of two isogenic lines and their reciprocal F1 hybrids revealed 5820 genes as significantly different between at least...

Data from: New species of Arthroleptis (Anura: Arthroleptidae) from Ngozi Crater in the Poroto Mountains of southwestern Tanzania

David C. Blackburn
A new species of squeaker frog (Arthroleptis) is described from Ngozi Crater in the Poroto Mountains of southwestern Tanzania. The holotype, and only specimen, was collected 80 years ago but remained undescribed because of past taxonomic confusion relating to large-bodied species of Arthroleptis from eastern Africa. Morphological study, including multivariate analysis of measurement data, indicates that this new species is distinguishable from other species of Arthroleptis, including large-bodied species such as Arthroleptis adolfifriederici, Arthroleptis affinis,...

Data from: Tropical nematode diversity: vertical stratification of nematode communities in a Costa Rican humid lowland rainforest

Thomas O. Powers, Deborah A. Neher, Peter Mullin, Alejandro Esquivel, Robin M. Giblin-Davis, Natsumi Kanzaki, Patricia P. Stock, Morielos M. Mora & Lorena Uribe-Lorio
Comparisons of nematode communities among ecosystems have indicated that, unlike many organisms, nematode communities have less diversity in the tropics than in temperate ecosystems. There are, however, few studies of tropical nematode diversity on which to base conclusions of global patterns of diversity. This study reports an attempt to estimate nematode diversity in the lowland tropical rainforest of La Selva Biological Research Station in Costa Rica. We suggest that one reason previous estimates of tropical...

Data from: Phylogenetic assessment of molecular and morphological data for eutherian mammals

Fu-Guo R. Liu & Michael M. Miyamoto
The interordinal relationships of eutherian (placental) mammals were evaluated by a phylogenetic analysis of four published data sets (three sequence and one morphological). The nature and degree of support and conflict for particular groups were assessed by separate bootstrap and homogeneity tests that were followed by combined analyses of the sequence and morphological data. Between orders, strong support (i.e., >95% bootstrap scores) was found for a paraphyletic Artiodactyla (relative to Cetacea) and a monophyletic Cetartiodactyla...

Data from: Asymmetric dispersal and colonization success of Amazonian plant-ants queens

Emilio M. Bruna, Thiago J. Izzo, Brian D. Inouye, Maria Uriarte & Heraldo L. Vasconcelos
Background: The dispersal ability of queens is central to understanding ant life-history evolution, and plays a fundamental role in ant population and community dynamics, the maintenance of genetic diversity, and the spread of invasive ants. In tropical ecosystems, species from over 40 genera of ants establish colonies in the stems, hollow thorns, or leaf pouches of specialized plants. However, little is known about the relative dispersal ability of queens competing for access to the same...

Data from: Molecular phylogenetics of Kosteletzkya (Malvaceae, Hibisceae) reveals multiple independent and successive polyploid speciation events

Kurt M. Neubig, , W. Mark Whitten, Stuart F. McDaniel & Orland J. Blanchard
Kosteletzkya s.s. is a genus of 17 species (excluding the endemic species of Madagascar), found in the New World, continental Africa, Madagascar, and Southeast Asia. Recent chromosome counts revealed diploid, tetraploid, and hexaploid species. To estimate the history of the genus, we sequenced nuclear and plastid loci for nearly all Kosteletzkya spp., in the majority of cases, with multiple accessions per species. The African species form a paraphyletic grade relative to a New World clade....

Data from: Genetic structure, admixture, and invasion success in a Holarctic defoliator, the gypsy moth (Lymantria dispar, Lepidoptera: Erebidae)

Yunke Wu, John J. Molongoski, Deborah F. Winograd, Steven M. Bogdanowicz, Artemis S. Louyakis, David R. Lance, Victor C. Mastro & Richard G. Harrison
Characterizing the current population structure of potentially invasive species provides a critical context for identifying source populations and for understanding why invasions are successful. Non-native populations inevitably lose genetic diversity during initial colonization events, but subsequent admixture among independently introduced lineages may increase both genetic variation and adaptive potential. Here we characterize the population structure of the gypsy moth (Lymantria dispar Linnaeus), one of the world's most destructive forest pests. Native to Eurasia and recently...

Data from: Functional attributes of savannah soils: contrasting effects of tree canopies and herbivores on bulk density, nutrients and moisture dynamics

Ricardo M. Holdo & Michelle C. Mack
1. Savannahs are highly heterogeneous tree-grass mixtures, and the structural variation imposed by a discontinuous canopy cover results in spatial variation in soil properties such as plant-available nutrients, temperature and soil moisture. Many savannahs are also dominated by large vertebrate herbivores, which impose a different suite of effects on soil properties related to consumption, excretion and physical disturbance. 2. In nutrient-poor, water-limited systems, variation in soil resource availability may play a fundamental role in structuring...

Data from: Arboreal camera trapping: taking a proven method to new heights

Tremaine Gregory, Farah Carrasco Rueda, Jessica Deichmann, Joseph Kolowski & Alfonso Alonso
1. Although camera trapping has been shown to be a highly effective non-invasive tool for wildlife monitoring, the technique has not yet been widely applied to studies of arboreal species. Despite the unique challenges that camera trapping in the canopy poses, its versatility and relatively non-invasive nature, combined with recent technological improvements on the cameras themselves, make camera trapping a highly useful tool for arboreal research. 2. We present data on the methodology and effectiveness...

Data from: Acquisition of germ plasm accelerates vertebrate evolution.

Teri Evans, Christopher M. Wade, Frank A. Chapman, Andrew D. Johnson & Matthew Loose
Primordial germ cell (PGC) specification occurs either by induction from pluripotent cells (epigenesis) or by a cell-autonomous mechanism mediated by germ plasm (preformation). Among vertebrates, epigenesis is basal, whereas germ plasm has evolved convergently across lineages and is associated with greater speciation. We compared protein-coding sequences of vertebrate species that employ preformation with their sister taxa that use epigenesis and demonstrate that genes evolve more rapidly in species containing germ plasm. Furthermore, differences in rates...

Data from: Outer bark thickness decreases more with height on stems of fire-resistant than fire-sensitive Floridian oaks (Quercus spp.; Fagaceae)

Sarah J. Graves, Sami W. Rifai & Francis E. Putz
Premise of the study: In ecosystems maintained by low-intensity surface fires, tree bark thickness is a determinant of fire-survival because it protects underlying tissues from heat damage. However, it has been unclear whether relatively thick bark is maintained at all heights or only near the ground where damage is most likely. Methods: We studied six Quercus species from the red and white clades, with three species characteristic of fire-maintained savannas and three species characteristic of...

Data from: Convergence of soil nitrogen isotopes across global climate gradients

Joseph M. Craine, Andrew J. Elmore, Lixin Wang, Laurent Augusto, W. Troy Baisden, E. N. J. Brookshire, Michael D. Cramer, Niles J. Hasselquist, Erik A. Hobbie, Ansgar Kahmen, Keisuke Koba, J. Marty Kranabetter, Michelle C. Mack, Erika Marin-Spiotta, Jordan R. Mayor, Kendra K. McLauchlan, Anders Michelsen, Gabriela B. Nardoto, Rafael S. Oliveira, Steven S. Perakis, Pablo L. Peri, Carlos A. Quesada, Andreas Richter, Louis A. Schipper, Bryan A. Stevenson … & Bernd Zeller
Quantifying global patterns of terrestrial nitrogen (N) cycling is central to predicting future patterns of primary productivity, carbon sequestration, nutrient fluxes to aquatic systems, and climate forcing. With limited direct measures of soil N cycling at the global scale, syntheses of the 15N:14N ratio of soil organic matter across climate gradients provide key insights into understanding global patterns of N cycling. In synthesizing data from over 6000 soil samples, we show strong global relationships among...

Data from: Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing

A. Millie Burrell, Alan E. Pepper, George Hodnett, John A. Goolsby, William A. Overholt, Alexis E. Racelis, Rodrigo Diaz & Patricia E. Klein
Imperata cylindrica (Cogongrass, Speargrass) is a diploid C4 grass that is a noxious weed in 73 countries and constitutes a significant threat to global biodiversity and sustainable agriculture. We used a cost-effective genotyping-by-sequencing (GBS) approach to identify the reproductive system, genetic diversity and geographic origins of invasions in the south-eastern United States. In this work, we demonstrated the advantage of employing the closely related, fully sequenced crop species Sorghum bicolor (L.) Moench as a proxy...

Data from: Climate mediates the effects of disturbance on ant assemblage structure

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Simon Watson, Manoli Photakis, Silvia Abril, Alan N. Andersen, Elena Angulo, Inge Armbrecht, Xavier Arnan, Fabricio B. Baccaro, Tom R. Bishop, Raphael Boulay, Cristina Castracani, Israel Del Toro, Thibaut Delsinne, Mireia Diaz, David A. Donoso, Martha L. Enríquez, Tom M. Fayle, Donald H. Feener, Matthew C. Fitzpatrick, Crisanto Gómez, Donato A. Grasso, Sarah Groc … & C. Gomez
Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction...

Data from: Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerata L.) through transcriptome analysis

Lin K. Huang, Hai D. Yan, J. Wang, T. Frazier, X. X. Zhao, X. Q. Zhang, X. Huang, D. F. Yan, W. J. Zang, X. Ma, Y. Peng, Y. H. Yan, W. Liu & G. Yin
Orchardgrass (Dactylis glomerata L.) is a long-lived, cool-season forage grass that is commonly used for hay production. Despite its economic importance, orchardgrass genome remains relatively unexplored. In this study, we used Illumina RNA sequencing to identify gene-associated molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), as well as heat stress-induced differentially expressed genes (DEGs) in two orchardgrass genotypes, ‘Baoxing’ (heat resistant) and ‘01998’ (heat susceptible). Approximately 163 million high-quality trimmed reads...

Data from: Abiotic stress does not magnify the deleterious effects of spontaneous mutations

Jacob R. Andrew, Melody M. Dossey, Veniel O. Garza, Michelle Keller-Pearson, Charles F. Baer & Joanna Joyner-Matos
Although the effects of deleterious alleles often are predicted to be greater in stressful environments, there is no theoretical basis for this prediction and the empirical evidence is mixed. Here we characterized the effects of three types of abiotic stress (thermal, oxidative and hyperosmotic) on two sets of nematode (Caenorhabditis elegans) mutation accumulation (MA) lines that differ by threefold in fitness. We compared the survival and egg-to-adult viability between environments (benign and stressful) and between...

Data from: Mutation is a sufficient and robust predictor of genetic variation for mitotic spindle traits in Caenorhabditis elegans

Reza Farhadifar, Jose Miguel Ponciano, Erik C. Andersen, Daniel J. Needleman & Charles F. Baer
Different types of phenotypic traits consistently exhibit different levels of genetic variation in natural populations. There are two potential explanations: either mutation produces genetic variation at different rates, or natural selection removes or promotes genetic variation at different rates. Whether mutation or selection is of greater general importance is a longstanding unresolved question in evolutionary genetics. We report mutational variances (VM) for 19 traits related to the first mitotic cell division in C. elegans, and...

Data from: A new resource for the development of SSR markers: millions of loci from a thousand plant transcriptomes

Richard G. Hodel, Matthew A. Gitzendanner, Charlotte C. Germain-Aubrey, Xiaoxian Liu, Andrew A. Crowl, Miao Sun, Jacob B. Landis, Maria Claudia Segovia-Salcedo, Norman A. Douglas, Shichao Chen, Douglas E. Soltis, Pamela S. Soltis & Richard G. J. Hodel
Premise of the study: The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility. Methods and Results: Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic...

Data from: Sex-biased avian host use by arbovirus vectors

Nathan D. Burkett-Cadena, Andrea M. Bingham & Thomas R. Unnasch
Prevalence of arthropod-borne parasites often differs drastically between host sexes. This sex-related disparity may be related to physiological (primarily hormonal) differences that facilitate or suppress replication of the pathogen in host tissues. Alternately, differences in pathogen prevalence between host sexes may be owing to differential exposure to infected vectors. Here, we report on the use of PCR-based assays recognizing bird sex chromosomes to investigate sex-related patterns of avian host use from field-collected female mosquitoes from...

Data from: Sexual selection is influenced by both developmental and adult environments

Stephanie R. Gillespie, M. Scarlett Tudor, Allen J. Moore & Christine W. Miller
Sexual selection is often assumed to be strong and consistent, yet increasing research shows it can fluctuate over space and time. Few experimental studies have examined changes in sexual selection in response to natural environmental variation. Here, we use a difference in resource quality to test for the influence of past environmental conditions and current environmental conditions on male and female mate choice and resulting selection gradients for leaf-footed cactus bugs, Narnia femorata. We raised...

Data from: Context-dependent effects of large wildlife declines on small mammal communities in central Kenya

Hillary S. Young, Douglas J. McCauley, Rodolfo Dirzo, Jacob R. Goheen, Bernard Agwanda, Cara Brook, Erik O. Castillo, Adam W. Ferguson, Stephen N. Kinyua, Molly M. McDonough, Todd M. Palmer, Robert M. Pringle, Truman P. Young & Kristofer M. Helgen
Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife...

Data from: Anatomy, systematics, paleoenvironment, growth, and age of the sauropod dinosaur Sonorasaurus thompsoni from the Cretaceous of Arizona, USA

Michael D. D'Emic, Brady Z. Foreman & Nathan A. Jud
Sauropod dinosaurs are rare in the Cretaceous North American fossil record in general and are absent from that record for most of the Late Cretaceous. Sonorasaurus thompsoni from the Turney Ranch Formation of the Bisbee Group of Arizona, USA, potentially represents one of the youngest sauropods before their ca. 30-million-year-long hiatus from the record. The anatomy of Sonorasaurus has only been briefly described, its taxonomic validity has been questioned, several hypotheses have been proposed regarding...

Data from: A global perspective on Campanulaceae: biogeographic, genomic, and floral evolution

Andrew A. Crowl, Nicholas W. Miles, Clayton J. Visger, Kimberly Hansen, Tina Ayers, Rosemarie Haberle & Nico Cellinese
PREMISE OF THE STUDY: The Campanulaceae are a diverse clade of flowering plants encompassing more than 2300 species in myriad habitats from tropical rainforests to arctic tundra. A robust, multigene phylogeny, including all major lineages, is presented to provide a broad, evolutionary perspective of this cosmopolitan clade. METHODS: We used a phylogenetic framework, in combination with divergence dating, ancestral range estimation, chromosome modeling, and morphological character reconstruction analyses to infer phylogenetic placement and timing of...

Data from: Resource quality affects weapon and testis size and the ability of these traits to respond to selection in the leaf-footed cactus bug, Narnia femorata

Daniel A. Sasson, Patricio R. Munoz, Salvador A. Gezan & Christine W. Miller
The size of weapons and testes can be central to male reproductive success. Yet, the expression of these traits is often extremely variable. Studies are needed that take a more complete organism perspective, investigating the sources of variation in both traits simultaneously and using developmental conditions that mimic those in nature. In this study, we investigated the components of variation in weapon and testis sizes using the leaf-footed cactus bug, Narnia femorata (Hemiptera: Coreidae) on...

Data from: The contribution of dominance to phenotype prediction in a pine breeding and simulated population

Janeo Eustáquio De Almeida Filho, J. F. R. Guimarães, F. F. E Silva, M. D. V. De Resende, P. Muñoz, M. Kirst &
Pedigrees and dense marker panels have been used to predict the genetic merit of individuals in plant and animal breeding, accounting primarily for the contribution of additive effects. However, nonadditive effects may also affect trait variation in many breeding systems, particularly when specific combining ability is explored. Here we used models with different priors, and including additive-only and additive plus dominance effects, to predict polygenic (height) and oligogenic (fusiform rust resistance) traits in a structured...

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