339 Works

Data from: Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing

Gregory Neils Puncher, Alessia Cariani, Gregory E. Maes, Jeroen Van Houdt, Koen Herten, Rita Cannas, Naiara Rodriguez-Ezpeleta, Aitor Albaina, M. Andone Estonba, Molly Lutcavage, Alex Hanke, Jay Rooker, James S. Franks, Joseph M. Quattro, Gualtiero Basilone, Igaratza Fraile, Urtzi Laconcha, Nicolas Goñi, Ai Kimoto, A. David Macías, Francisco Alemany, Simeon Deguara, Salem W. Zgozi, Fulvio Garibaldi, Isik K. Oray … & Fausto Tinti
The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species’ stock dynamics, a genome-wide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly...

Data from: Multi-scale effects of habitat structure and landscape context on a vertebrate with limited dispersal ability (the brown-throated sloth, Bradypus variegatus)​

Kelsey D. Neam, & Thomas E. Lacher
As human population, food consumption, and demand for forest products continue to rise over the next century, the pressures of land use change on biodiversity are projected to intensify. In tropical regions, countryside habitats that retain abundant tree cover and structurally complex canopies may complement protected areas by providing suitable habitats and landscape connectivity for a significant portion of the native biota. Species with low dispersal capabilities are among the most at risk of extinction...

Data from: Three-dimensional self-gated cardiac MR imaging for the evaluation of myocardial infarction in mouse model on a 3T clinical MR system

Xiaoyong Zhang, Bensheng Qiu, Zijun Wei, Fei Yan, Caiyun Shi, Shi Su, Xin Liu, Jim X. Ji & Guoxi Xie
Purpose: To develop and assess a three-dimensional (3D) self-gated technique for the evaluation of myocardial infarction (MI) in mouse model without the use of external electrocardiogram (ECG) trigger and respiratory motion sensor on a 3T clinical MR system. Methods: A 3D T1-weighted GRE sequence with stack-of-stars sampling trajectories was developed and performed on six mice with MIs that were injected with a gadolinium-based contrast agent at a 3T clinical MR system. Respiratory and cardiac self-gating...

Data from: Randomized phase 2 study of FcRn antagonist efgartigimod in generalized myasthenia gravis

James F. Howard, Vera Bril, Ted M. Burns, Renato Mantegazza, Malgorzata Bilinska, Andrzej Szczudlik, Said Beydoun, Francisco Javier Rodriguez De Rivera Garrido, Fredrik Piehl, Mariarosa Rottoli, Philip Van Damme, Tuan Vu, Amelia Evoli, Miriam Freimer, Tahseen Mozaffar, E. Sally Ward, Torsten Dreier, Peter Ulrichts, Katrien Verschueren, Antonio Guglietta, Hans De Haard, Nicolas Leupin & Jan J. G. M. Verschuuren
Objective: To investigate safety and explore efficacy of efgartigimod (ARGX-113), an anti-neonatal Fc receptor immunoglobulin G1 Fc fragment, in patients with generalized myasthenia gravis (gMG) with a history of anti-acetylcholine receptor (AChR) autoantibodies, who were on stable standard-of-care myasthenia gravis (MG) treatment. Methods: A phase 2, exploratory, randomized, double-blind, placebo-controlled, 15-center study is described. Eligible patients were randomly assigned (1:1) to receive 4 doses over a 3-week period of either 10 mg/kg IV efgartigimod or...

Data from: MarTurtSI, a global database of stable isotope analyses of marine turtles

Christine Figgener, Jospeh Bernardo & Pamela T. Plotkin
Marine turtles are both flagship species of conservation concern and indicators of ocean health. As highly migratory species, and despite substantial research effort focusing on nesting females and satellite tagging studies, we still know little about the trophic ecology and habitat use of immature stages and males. Consequently, marine turtle biologists began using stable isotope analyses in the last decade to elucidate various aspects of trophic ecology, including habitat use and trophic position. This has...

Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods

Kimberly Ballare, Nathaniel Pope, Antonio Castilla, Sarah Cusser, Richard Metz & Shalene Jha
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next-generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we...

Data from: Pollination biology and reproductive phenology of the federally endangered endemic Physaria globosa (Brassicaceae) in Tennessee

James H. Thacker, Shawn E. Krosnick, Silas C. Maynord, Geoff P. Call & Joshua S. Perkin
A study on the reproductive biology of the federally endangered Physaria globosa was conducted near Hartsville, TN, at one of the largest known populations of the species from February through July 2016. Objectives included (a) establishment of baseline reproductive phenology for P. globosa, (b) documentation of the diversity and frequency of floral visitors, and (c) determination of effective insect pollen vectors. Flowers were open for three days and displayed characteristics typical of outcrossing. Six insect...

Data from: Screening sticky cards as a simple method for improving efficiency of Diaphorina citri (Hemiptera: Liviidae) monitoring and reducing non-target organisms

Mamoudou Sétamou, Robert R. Saldaña, James M. Hearn, Jon Dale, Teresa Patricia Feria Arroyo & Darek Czokajlo
Management of Diaphorina citri Kuwayama (Hemiptera: Liviidae) populations is one of the major strategies for reducing the spread and incidence of huanglongbing (HLB). HLB is putatively caused by Candidatus Liberibacter spp. (Rhizobiales: Phyllopbacteriaceae) that are transmitted to citrus by psyllid vectors. Diaphorina citri population monitoring is done to detect its presence and inform on management decisions. Various methods are used for detecting and estimating D. citri densities but trapping with yellow or lime-green sticky cards...

Data from: Threshold elemental ratios and the temperature dependence of herbivory in fishes

Eric K. Moody, Nathan K. Lujan, Katherine A. Roach & Kirk O. Winemiller
1. Herbivorous ectothermic vertebrates are more diverse and abundant at lower latitudes. While thermal constraints may drive this pattern, its underlying cause remains unclear. We hypothesized that this constraint stems from an inability to meet the elevated phosphorus demands of bony vertebrates feeding on P-poor plant material at cooler temperatures because low gross growth efficiency at warmer temperatures facilitates higher P ingestion rates. We predicted that dietary carbon:phosphorus (C:P) should exceed the threshold elemental ratio...

Data from: Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms

Mengmeng Lu, Konstantin V. Krutovsky, C. Dana Nelson, Jason B. West, Nathalie A. Reilly & Carol A. Loopstra
In the United States, forest genetics research began over 100 years ago and loblolly pine breeding programs were established in the 1950s. However, the genetics underlying complex traits of loblolly pine remains to be discovered. To address this, adaptive and growth traits were measured and analyzed in a clonally tested loblolly pine (Pinus taeda L.) population. Over 2.8 million single nucleotide polymorphism (SNP) markers detected from exome sequencing were used to test for single locus...

Data from: Inbreeding tolerance as a pre-adapted trait for invasion success in the invasive ant Brachyponera chinensis

Pierre-André Eyer, Kenji Matsuura, Edward Vargo, Kazuya Kobayashi, Toshihisa Yashiro, Wataru Suehiro, Chihiro Himuro, Tomoyuki Yokoi, Benoit Guénard, Robert R. Dunn, Kazuki Tsuji, Pierre‐André Eyer & Edward L. Vargo
Identifying traits that facilitate species introductions and successful invasions of ecosystems represents a key issue in ecology. Following their establishment into new environments, many non-native species exhibit phenotypic plasticity with post-introduction changes in behavior, morphology or life history traits that allow them to overcome the presumed loss of genetic diversity resulting in inbreeding and reduced adaptive potential. Here we present a unique strategy in the invasive ant Brachyponera chinensis (Emery), in which inbreeding tolerance is...

Data from: Phylogeography, population genetics, and distribution modeling reveal vulnerability of Scirpus longii (Cyperaceae) and the Atlantic Coastal Plain Flora to climate change.

Daniel Spalink, Ron MacKay & Kenneth J. Sytsma
A proactive approach to conservation must be predictive, anticipating how habitats will change and which species are likely to decline or prosper. We use composite species distribution modeling to identify suitable habitats for 18 members of the North American Atlantic Coastal Plain Flora (ACPF) since the Last Glacial Maximum and project these into the future. We then use Scirpus longii (Cyperaceae), a globally imperiled ACPF sedge with many of the characteristics of extinction vulnerability, as...

Data from: A multilocus phylogeny of the fish genus Poeciliopsis: solving taxonomic uncertainties and preliminary evidence of reticulation

Mariana Mateos, Omar Domínguez-Domínguez & Alejandro Varela-Romero
The fish genus Poeciliopsis constitutes a valuable research system for evolutionary ecology, whose phylogenetic relationships have not been fully elucidated. We conducted a multilocus phylogenetic study of the genus based on seven nuclear and two mitochondrial loci with a thorough set of analytical approaches, i.e., concatenated (also known as super-matrix), species trees, and phylogenetic networks. Although several relationships remain unresolved, the overall results uncovered phylogenetic affinities among several members of this genus. A population previously...

Data from: Meiotic drive shapes rates of karyotype evolution in mammals

Heath Blackmon, Joshua Justison, Itay Mayrose & Emma E. Goldberg
Chromosome number is perhaps the most basic characteristic of a genome, yet generalizations that can explain the evolution of this trait across large clades have remained elusive. Using karyotype data from over 1,000 mammals, we developed and applied a phylogenetic model of chromosome evolution that links chromosome number changes with karyotype morphology. Using our model, we infer that rates of chromosome number evolution are significantly lower in species with karyotypes that consist of either all...

Data from: The challenges that spatial context present for synthesizing community ecology across scales

Christopher J. Patrick & Lester L. Yuan
Accurately characterizing spatial patterns on landscapes is necessary to understand the processes that generate biodiversity, a problem that has applications in ecological theory, conservation planning, ecosystem restoration, and ecosystem management. However, the measurement of biodiversity patterns and the ecological and evolutionary processes that underlie those patterns is highly dependent on the study unit size, boundary placement, and number of observations. These issues, together known as the modifiable areal unit problem, are well known in geography....

Data from: Can ancestry and morphology be used as surrogates for species niche relationships?

Friedrich Keppeler & Kirk Winemiller
Species interactions are difficult to quantify, and, consequently, many studies have used species traits and phylogeny as proxies under an assumption of niche conservatism (i.e., closely related and morphologically similar species should have similar niches). However, few studies have investigated whether niches actually are conserved within and across diverse communities. Here, we tested the degree to which phylogenetic relatedness and morphological similarity predict diets and stable isotopic ratios (δ15N and δ13C), two common descriptors of...

Data from: Accurate genomic predictions for chronic wasting disease in U.S. white-tailed deer

Christopher M. Seabury, David L. Oldeschulte, Eric K. Bhattarai, Dhruti Legare, Pamela J. Ferro, Richard P. Metz, Charles D. Johnson, Mitchell A. Lockwood & Tracy A. Nichols
The geographic expansion of chronic wasting disease (CWD) in U.S. white-tailed deer (Odocoileus virginianus) has been largely unabated by best management practices, diagnostic surveillance, and depopulation of positive herds. Using a custom Affymetrix Axiom® single nucleotide polymorphism (SNP) array, we demonstrate that both differential susceptibility to CWD, and natural variation in disease progression, are moderately to highly heritable ( among farmed U.S. white-tailed deer, and that loci other than PRNP are involved. Genome-wide association analyses...

Detoxification-related gene expression accompanies anhydrobiosis in the foliar nematode (Aphelenchoides fragariae)

Zhen Fu, Paula Agudelo & Christina Wells
The foliar nematode (Aphelenchoides fragariae) is a quarantined pest that infects a broad range of herbaceous and woody plants. Previous work has demonstrated its remarkable ability to survive rapid and extreme desiccation, although the specific mechanisms underlying its anhydrobiotic response have not been characterized. We used RNA sequencing and de novo transcriptome assembly to compare patterns of gene expression between hydrated and 24-hr desiccated nematodes. Two thousand eighty-three and 953 genes were significantly up- and...

SARS-CoV-2 transmission and control in a hospital setting: an individual-based modelling study

Qimin Huang, Anirban Mondal, Xiaobing Jiang, Mary Ann Horn, Fei Fan, Peng Fu, Xuan Wang, Hongyang Zhao, Martial Ndeffo Mbah & David Gurarie
Background: Development of strategies for mitigating the severity of COVID-19 is now a top public health priority. We sought to assess strategies for mitigating the COVID-19 outbreak in a hospital setting via the use of non-pharmaceutical interventions. Methods: We developed an individual-based model for COVID-19 transmission in a hospital setting. We calibrated the model using data of a COVID-19 outbreak in a hospital unit in Wuhan. The calibrated model was used to simulate different intervention...

Under the radar: genetic assessment of Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), two Rio Grande basin endemic cyprinids that have experienced recent range contractions

Megan Osborne, David Portnoy, Andrew Fields, Kevin Conway, Megan Bean & Christopher Hoagstrom
The Rio Grande drainage of the southwestern United States and Mexico has undergone intense anthropogenic alteration by water diversions, extraction and associated habitat changes. These alterations have disproportionately impacted the pelagic broadcast spawning guild of minnows (pelagophils). Several Rio Grande endemic pelagophils, including the co-occurring Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), have experienced dramatic recent range-wide declines yet have slipped under the radar of conservation efforts. The status of N. jemezanus...

Research Intelligence and the VIVO Platform: A Case Study from Texas A&M University and a Proposal for the VIVO Community

Bruce E. Herbert, Dong Joon Lee & Ethel Mejia

Religion in Quarantine

Heidi Campbell

Emergent social cohesion for coping with community disruptions in disasters

Chao Fan, Yucheng Jiang & Ali Mostafavi
Social cohesion is an important determinant of community well-being, especially in times of distress such as disasters. This study investigates the phenomena of emergent social cohesion, which is characterized by abrupt, temporary, and extensive social ties with the goal of sharing and receiving information regarding a particular event influencing a community. In the context of disasters, emergent social cohesion, enabled by social media usage, could play a significant role in improving the ability of communities...

Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites

Stephan Funk, Jose Luis Vega-Pla, Cristina Luis, Gus Cothran & Rytis Juras
STRUCTURE remains the most applied tool aimed at recovering the true, but unknown, population structure from observed microsatellite data or other genetic markers. About 30% of STRUCTURE-based studies could not be reproduced (Gilbert et al., 2012). Here we use a large set of data from 2323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellite markers, to evaluate how program settings, in particular the so far insufficiently evaluated number of replicates,...

Maps of northern peatland extent, depth, carbon storage and nitrogen storage

Gustaf Hugelius, Julie Loisel, Sarah Chadburn, Robert B. Jackson, Miriam Jones, Glen MacDonald, Maija Marushchak, David Olefeldt, Maara Packalen, Matthias B. Siewert, Claire Treat, Merritt Turestsky, Carolina Voigt & Zicheng Yu
This dataset is grids of peatland extent, peat depth, peatland organic carbon storage, peatland total nitrogen storage and approximate extent of ombrotrophic/minerotrophic peatlands. The grids are geotiff files in 10 km pixel resolution projected in the World Azimuthal Equidistant projection. Note that the peat depth grid shows potential peat depth everywhere,also where there is no peatland cover. For files on peatland organic carbon, total nitrogen extent and extent of ombrotrophic/minerotrophic peatlands, there are separate files...

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