108 Works

Data from: Social organisation and genetic structure: insights from co-distributed bat populations

Stephen J. Rossiter, Akbar Zubaid, Adura Mohd-Adnan, Matthew J. Struebig, Thomas H. Kunz, Sucharita Gopal, Eric J. Petit & Tigga Kingston
The impact of ecology and social organisation on genetic structure at landscape spatial scales, where gene dynamics shape evolution as well as determine susceptibility to habitat fragmentation, is poorly understood. Attempts to assess these effects must take into account the potentially confounding effects of history. We used microsatellites to compare genetic structure in seven bat species with contrasting patterns of roosting ecology and social organisation, all of which are co-distributed in an ancient forest habitat...

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: Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent

Robert J. Baker, Benjamin Dickins, Jeffrey K. Wickliffe, Faisal Anwarali Khan, Sergey Gaschak, Kateryna Makova & Caleb D. Phillips
Currently, the effects of chronic, continuous low dose environmental irradiation on the mitochondrial genome of resident small mammals are unknown. Using the bank vole (Myodes glareolus) as a model system, we tested the hypothesis that approximately 50 generations of exposure to the Chernobyl environment has significantly altered genetic diversity of the mitochondrial genome. Using deep sequencing, we compared mitochondrial genomes from 131 individuals from reference sites with radioactive contamination comparable to that present in Northern...

Data from: Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats

, Brant C. Faircloth, Kevin A.M. Sullivan, Troy J. Kieran, Travis C. Glenn, Michael W. Vandewege, , Robert J. Baker, Richard D. Stevens, David A. Ray, Thomas E Lee, Roy N Platt & Kevin A M Sullivan
The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial...

Data from: Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern US

Soo-Rang Lee, Yeong-Seok Jo, Chan-Ho Park, Jonathan M. Friedman & Matthew S. Olson
Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in the invasive riparian shrub saltcedar (Tamarix L.) by analyzing 1,997 genome-wide...

Data from: Habitat selection and the value of information in heterogenous landscapes

Kenneth A. Schmidt & Francois Massol
Despite the wide usage of the term information in evolutionary ecology, there is no general treatise between fitness (i.e., density-dependent population growth) and selection of the environment sensu lato. Here we (1) initiate the building of a quantitative framework with which to examine the relationship between information use in spatially heterogeneous landscapes and density-dependent population growth, and (2) illustrate its utility by applying the framework to an existing model of breeding habitat selection. We begin...

Data from: Evaluating a handheld decision support device in pediatric intensive care settings

Tera L. Reynolds, Patricia R. DeLucia, Karen A. Esquibel, Todd Gage, Noah J. Wheeler, J. Adam Randell, James G. Stevenson & Kai Zheng
Objective: To evaluate end-user acceptance and the effect of a commercial handheld decision support device in pediatric intensive care settings. The technology, pac2, was designed to assist nurses in calculating medication dose volumes and infusion rates at the bedside. Materials and Methods: The devices, manufactured by InformMed Inc., were deployed in the pediatric and neonatal intensive care units in two health systems. This mixed methods study assessed end-user acceptance, as well as pac2’s effect on...

Data from: Ontogenetic variability in crystallography and mosaicity of conodont apatite: Implications for microstructure, paleothermometry and geochemistry

Mohammad Shohel, Neo McAdams & Bradley Cramer
X-ray diffraction data from Silurian conodonts belonging to various developmental stages of the species Dapsilodus obliquicostatus demonstrate changes in crystallography and degree of nanocrystallite ordering (mosaicity) in both hyaline and albid crown tissue. The exclusive use of a single species in this study, combined with systematic testing of each element type at multiple locations, provided insight into microstructural and crystallographic differentiation between element position (Sa, Sb-c, M) as well as between juveniles and adults. A...

Mammals on mountainsides revisited: trait-based tests of assembly reveal the importance of abiotic filters

Brooks Kohli, Richard Stevens, Eric Rickart & Rebecca Rowe
Aim: Mountains provide uniquely informative systems for examining how biodiversity is distributed and identifying the causes of those patterns. Elevational patterns of species richness are well-documented for many taxa but comparatively few studies have investigated patterns in multiple dimensions of biodiversity along mountainsides, which can reveal the underlying processes at play. Here, we use trait-based diversity patterns to determine the role of abiotic filters and competition in the assembly of communities of small mammals across...

Experimental parasite community perturbation reveals associations between Sin Nombre virus and gastrointestinal nematodes in a rodent reservoir host

Amy Sweeny, Courtney Thomason, Edwin Carbajal, Christina Hansen, Andrea Graham & Amy Pedersen
Individuals are often co-infected with several parasite species, yet measuring within-host interactions remains difficult in the wild. Consequently, the impact of such interactions on host fitness and epidemiology are often unknown. We used anthelmintic drugs to experimentally reduce nematode infection and measured the effects on both nematodes and the important zoonosis Sin Nombre virus (SNV) in its primary reservoir (Peromyscus spp.). Treatment significantly reduced nematode infection, but increased SNV seroprevalence. Furthermore, mice that were co-infected...

Data from: Invasion-induced root-fungal disruptions alter plant water and nitrogen economies

Lalasia Bialic-Murphy, Nick Smith, Priya Voothuluru, Robert McElderry, Morgan Roche, Steven Cassidy, Stephanie Kivlin & Susan Kaliz
Despite widespread evidence that biological invasion influences both the biotic and abiotic soil environments, the extent to which these two pathways underpin the effects of invasion on plant traits and performance is unknown. Leveraging a long-term (14-yr) field experiment, we show that an allelochemical-producing invader affects plants through biotic mechanisms, altering the soil fungal community composition, with no apparent shifts in soil nutrient availability. Changes in belowground fungal communities resulted in high costs of nutrient...

A comprehensive phylogenomic platform for exploring the angiosperm tree of life

William Baker, Paul Bailey, Vanessa Barber, Abigail Barker, Sidonie Bellot, David Bishop, Laura Botigue, Grace Brewer, Tom Carruthers, James Clarkson, Jeffrey Cook, Robyn Cowan, Steven Dodsworth, Niroshini Epitawalage, Elaine Françoso, Berta Gallego, Matthew Johnson, Jan Kim, Kevin Leempoel, Olivier Maurin, Catherine McGinnie, Lisa Pokorny, Shyamali Roy, Malcolm Stone, Eduardo Toledo … & Félix Forest
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data...

Analytic dataset informing modeling of winter species distributions of North American bat species

Sarah Olson, Meredith McClure, Catherine Haase, Carter Hranac, David Hayman, Brett Dickson, Liam McGuire, Daniel Crowley, Nathan Fuller, Cori Lausen & Raina Plowright
The fungal pathogen Pseudogymnoascus destructans and resultant white-nose syndrome (WNS) continues to advance across North America, infecting new bat populations, species, and hibernacula. Western North America hosts the highest bat diversity in the U.S. and Canada, yet little is known about hibernacula and hibernation behavior in this region. An improved understanding of where bats hibernate and the conditions that create suitable hibernacula is critical if land managers are to anticipate and address the conservation needs...

Large‐scale genome sampling reveals unique immunity and metabolic adaptations in bats

Diana Daniela Moreno Santillan, Tanya Lama, Yocelyn T Gutierrez Guerrero, Zixia Huang, Graham Hughes, Alexis Brown, Paul Donat, Huabin Zhao, Stephen Rossiter, Laurel Yohe, Joshua Potter, Emma Teeling, Sonja Vernes, Kalina Davies, Eugene Myers, Federico Hoffmann, Angelique Corthals, David Ray & Liliana Davalos
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large...

Nitrogen and water availability control plant carbon storage with warming

Guiyao Zhou, Cesar Terrer, An Huang, Bruce A. Hungate, Natasja Van Gestel, Xuhui Zhou & Kees Jan Van Groenigen
Plants may slow global warming through enhanced growth, because increased levels of photosynthesis stimulate the land carbon (C) sink. However, how climate warming affects plant C storage globally and key drivers that determining the response of plant C storage to climate warming remains unclear, causing uncertainty in climate projections. We performed a comprehensive meta-analysis, compiling 393 observations from 99 warming studies to examine the global patterns of plant C storage responses to climate warming and...

Data from: Rocky Mountain forests are poised to recover following bark beetle outbreaks, but with altered composition

Kyle Rodman, Robert Andrus, Amanda Carlson, Trevor Carter, Teresa Chapman, Jonathan Coop, Paula Fornwalt, Nathan Gill, Brian Harvey, Ashley Hoffman, Katharine Kelsey, Dominik Kulakowski, Daniel Laughlin, Jenna Morris, José Negrón, Katherine Nigro, Gregory Pappas, Miranda Redmond, Charles Rhoades, Monique Rocca, Zoe Schapira, Jason Sibold, Camille Stevens-Rumann, Thomas Veblen, Jianmin Wang … & Sarah Hart
Amplified by warming temperatures and drought, recent outbreaks of native bark beetles (Curculionidae: Scolytinae) have caused extensive tree mortality throughout Europe and North America. Despite their ubiquitous nature and important effects on ecosystems, forest recovery following such disturbances is poorly understood, particularly across regions with varying abiotic conditions and outbreak effects. To better understand post-outbreak recovery across a topographically complex region, we synthesized data from 16 field studies spanning subalpine forests in the Southern Rocky...

Tumor cell-derived asymmetric dimethylarginine regulates macrophage functions and polarization

Yi-Ling Chen, AKaychia T. Lowery, Samuel Lin, Ameae M. Walker & Kuan-Hui E. Chen
Abstract Background Asymmetric dimethylarginine (ADMA), which is significantly elevated in the plasma of cancer patients, is formed via intracellular recycling of methylated proteins and serves as a precursor for resynthesis of arginine. However, the cause of ADMA elevation in cancers and its impact on the regulation of tumor immunity is not known. Methods Three mouse breast cell lines (normal breast epithelial HC11, breast cancer EMT6 and triple negative breast cancer 4T1) and their equivalent 3D...

Data from: Pleistocene speciation in the genus Populus (Salicaceae)

Nicholas D. Levsen, Peter Tiffin & Matthew S. Olson
The macro-evolutionary consequences of recent climate change remain controversial and there is little paleobotanical or morphological evidence that Pleistocene (1.8-0.12 Ma) glacial cycles acted as drivers of speciation, especially among lineages with long generation times, such as trees. We combined genetic and ecogeographic data from two closely related North American tree species, Populus balsamifera and P. trichocarpa (Salicacaeae) to determine if their divergence coincided with and was possibly caused by Pleistocene climatic events. We analyzed...

Data from: Multilocus characterization of a woodrat (genus Neotoma) hybrid zone

Matthew R. Mauldin, Michelle L. Haynie, J. Delton Hanson, Robert J. Baker & Robert D. Bradley
In order to investigate hybridization between 2 species of woodrats, Neotoma floridana and Neotoma micropus, 103 specimens were collected, in March of 1988, from a known area of sympatry, and compared with reference collections from areas of allopatry. Ten genetic markers, consisting of 7 microsatellite loci, 1 mitochondrial gene (cytochrome-b [Cytb]), and 2 nuclear introns (intron 2 of the vertebrate alcohol dehydrogenase gene [Adh1-I2] and intron 7 of the beta-fibrinogen gene [Fgb-I7]) were used to...

Data from: Beyond size – morphological predictors of bite force in a diverse insectivorous bat assemblage from Malaysia

Juliana Senawi, Daniela Schmieder, Björn Siemers & Tigga Kingston
1. Bite force is used to investigate feeding performance in a variety of vertebrates. In all taxa studied, bite force is strongly correlated with body and head size. Studies of bite force in bats have largely centred on neotropical species with a particular focus on species that maximize dietary differences. Little is known about the bite force of bats from the Old World tropics, nor of variation in bite force within diverse assemblages of obligate...

Data from: A 1,000-year-old antimicrobial remedy with antistaphylococcal activity

Freya Harrison, Aled E. L. Roberts, Rebecca Gabrilska, Kendra P. Rumbaugh, Christina Lee & Stephen P. Diggle
Plant-derived compounds and other natural substances are a rich potential source of compounds that kill or attenuate pathogens that are resistant to current antibiotics. Medieval societies used a range of these natural substances to treat conditions clearly recognizable to the modern eye as microbial infections, and there has been much debate over the likely efficacy of these treatments. Our interdisciplinary team, comprising researchers from both sciences and humanities, identified and reconstructed a potential remedy for...

Data from: Investigating sensitivity of phylogenetic community structure metrics using North American desert bats

Lorelei E. Patrick & Richard D. Stevens
A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and...

Data from: Threshold effect of habitat loss on bat richness in cerrado-forest landscapes

Renata L. Muylaert, Richard D. Stevens & Milton C. Ribeiro
Understanding how animal groups respond to contemporary habitat loss and fragmentation is essential for development of strategies for species conservation. Until now, there has been no consensus about how landscape degradation affects the diversity and distribution of Neotropical bats. Some studies demonstrate population declines and species loss in impacted areas, although the magnitude and generality of these effects on bat community structure are unclear. Empirical fragmentation thresholds predict an accentuated drop in biodiversity, and species...

Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

Matthew G. Johnson, Lisa Pokorny, Steven Dodsworth, Laura R. Botigue, Robyn S. Cowan, Alison Devault, Wolf L. Eiserhardt, Niroshini Epitawalage, Félix Forest, Jan T. Kim, James Leebens-Mack, Ilia J. Leitch, Olivier Maurin, Doug Soltis, Pamela S. Soltis, Gane Ka-Shu Wong, William J. Baker & Norman Wickett
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used...

Data from: True homoplasy of retrotransposon insertions in primates

Liliya Doronina, Olga Reising, Hiram Clawson, David A. Ray & Jürgen Schmitz
How reliable are the presence/absence insertion patterns of the supposedly homoplasy-free retrotransposons, that were randomly inserted in the quasi infinite genomic space? To systematically examine this question in an up-to-date, multi-genome comparison, we screened millions of primate transposed Alu SINE elements for incidences of homoplasious precise insertions and deletions. In genome-wide analyses, we identified and manually verified nine cases of precise parallel Alu insertions of apparently identical elements at orthologous positions in two ape lineages...

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