204 Works

Oxylobus (Asteraceae) analysis DNA sequence data

Edward Schilling
A molecular phylogenetic investigation was carried out to clarify aspects of the systematics of Oxylobus, a primarily Mexican alpine genus of Eupatorieae. Analysis of sequence data from two nuclear (nrDNA ITS, ETS) and three plastid markers (rbcL, ndhF, matK) confirmed the monophyly of Oxylobus and placed species of Ageratina as its sister group. A survey of 56 samples of Oxylobus using nrDNA ITS and ETS provided support for the currently accepted species, and showed the...

Data from: Illuminating prey selection in an insectivorous bat community, exposed to artificial light at night

Zachary M. Cravens, Veronica A. Brown, Timothy J. Divoll & Justin G. Boyles
1.Light pollution has been increasing around the globe and threatens to disturb natural rhythms of wildlife species. Artificial light impacts the behaviour of insectivorous bats in numerous ways, including foraging behaviour, which may in turn lead to altered prey selection. 2.In a manipulative field experiment, we collected faecal samples from six species of insectivorous bats in naturally dark and artificially lit conditions, and identified prey items using molecular methods to investigate effects of light pollution...

Data from: Development and validation of a weather-based warning system to advise fungicide applications to control dollar spot on turfgrass

Damon L. Smith, James P. Kerns, Nathan R. Walker, Andrea F. Payne, Brandon Horvath, John C. Inguagiato, John E. Kaminski, Maria Tomaso-Peterson & Paul L. Koch
Dollar spot is one of the most common diseases of golf course turfgrass and numerous fungicide applications are often required to provide adequate control. Weather-based disease warning systems have been developed to more accurately time fungicide applications; however, they tend to be ineffective and are not currently in widespread use. The primary objective of this research was to develop a new weather-based disease warning system to more accurately advise fungicide applications to control dollar spot...

Data from: The adaptive value of gluttony: predators mediate the life history trade-offs of satiation threshold

Jonathan N Pruitt & Jennifer J Krauel
Animals vary greatly in their tendency to consume large meals. Yet, whether or how meal size influences fitness in wild populations is infrequently considered. Using a predator exclusion, marked-recapture experiment, we estimated selection on the amount of food accepted during an ad libitum feeding bout (hereafter termed "satiation threshold") in the wolf spider Schizocosa ocreata. Individually marked, size-matched females of known satiation threshold were assigned to predator exclusion and predator inclusions treatments and tracked for...

Data from: Shared genetic diversity across the global invasive range of the Monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection

Pim Edelaar, Severine Roques, Elizabeth A. Hobson, Anders Gonçalves Da Silva, Michael L. Avery, Michael A. Russello, Juan Carlos Senar, Timothy F. Wright, Martina Carrete & Jose Luis Tella
While genetic diversity is hypothesized to be an important factor explaining invasion success, there is no consensus yet on how variation in source populations or demographic processes affects invasiveness. We used mitochondrial DNA haplotypic and microsatellite genotypic data to investigate levels of genetic variation and reconstruct the history of replicate invasions on three continents in a globally invasive bird, the monk parakeet (Myiopsitta monachus). We evaluated whether genetic diversity at invasive sites could be explained...

Data from: Incorporating abundance information and guiding variable selection for climate-based ensemble forecasting of species' distributional shifts

Evan P. Tanner, Monica Papes, R. Dwayne Elmore, Samuel D. Fuhlendorf & Craig A. Davis
Ecological niche models (ENMs) have increasingly been used to estimate the potential effects of climate change on species’ distributions worldwide. Recently, predictions of species abundance have also been obtained with such models, though knowledge about the climatic variables affecting species abundance is often lacking. To address this, we used a well-studied guild (temperate North American quail) and the Maxent modeling algorithm to compare model performance of three variable selection approaches: correlation/variable contribution (CVC), biological (i.e.,...

Data from: A novel molecular toolkit for rapid detection of the pathogen and primary vector of thousand cankers disease

Emel Oren, William Klingeman, Romina Gazis, John Moulton, Paris Lambdin, Mark Coggeshall, Jiri Hulcr, Steven J. Seybold & Denita Hadziabdic
Thousand Cankers Disease (TCD) of Juglans and Pterocarya (Juglandaceae) involves a fungal pathogen, Geosmithia morbida, and a primary insect vector, Pityophthorus juglandis. TCD was described originally from dying Juglans nigra trees in the western United States (USA), but it was reported subsequently from the eastern USA and northern Italy. The disease is often difficult to diagnose due to the absence of symptoms or signs on the bark surface of the host. Furthermore, disease symptoms can...

Data from: Use of a pressure-sensing walkway system for biometric assessment of gait characteristics in goats

Rebecca E. Rifkin, Remigiusz M. Grzeskowiak, Pierre-Yves Mulon, H. Steve Adair, Alexandru S. Biris, Madhu Dhar & David E. Anderson
The purpose of this study was to quantitatively assess gait characteristics and weight-bearing forces during ambulation in healthy goats using a pressure-sensing walkway as a biometric tool for stride, gait, and force analysis. Forty-six healthy adult goats ranging in age from 5 to 6 years, mixed-breeds, and with a mean body weight of 52 ± 7.1 kgs were used. Goats were trained to walk over a pressure-sensing walkway. Data for analysis was collected on 2...

Data from: Plant host identity and soil macronutrients explain little variation in sapling endophyte community composition: is disturbance an alternative explanation?

Eric A. Griffin, Joshua G. Harrison, Steven W. Kembel, Alyssa A. Carrell, S. Joseph Wright & Walter P. Carson
1. Bacterial endophytes may be fairly host specific; nonetheless, an important subset of taxa may be shared among numerous host species forming a community-wide core microbiome. Moreover, other key factors, particularly the supply of limiting macronutrients and disturbances, may supersede the importance of host identity. 2. We tested the following four non-mutually exclusive hypotheses: 1. The Host Identity Hypothesis: endophytes vary substantially among different host plant species. 2. The Core Microbiome Hypothesis: a subset of...

Data from: Earth history and the passerine superradiation

Carl H. Oliveros, Daniel J. Field, Daniel T. Ksepka, F. Keith Barker, Alexandre Aleixo, Michael J. Andersen, Per Alström, Brett W. Benz, Edward L. Braun, Michael J. Braun, Gustavo A. Bravo, Robb T. Brumfield, R. Terry Chesser, Santiago Claramunt, Joel Cracraft, Andrés M. Cuervo, Elizabeth P. Derryberry, Travis C. Glenn, Michael G. Harvey, Peter A. Hosner, Leo Joseph, Rebecca T. Kimball, Andrew L. Mack, Colin M. Miskelly, A. Townsend Peterson … & Brant C. Faircloth
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships...

Data from: A parametric method for assessing diversification rate variation in phylogenetic trees

Premal Shah, Benjamin Minault Fitzpatrick & James Andrew Fordyce
Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification-rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a...

Data from: Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

Matt Friedman, Benjamin P. Keck, Alex Dornburg, Ron I. Eytan, Christopher H. Martin, C. Darrin Hulsey, Peter C. Wainwright & Thomas J. Near
Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance. Although the Early Cretaceous (ca 135...

Data from: Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

Thomas J. Near, Alex Dornburg, Ron I. Eytan, Benjamin P. Keck, W. Leo Smith, Kristen L. Kuhn, Jon A. Moore, Samantha A. Price, Frank T. Burbrink, Matt Friedman & Peter C. Wainwright
Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the “bush at...

Data from: An evaluation of transferability of ecological niche models

Huijie Qiao, Xiao Feng, Luis E. Escobar, A. Townsend Peterson, Jorge Soberon, Gengping Zhu & Monica Papeș
Ecological niche modeling (ENM) is used widely to study species’ geographic distributions. ENM applications frequently involve transferring models calibrated with environmental data from one region to other regions or times that may include novel environmental conditions. When novel conditions are present, transferability implies extrapolation, whereas, in absence of such conditions, transferability is an interpolation step only. We evaluated transferability of models produced using 11 ENM algorithms from the perspective of interpolation and extrapolation in a...

Data from: PHRAPL: phylogeographic inference using approximate likelihoods

Nathan D. Jackson, Ariadna E. Morales, Bryan C. Carstens & Brian C. O'Meara
The demographic history of most species is complex, with multiple evolutionary processes combining to shape the observed patterns of genetic diversity. To infer this history, the discipline of phylogeography has (to date) used models that simplify the historical demography of the focal organism, for example by assuming or ignoring ongoing gene flow between populations or by requiring a priori specification of divergence history. Since no single model incorporates every possible evolutionary process, researchers rely on...

Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

Carl J. Rothfels, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Anders Larsson, Dylan O. Burge, Markus Ruhsam, Michael Deyholos, Douglas E. Soltis, , Shane W. Shaw, Lisa Pokorny, Tao Chen, Claude DePamphilis, Lisa DeGironimo, Li Chen, Xiaofeng Wei, Xiao Sun, Petra Korall, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer, C. Neal Stewart, Gane K-S. Wong … & Claude De Pamphilis
Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the...

Data from: Xianella: a new mat-forming calcified cyanobacterium from the Middle–Late Ordovician of North China

Jeong-Hyun Lee & Robert Riding
Xianella hongii gen. et sp. nov. is described from the Middle–Late Ordovician of Shaanxi, China and interpreted as a calcified cyanobacterial sheath. Xianella filaments formed cable-like strands that constructed thick fenestral layers. The specimens occur in metre-sized limestone blocks, possibly derived from local collapse of a reefal platform margin. In combination with micrite, some of which is intraclastic and peloidal, Xianella created thick and extensive stacks of layered calcified fenestral fabric that appear to be...

Data from: Effects of climatic and geological processes during the Pleistocene on the evolutionary history of the northern cavefish, Amblyopsis spelaea (Teleostei: Amblyopsidae)

Matthew Lance Niemiller, James R. McCandless, Robert Graham Reynolds, James Caddle, Thomas J. Near, Christopher R. Tillquist, William D. Pearson & Benjamin Minault Fitzpatrick
Climatic and geological processes associated with glaciation cycles during the Pleistocene have been implicated in influencing patterns of genetic variation and promoting speciation of temperate flora and fauna. However, determining the factors promoting divergence and speciation is often difficult in many groups because of our limited understanding of potential vicariant barriers and connectivity between populations. Pleistocene glacial cycles are thought to have significantly influenced the distribution and diversity of subterranean invertebrates; however, impacts on subterranean...

Data from: Unraveling the determinants of insular body size shifts

Craig R. McClain, Paul A. P. Durst, Alison G. Boyer & Clinton D. Francis
The island rule, a pattern of size shifts on islands, is an oft-cited but little understood phenomenon of evolutionary biology. Here we explore the evolutionary mechanisms behind the rule in 184 mammal species, testing climatic, ecological, and phylogenetic hypotheses in a robust quantitative framework. Our findings confirm the importance of species’ ecological traits in determining both the strength and the direction of body size changes on islands. Although the island rule pattern appears relatively weak...

Data from: Trait integration and macroevolutionary patterns in the pollination biology of conifers

Andrew B. Leslie, Jeremy Michael Beaulieu, Peter R. Crane, Patrick Knopf & Michael J. Donoghue
Integration influences patterns of trait evolution, but the relationship between these patterns and the degree of trait integration is not well understood. In order to explore this further, we study a specialized pollination mechanism in conifers whose traits are linked through function but not development. This mechanism depends on interactions among three characters: pollen that is buoyant, ovules that face downward at pollination, and the production of a liquid droplet that buoyant grains float through...

Data from: Male mealworm beetles increase resting metabolic rate under terminal investment

Indrikis A. Krams, Tatjana Krama, Fhionna R. Moore, Inese Kivleniece, Aare Kuusik, Todd M. Freeberg, Raivo Mänd, M. J. Rantala, Janina Daukšte & Marika Mänd
Harmful parasite infestation can cause energetically costly behavioural and immunological responses, with the potential to reduce host fitness and survival. It has been hypothesized that the energetic costs of infection cause resting metabolic rate (RMR) to increase. Furthermore, under terminal investment theory, individuals exposed to pathogens should allocate resources to current reproduction when life expectancy is reduced, instead of concentrating resources on an immune defence. In this study, we activated the immune system of Tenebrio...

Data from: Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

Nathan P. McNulty, Wu Meng, Alison R. Erickson, Chongle Pan, Brian K. Erickson, Eric C. Martens, Nicholas A. Pudlo, Brian D. Muegge, Bernard Henrissat, Robert L. Hettich, Jeffrey I. Gordon & Meng Wu
The human gut microbiota is an important metabolic organ. However, little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In the current study, gnotobiotic mice colonized with a simplified model microbiota composed of 12 sequenced human gut bacterial species were fed oscillating diets of disparate composition. Rapid, reproducible and reversible changes in community structure were observed. Time series microbial RNA-Seq analyses revealed...

Data from: Genetics-based interactions of foundation species affect community diversity, stability, and network structure

Arthur R. Keith, Joseph K. Bailey, Matthew K. Lau & Thomas G. Whitham
We examined the hypothesis that genetics-based interactions between strongly interacting foundation species, the tree Populus angustifolia and the aphid Pemphigus betae, affect arthropod community diversity, stability and species interaction networks of which little is known. In a 2-year experimental manipulation of the tree and its aphid herbivore four major findings emerged: (i) the interactions of these two species determined the composition of an arthropod community of 139 species; (ii) both tree genotype and aphid presence...

Data from: A combined morphometric and phylogenetic revision of the late Ordovician brachiopod genera Eochonetes and Thaerodonta

Jennifer E. Bauer & Alycia L. Stigall
Systematic revision of the Late Ordovician brachiopod genera Eochonetes Reed, 1917 and Thaerodonta Wang, 1949 was conducted utilizing specimen-based morphometric and species-level phylogenetic analyses. Previous studies had recognized Thaerodonta and Eochonetes as either distinct taxonomic entities or synonyms. New multivariate and phylogenetic analyses confirm the synonymy of Thaerodonta with Eochonetes and provide a framework to assess evolutionary and ecological patterns within the clade. Multivariate analyses were employed to delineate species in morphospace and provided information...

Data from: Intragenomic nuclear RNA variation in a cryptic Amanita taxon

Karen W. Hughes, Rodham E. Tulloss & Ronald H. Petersen
Amanita cf. lavendula collections in eastern North America, Mexico, and Costa Rica were found to consist of four cryptic taxa, one of which exhibited consistently unreadable nuclear rDNA ITS1-5.8S-ITS2 (fungal barcode) sequences after ITS1 base 130. This taxon is designated here as Amanita cf. lavendula taxon 1. ITS sequences from dikaryotic basidiomata were cloned, but sequences recovered from cloning did not segregate into distinct haplotypes. Rather, there was a mix of haplotypes that varied among...

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  • University of Tennessee at Knoxville
  • Yale University
  • University of Florida
  • University of Kansas
  • Utah State University
  • University of Georgia
  • University of Nevada Reno
  • Oak Ridge National Laboratory
  • Pennsylvania State University
  • University of California, Davis