500 Works

Data from: Fat in the leg: function of the expanded hind leg in gasteruptiid wasps (Hymenoptera: Gasteruptiidae)

István Mikó, Sarthok Rasique Rahman, Salvatore S. Anzaldo, Thomas Van De Kamp, Ben A. Parslow, Nikolai J. Tatarnic, Maxwell T. Wetherington, Julie Anderson, Rudolf J. Schilder, Jonah M. Ulmer, Andrew R. Deans & Heather M. Hines
Among some of the most unusual traits of the gasteruptiid wasps is their unique hovering flight and the expansion of their hind tibiae. Tibial expansions in female parasitoid hymenopterans often involve an enlarged sensory structure for vibration detection, the subgenual organ, thus enabling refined substrate-borne detection of concealed hosts. In the present paper, we utilize a combination of microscopy, chemical analysis, gene expression, and behavior to explore the function of the expanded hind tibia of...

Data from: Using spatial capture–recapture to elucidate population processes and space-use in herpetological studies

David J. Muñoz, David A. W. Miller, Chris Sutherland & Evan H. Campbell Grant
The cryptic behavior and ecology of herpetofauna make estimating the impacts of environmental change on demography difficult; yet, the ability to measure demographic relationships is essential for elucidating mechanisms leading to the population declines reported for herpetofauna worldwide. Recently developed spatial capture–recapture (SCR) methods are well suited to standard herpetofauna monitoring approaches. Individually identifying animals and their locations allows accurate estimates of population densities and survival. Spatial capture–recapture methods also allow estimation of parameters describing...

Data from: Horizontal gene acquisitions, mobile element proliferation, and genome decay in the host - restricted plant pathogen Erwinia tracheiphila

Lori R. Shapiro, Erin D. Scully, Timothy J. Straub, Jihye Park, Andrew G. Stephenson, Gwyn A. Beattie, Mark L. Gleason, Roberto Kolter, Miguel C. Coelho, Consuelo M. De Moraes, Mark C. Mescher & Olga Zhaxybayeva
Modern industrial agriculture depends on high density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared to ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and...

Data from: Genetic species delineation among branching Caribbean Porites corals

Carlos Prada, Melissa B. Debiasse, Joseph E. Neigel, Bree Yednock, Joseph L. Stake, Zach H. Foesman, Iliana B. Baums & Michael E. Hellberg
Coral species are difficult to discern because of their morphological plasticity, long generation times, and slow rates of mitochondrial DNA evolution. Amongst Caribbean representatives of the genus Porites are three named species (P. divaricata, P. furcata, and P. porites) with branching colony morphologies whose validity as genetically isolated species has been debated. We present sequence data from the mitochondrial control region, nuclear ITS, and nine single copy nuclear loci for the Caribbean Porites and a...

Data from: Microbial invasion of the Caribbean by an Indo-Pacific coral zooxanthella

D. Tye Pettay, Drew C. Wham, Robin T. Smith, Roberto Iglesias-Prieto & Todd C. LaJeunesse
Human-induced environmental changes have ushered in the rapid decline of coral reef ecosystems, particularly by disrupting the symbioses between reef-building corals and their photosymbionts. However, escalating stressful conditions enable some symbionts to thrive as opportunists. We present evidence that a stress-tolerant “zooxanthella” from the Indo-Pacific Ocean, Symbiodinium trenchii, has rapidly spread to coral communities across the Greater Caribbean. In marked contrast to populations from the Indo-Pacific, Atlantic populations of S. trenchii contained exceptionally low genetic...

Data from: Geographic differences in vertical connectivity in the Caribbean coral Montastraea cavernosa despite high levels of horizontal connectivity at shallow depths

Xaymara Serrano, Iliana B. Baums, Katherine O'Reilly, Tyler B. Smith, Ross J. Jones, Tonya L. Shearer, Flavia L. D. Nunes & Andrew C. Baker
The Deep Reef Refugia Hypothesis proposes that deep reefs can act as local recruitment sources for shallow reefs following disturbance. To test this hypothesis, nine polymorphic DNA microsatellite loci were developed and used to assess vertical connectivity in 583 coral colonies of the Caribbean depth-generalist coral Montastraea cavernosa. Samples were collected from three depth zones (≤10 m, 15-20 m and ≥25 m) at sites in Florida Upper Keys, Lower Keys and Dry Tortugas), Bermuda, and...

Data from: Energetic constraint of non-monotonic mass change during offspring growth: a general hypothesis and application of a new tool

Jennifer M. Arnold, Ian C. Nisbet & Stephen A. Oswald
1. Postnatal growth is an important life-history trait and can be a sensitive indicator of ecological stress. For over 50 years, monotonic (never-decreasing) growth has been viewed as the predominant trajectory of postnatal mass change in most animal species, notably among birds. However, prevailing analytical approaches and energetic constraints may limit detection of non-monotonic (or multi-phasic), determinate growth patterns, such as mass recession in birds (weight-loss prior to fledging, preceded by overshooting adult mass), which...

Data from: Scatterhoarders drive long- and short-term population dynamics of a nut-producing tree, while pre-dispersal seed predators and herbivores have little effect

Elise C. Elwood, Nathanael I. Lichti, Sara F. Fitzsimmons & Harmony J. Dalgleish
1.Both seed predators and herbivores can have profound effects on individual plant growth, reproduction and survival, but their population level effects are less well understood. While most plants interact with a suite of seed predators and herbivores over their life cycle, few studies incorporate the effects of multiple interacting partners and multiple life stages on plant population growth. 2.We constructed a matrix model using six years of data from a rare, seed-producing population of American...

Data from: Dynamics of short- and long-term association between a bacterial plant pathogen and its arthropod vector

Lori R. Shapiro, Irmgard Seidl-Adams, Consuelo M. De Moraes, Andrew G. Stephenson & Mark C. Mescher
The dynamics of association between pathogens and vectors can strongly influence epidemiology. It has been proposed that wilt disease epidemics in cucurbit populations are sustained by persistent colonization of beetle vectors (Acalymma vittatum) by the bacterial phytopathogen Erwinia tracheiphila. We developed a qPCR method to quantify E. tracheiphila in whole beetles and frass and used it to assess pathogen acquisition and retention following variable exposure to infected plants. We found that (i) E. tracheiphila is...

Data from: Limited hatchery introgression into wild brook trout (Salvelinus fontinalis) populations despite reoccurring stocking

Shannon L. White, William L. Miller, Stephanie A. Dowell, Meredith L. Bartron & Tyler Wagner
Due to increased anthropogenic pressures on many fish populations, supplementing wild populations with captive-raised individuals has become an increasingly common management practice. Stocking programs can be controversial due to uncertainty about the long-term fitness effects of genetic introgression on wild populations. In particular, introgression between hatchery and wild individuals can cause declines in wild population fitness, resiliency, and adaptive potential, and contribute to local population extirpation. However, low survival and fitness of captive-raised individuals can...

Data from: Empirical and theoretical investigation into the potential impacts of insecticide resistance on the effectiveness of insecticide-treated bed nets

Katey D. Glunt, Maureen Coetzee, Silvie Huijben, A. Alphonsine Koffi, Penelope A. Lynch, Raphael N'Guessan, Welbeck A. Oumbouke, Eleanore D. Sternberg & Matthew B. Thomas
In spite of widespread insecticide resistance in vector mosquitoes throughout Africa, there is limited evidence that long lasting insecticidal bed nets (LLINs) are failing to protect against malaria. Here, we showed that LLIN contact in the course of host-seeking resulted in higher mortality of resistant Anopheles spp. mosquitoes than predicted from standard laboratory exposures with the same net. We also found that sub-lethal contact with an LLIN caused a reduction in blood feeding and subsequent...

Data from: Detecting recent selective sweeps while controlling for mutation rate and background selection

Christian D. Huber, Michael DeGiorgio, Ines Hellmann & Rasmus Nielsen
A composite likelihood ratio test implemented in the program SweepFinder is a commonly used method for scanning a genome for recent selective sweeps. SweepFinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum (SFS) around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power...

Data from: Unrecognized coral species diversity masks differences in functional ecology

Jennifer N. Boulay, Michael E. Hellberg, Jorge Cortés, Iliana B. Baums & J. Cortes
Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P. lobata reproduces mainly sexually, P. evermanni dominates in areas where triggerfish prey on bioeroding mussels living within the coral skeleton, thereby generating...

Data from: A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales

Michael R. McKain, Haibao Tang, Joel R. McNeal, Saravanaraj Ayyampalayam, Jerrold I. Davis, Claude W. DePamphilis, Thomas J. Givnish, J. Chris Pires, Dennis Wm. Stevenson & Jim H. Leebens-Mack
Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intra-genomic syntenic blocks. Three such whole genome duplication (WGD) events, designated as rho (ρ), sigma (σ), and tau (τ), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein coding sequences. The timing of...

Data from: Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers

Joram M. Mwacharo, Koh Nomura, Hirofumi Hanada, Takashi Amano, Jianlin L. Han & Olivier Hanotte
Unravelling the genetic history of any livestock species is central to understanding the origin, development and expansion of agricultural societies and economies. Domestic village chickens are widespread in Africa. Their close association with, and reliance on, humans for long range dispersal makes the species an important biological marker in tracking cultural and trading contacts between human societies and civilisations across time. Archaezoological and linguistic evidences suggest a complex history of arrival and dispersion of the...

Data from: Complex environmental drivers of immunity and resistance in malaria mosquitoes

Courtney C. Murdock, Lillian L. Moller-Jacobs & Matthew B. Thomas
Considerable research effort has been directed at understanding the genetic and molecular basis of mosquito innate immune mechanisms. Whether environmental factors interact with these mechanisms to shape overall resistance remains largely unexplored. Here we examine how changes in mean ambient temperature, diurnal temperature fluctuation, and time of day of infection affected the immunity and resistance of Anopheles stephensi to infection with Escherichia coli. We used quantitative PCR to estimate the gene expression of three immune...

Separating planetary reflex Doppler shifts from stellar variability in the wavelength domain (code)

Andrew Collier Cameron, E. B. Ford, S. Shahaf & A. Mortier

Investigating the relationship between polarimetric radar signatures of hydrometeor size sorting and tornadic potential in simulated supercells

S. Loeffler, M.R. Kumjian, P. Markowski, B.E. Coffer & M.D. Parker
The national upgrade of the operational weather radar network to polarimetric capabilities has lead to numerous studies focusing on polarimetric radar signatures commonly observed in supercells. One such signature is the horizontal separation of regions of enhanced differential reflectivity (ZDR) and specific differential phase (KDP) values due to hydrometeor size sorting. Recent observational studies have shown that the orientation of this separation tends to be more perpendicular to storm motion in supercells that produce tornadoes....

Data from: Ancestral polyploidy in seed plants and angiosperms

Yuannian Jiao, Norman J. Wickett, Ayyampalayam Saravanaraj, André S. Chanderbali, Lena Landherr, Paula E. Ralph, Lynn P. Tomsho, Yi Hu, Haiying Liang, Pamela S. Sotis, Douglas E. Soltis, Sandra W. Clifton, Scott E. Schlarbaum, Stephan C. Schuster, Hong Ma, Jim Leebens-Mack & Claude W. DePamphilis
Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms1, 2, 3, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications4, 5, 6, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive...

Data from: Environmental and biological controls on the diversity and ecology of Late Cretaceous through early Paleogene marine ecosystems in the U.S. Gulf Coastal Plain

Jocelyn A. Sessa, Timothy J. Bralower, Mark E. Patzkowsky, John C. Handley & Linda C. Ivany
The late Mesozoic through early Cenozoic is an interval of significant biologic turnover and ecologic reorganization within marine assemblages, but the timing and causes of these changes remain poorly understood. Here, we quantify the pattern and timing of changes in the diversity (richness and evenness) and ecology of local (i.e., sample level) mollusk-dominated assemblages during this critical interval using field-collected and published datasets from the US Gulf Coastal Plain. We test whether the biologic and...

Data from: A connection between colony biomass and death in Caribbean reef-building corals

Daniel J. Thornhill, Randi D. Rotjan, Brian D. Todd, Geoff C. Chilcoat, Roberto Iglesias-Prieto, Todd C. LaJeunesse, Dustin W. Kemp, Jennifer McCabe Reynolds, Gregory W. Schmidt, Thomas Shannon, Mark E. Warner & William K. Fitt
Increased sea-surface temperatures linked to warming climate threaten coral reef ecosystems globally. To better understand how corals and their endosymbiotic dinoflagellates (Symbiodinium spp.) respond to environmental change, tissue biomass and Symbiodinium density of seven coral species were measured on various reefs approximately every four months for up to thirteen years in the Upper Florida Keys, United States (1994–2007), eleven years in the Exuma Cays, Bahamas (1995–2006), and four years in Puerto Morelos, Mexico (2003–2007). For...

Data from: Species delimitation of common reef corals in the genus Pocillopora using nucleotide sequence phylogenies, population genetics, and symbiosis ecology

Jorge H Pinzón & Todd C LaJeunesse
Stony corals in the genus Pocillopora are among the most common and widely distributed of Indo-Pacific corals and, as such, are often the subject of research. In the far Tropical Eastern Pacific (TEP), they are major constituents of shallow coral communities, exhibiting considerable variability in colony shape and branch morphology and marked differences in response to thermal stress. Numerous intermediates occur between morphospecies that may relate to extensive hybridization. The diversity of the Pocillopora genus...

Data from: Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)

Hervé Sauquet, Simon Y. W. Ho, Maria A. Gandolfo, Gregory J. Jordan, Peter Wilf, David J. Cantrill, Michael J. Bayly, Lindell Bromham, Gillian K. Brown, Raymond J. Carpenter, Daphne M. Lee, Daniel J. Murphy, J. M. Kale Sniderman & Frank Udovicic
Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen)....

Data from: Ecological effects on metabolic scaling amphipod responses to fish predators in freshwater springs

Douglas S. Glazier, Eric M. Butler, Sara A. Lombardi, Travis J. Deptola, Andrew J. Reese & Erin V. Satterthwaite
Metabolic rate is commonly thought to scale with body mass to the 3/4-power as a result of universal body-design constraints. However, recent comparative work has shown that the metabolic scaling slope may vary significantly among species and higher taxa, apparently in response to different lifestyles and ecological conditions, though the precise mechanisms involved are not well understood. To better understand these under-appreciated ecological effects and their causes, it is important to control for extraneous phylogenetic...

Data from: Genotypic diversity and spatial-temporal distribution of Symbiodinium clones in an abundant reef coral

Daniel T. Pettay, Jorge H. Pinzón, Drew C. Wham & Todd C. LaJeunesse
Genetic data are rapidly advancing our understanding of various biological systems including the ecology and evolution of coral-algal symbioses. The fine-scale interactions between individual genotypes of host and symbiont remain largely unstudied and constitute a major gap in knowledge. By applying microsatellite markers developed for both host and symbiont, we investigated the intra-colony diversity, prevalence and stability of Symbiodinium glynni (type D1) multilocus genotypes in association with dense populations of Pocillopora at two sites in...

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