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Vairimorpha (formerly Nosema) apis and V. ceranae are microsporidian pathogens that are of concern for managed honey bee colonies. Multiple treatments have been proposed to be effective in reducing the prevalence and intensity of Vairimorpha spp. infections. Here, we test the efficacy of these products in one lab-based experiment and three field experiments. In the lab experiment, we found no reductions in Vairimorpha spp. prevalence (proportion of individuals infected with Vairimorpha spp.) or intensity (number of Vairimorpha spp. spores per individual), but we did find a decrease in honey bee survival after treatment with Fumagilin-B, Honey-B-Healthy®, and Nozevit Plus. The first field experiment showed increased Vairimorpha spp. intensity in colonies treated with Fumagilin-B and HiveAlive® compared to a negative control (sucrose syrup alone). The second field experiment showed a weak reduction in Vairimorpha spp. intensity after 3 weeks post treatment with Fumagilin-B compared to Nozevit. However, Vairimorpha spp. intensity returned to levels comparable to those of other treatment groups after 5 weeks post treatment and remained similar to those of other groups for the duration of the experiment. The final field trial showed no positive or negative effects of treatment with Fumagilin-B or Nosevit on Vairimorpha spp. prevalence or intensity. These findings raise questions regarding the efficacy of the products currently being used by beekeepers to control Vairimorpha spp. We argue that the observed reduction of Vairimorpha spp. is more likely relevant to the phenology of spore prevalence and intensity in honey bee colonies than to chemical treatment.

The Featured Creatures collection provides in-depth profiles of insects, nematodes, arachnids and other organisms relevant to Florida. These profiles are intended for the use of interested laypersons with some knowledge of biology as well as academic audiences. Apis nigrocincta Smith (1860) is a cavity-nesting honey bee native to the Philippines and Indonesia. The Florida Department of Agriculture and Consumer Services – Division of Plant Industry’s Apiary Inspection Section is actively screening for invasive honey bee species in an effort to eradicate unwanted pests. This bee is not currently considered a threat to Florida, but state researchers are actively screening honey bees of unknown origins using molecular markers to detect the presence of Apis nigrocincta.

Beekeepers need new registered products to control the small hive beetle (SHB), Aethina tumida, a significant pest of western honey bee (Apis mellifera) colonies. Few approved chemical controls exist, and there is no standardized system for screening compounds against SHBs. We outline a detailed method for an acute toxicity bioassay that delivers compounds via pollen. We provide a detailed method for a field trial that delivers treated pollen in traps made from modified compact disc cases. We applied both methods in proof-of-concept experiments to assess acetamiprid as a SHB control agent. Using the laboratory bioassay, we found acetamiprid (LC50 = 20.5 µg/g) to be more toxic to SHBs than coumaphos was (LC50 = 1250 µg/g), yet less toxic to SHBs than fipronil was (LC50 = 1.78 µg/g). In our field trial, colonies treated with acetamiprid and fipronil significantly reduced (p < 0.001) live SHB populations over those of control colonies. Traps containing acetamiprid retained significantly higher (p < 0.001) numbers of dead SHBs than did traps containing fipronil. We outline the first detailed methods to assess the toxicity of compounds delivered in pollen for adult SHB control. Our proof-of-concept experiments showed acetamiprid to be a promising control agent for SHBs.

The Featured Creatures collection provides in-depth profiles of insects, nematodes, arachnids and other organisms relevant to Florida. These profiles are intended for the use of interested laypersons with some knowledge of biology as well as academic audiences. Although the Himalayan giant honey bee Apis laboriosa Smith is the largest honey bee species in the world, it is also one of the least studied. It has a distribution mostly concentrated in the Hindu Kush Himalayan region of southern Asia.

Conservation management often uses information on genetic population structure to assess the importance of local provenancing for ecological restoration and reintroduction programs. For species that do not exhibit complete reproductive isolation, the estimation of population genetic parameters may be influenced by the extent of admixture. Therefore, to avoid perverse outcomes for conservation, genetically informed management strategies must determine whether hybridization between species is relevant, and the extent to which observed population genetic patterns are shaped by interspecific versus intraspecific gene flow. We used genotyping by sequencing to identify over 2,400 informative single nucleotide polymorphisms across 18 populations of Eucalyptus regnans F. Muell., a foundation tree species of montane forests in south‐eastern Australia. We used these data to determine the extent of hybridization with another species, Eucalyptus obliqua L'Hér., and investigate how admixture influences genetic diversity parameters, by estimating metrics of genetic diversity and examining population genetic structure in datasets with and without admixed individuals. We found hybrid individuals at all sites and two highly introgressed populations. Hybrid individuals were not distributed evenly across environmental gradients, with logistic regression identifying hybrids as being associated with temperature. Removal of hybrids resulted in increases in genetic differentiation (F ST), expected heterozygosity, observed heterozygosity and the inbreeding coefficient, and different patterns of isolation by distance. After removal of hybrids and introgressed populations, mountain ash showed very little population genetic structure, with a small effect of isolation by distance, and very low global F ST(0.03). Our study shows that, in plants, decisions around provenancing of individuals for restoration depend on knowledge of whether hybridization is influencing population genetic structure. For species in which most genetic variation is held within populations, there may be little benefit in planning conservation strategies around environmental adaptation of seed sources. The possibility for adaptive introgression may also be relevant when species regularly hybridize.

DNA methylation plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from Nanopore sequencing, their accuracy remains largely unknown. Here, we present a systematic benchmarking of tools for the detection of CpG methylation from Nanopore sequencing using individual reads, control mixtures of methylated and unmethylated reads, and bisulfite sequencing. We found that tools have a tradeoff between false positives and false negatives and present a high dispersion with respect to the expected methylation frequency values. We described various strategies to improve the accuracy of these tools, including a consensus approach, METEORE (https://github.com/comprna/METEORE), based on the combination of the predictions from two or more tools that shows improved accuracy over individual tools. Snakemake pipelines are also provided for reproducibility and to enable the systematic application of our analyses to other datasets., Several existing algorithms predict the methylation of DNA using Nanopore sequencing signals, but it is unclear how they compare in performance. Here, the authors benchmark the performance of several such tools, and propose METEORE, a consensus tool that improves prediction accuracy.

Chytridiomycosis, a disease caused by the emerging fungus Batrachochytrium dendrobatidis (Bd), has been implicated in the decline of over 500 amphibian species. Population declines could have important genetic consequences, including reduced genetic diversity. We contrasted genetic diversity among both long-Bd-exposed and unexposed populations of the south-east Australian alpine tree frog (Litoria verreauxii alpina) across its range. At the population level, we found no significant differences in genetic diversity between Bd-exposed and unexposed populations. Encouragingly, even Bd-infected remnant populations that are now highly isolated maintain genetic diversity comparable to populations in which Bd is absent. Spatial genetic structure among populations followed an isolation-by-distance pattern, suggesting restricted movement among remnant populations. At the individual level, greater heterozygosity was associated with reduced probability of infection. Loss of genetic diversity in remnant populations that survived chytridiomycosis epidemics does not appear to be a threat to L. v. alpina. We suggest several factors underpinning maintenance of genetic diversity: (1) remnant populations have remained large enough to avoid losses of genetic diversity; (2) many individuals in the population are able to breed once before succumbing to disease; and (3) juveniles in the terrestrial environment have low exposure to Bd, providing an annual ‘reservoir’ of genetic diversity. The association between individual heterozygosity and infection status suggests that, while other work has shown all breeding adults are typically killed by Bd, males with greater heterozygosity may survive longer and obtain fitness benefits through extended breeding opportunities. Our results highlight the critical role of life history in mitigating the impacts of Bd infection for some amphibian species, but we infer that increased isolation as a result of disease-induced population extirpations will enhance population differentiation and thus biogeographic structure.

Antarctica has long been considered biologically isolated1. Global warming will make parts of Antarctica more habitable for invasive taxa, yet presumed barriers to dispersal—especially the Southern Ocean’s strong, circumpolar winds, ocean currents and fronts—have been thought to protect the region from non-anthropogenic colonizations from the north1,2. We combine molecular and oceanographic tools to directly test for biological dispersal across the Southern Ocean. Genomic analyses reveal that rafting keystone kelps recently travelled >20,000 km and crossed several ocean-front ‘barriers’ to reach Antarctica from mid-latitude source populations. High-resolution ocean circulation models, incorporating both mesoscale eddies and wave-driven Stokes drift, indicate that such Antarctic incursions are remarkably frequent and rapid. Our results demonstrate that storm-forced surface waves and ocean eddies can dramatically enhance oceanographic connectivity for drift particles in surface layers, and show that Antarctica is not biologically isolated. We infer that Antarctica’s long-standing ecological differences have been the result of environmental extremes that have precluded the establishment of temperate-adapted taxa, but that such taxa nonetheless frequently disperse to the region. Global warming thus has the potential to allow the establishment of diverse new species—including keystone kelps that would drastically alter ecosystem dynamics—even without anthropogenic introductions. Genomic tools and ocean circulation models show that organisms surface-drift across the Southern Ocean frequently. The extreme cold therefore keeps Antarctica biologically isolated, but as the climate warms new species may establish quickly.

Barriers to dispersal can disrupt gene flow between populations, resulting in genetically distinct populations. Although many marine animals have potential for long-distance dispersal via a planktonic stage, gene flow among populations separated by large geographic distances is not always evident. Polychaetes are ecologically important and have been used as biological surrogates for marine biodiversity. Some polychaete species are used as bait for recreational fisheries, with this demand supporting commercial fisheries for polychaetes to service the retail bait market. However, despite their ecological and economic importance, very little is known about the life history or population dynamics of polychaetes, and few studies have used genetic or genomic approaches to understand polychaete population connectivity. Here, we investigate the population structure of one commonly collected beachworm species used for bait on the eastern coast of Australia, namely, Australonuphis teres, by using genome-wide single-nucleotide polymorphism data. We sampled A. teres from hierarchical nested spatial scales along 900km of the coast in New South Wales. We identified six genetic groups, but there was no clear geographic pattern of distribution. Our results suggest that there is considerable gene flow among the sampled populations. These high-resolution genomic data support the findings of previous studies, and we infer that oceanographic processes promote genetic exchange among polychaete populations in south-eastern Australia.

Although it has been clearly established that well-positioned histone H2A.Z-containing nucleosomes flank the nucleosome-depleted region (NDR) at the transcriptional start site (TSS) of active mammalian genes, how this chromatin-based information is transmitted through the cell cycle is unknown. We show here that in mouse trophoblast stem cells, the amount of histone H2A.Z at promoters decreased during S phase, coinciding with homotypic (H2A.Z-H2A.Z) nucleosomes flanking the TSS becoming heterotypic (H2A.Z-H2A). To our surprise these nucleosomes remained heterotypic at M phase. At the TSS, we identified an unstable heterotypic histone H2A.Z-containing nucleosome in G1 phase that was lost after DNA replication. These dynamic changes at the TSS mirror a global expansion of the NDR at S and M phases, which, unexpectedly, is unrelated to transcriptional activity. Coincident with the loss of histone H2A.Z at promoters, histone H2A.Z is targeted to the centromere when mitosis begins.

Background The advent of genotyping by Next Generation Sequencing has enabled rapid discovery of thousands of single nucleotide polymorphism (SNP) markers and high throughput genotyping of large populations at an affordable cost. Genotyping by sequencing (GBS), a reduced representation library sequencing method, allows highly multiplexed sequencing of genomic subsets. This method has limitations for small organisms with low amounts of genomic DNA, such as the bluetongue virus (BTV) vectors, Culicoides midges. Results This study employed the GBS method to isolate SNP markers de novo from whole genome amplified Culicoides brevitarsis genomic DNA. The individuals were collected from regions representing two different Australian patterns of BTV strain distribution: the Northern Territory (NT) and the east coast. We isolated 8145 SNPs using GBS. Phylogenetic analysis conducted using the filtered 3263 SNPs revealed the presence of a distinct C. brevitarsis sub-population in the NT and this was confirmed by analysis of mitochondrial DNA. Two loci showed a very strong signal for selection and were unique to the NT population. Bayesian analysis with STRUCTURE indicated a possible two-population cluster. Conclusions The results suggest that genotyping vectors with high density markers in combination with biological and environmental data is useful. However, more extensive sampling over a wider spatial and temporal range is needed. The presence of sub-structure in populations and loci under natural selection indicates the need for further investigation of the role of vectors in shaping the two Australian systems of BTV transmission. The described workflow is transferable to genotyping of small, non-model organisms, including arthropod vectors of pathogens of economic and medical importance. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3124-1) contains supplementary material, which is available to authorized users.

Background Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding receptors that trigger a highly effective defence response upon recognition of specific pathogen avirulence proteins. Identifying avirulence genes is crucial for understanding how virulence evolves in the field. Results To facilitate avirulence gene cloning in the flax rust fungus, Melampsora lini, we constructed a high-density genetic linkage map using single nucleotide polymorphisms detected in restriction site-associated DNA sequencing (RADseq) data. The map comprises 13,412 RADseq markers in 27 linkage groups that together span 5860 cM and contain 2756 recombination bins. The marker sequences were used to anchor 68.9 % of the M. lini genome assembly onto the genetic map. The map and anchored assembly were then used to: 1) show that M. lini has a high overall meiotic recombination rate, but recombination distribution is uneven and large coldspots exist; 2) show that substantial genome rearrangements have occurred in spontaneous loss-of-avirulence mutants; and 3) identify the AvrL2 and AvrM14 avirulence genes by map-based cloning. AvrM14 is a dual-specificity avirulence gene that encodes a predicted nudix hydrolase. AvrL2 is located in the region of the M. lini genome with the lowest recombination rate and encodes a small, highly-charged proline-rich protein. Conclusions The M. lini high-density linkage map has greatly advanced our understanding of virulence mechanisms in this pathogen by providing novel insights into genome variability and enabling identification of two new avirulence genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3011-9) contains supplementary material, which is available to authorized users.

In this study, application of a dual absorbance/fluorescence assay to a chemical library screen identified several previously unknown inhibitors of mycobacteria. In addition, growth conditions had a significant effect on the activity profile of the library. Some inhibitors such as Se-methylselenocysteine were detected only when screening was performed under nutrient-limited culture conditions as opposed to nutrient-rich culture conditions. We propose that multiple culture condition library screening is required for complete inhibitory profiling and for maximal antimycobacterial compound detection.

Summary • Animals often use colours to hide from predators (crypsis) or advertise defences (aposematism), but there is little evidence for colour-based defence in plants.  Here, we test whether ontogenetic changes in leaf colour of lancewood (Pseudopanax crassifolius) may have been part of a defensive strategy against flightless browsing birds called moa, which were once the only large herbivores in New Zealand. We tested this hypothesis by conducting spectrographic measurements on differentsized plants grown in a common garden. We also compared these results with observations on a closely related, derived species that evolved in the absence of moa on the Chatham Islands.  Spectrographic analyses showed that birds would have difficulty distinguishing seedling leaves against a background of leaf litter. Conversely, brightly coloured tissues flanking spines on sapling leaves are highly conspicuous to birds. Once above the reach of the tallest known moa, adults produce leaves that are typical in appearance to adult leaves. The Chatham Island species lacks ontogenetic colour changes entirely.  Overall, the results indicate that P. crassifolius goes through a remarkable series of colour changes during development, from cryptically coloured seedlings to aposematically coloured saplings, which may have formed a defensive strategy to protect against giant browsing birds.

Thirty genes composed of cytokines, chemokines, granzymes, perforin and integrins were evaluated in gut and splenic K(d)Gag197-205-specific single CD8(+) T cells using Fluidigm 48.48 Dynamic arrays, with the aim of identifying biomarkers to predict effective mucosal and systemic vaccine efficacy. The mRNA expression profiles were analyzed in three ways: (i) the "number" of K(d)Gag197-205-specific CD8(+) T cells expressing the biomarker, (ii) "level" of mRNA expression using principal component analysis (PCA) and (iii) poly-functionality in relation to RANTES expression. In total, 21 genes were found to be differentially expressed between the vaccine groups and the immune compartments tested. Overall, the PCA indicated that IL-13Rα2 or IL-4R antagonist adjuvanted vaccines that previously induced high-avidity mucosal/systemic CD8(+) T cells with better protective efficacy, the "level" of mRNA expression, specifically RANTES, MIP-1β, and integrin α4 in gut K(d)Gag197-205-specific single CD8(+) T cells, were significantly elevated compared to unadjuvanted vaccine. Furthermore, significantly elevated granzymes/perforin levels were detected in IL-13(-/-) mice given the unadjuvanted vaccine, indicating that the degree of IL-13 inhibition (total, transient or no inhibition) can considerably alter the level of T-cell activity/poly-functionality. When splenic- and gut-K(d)Gag197-205-specific CD8(+) T cells were compared, PC1 vs. PC2 scores revealed that not only RANTES, MIP-1β, and integrin α4 mRNA, but also perforin, granzymes A/B, and integrins β1 and β2 mRNA were elevated in spleen. Collectively, data suggest that RANTES, MIP-1β, perforin, and integrins α4, β1 and β7 mRNA in single HIV-specific CD8(+) T cells could be used as a measure of effective mucosal and systemic vaccine efficacy.

Nosema are single-celled fungal parasites that infect various animal hosts. One species, Nosema ceranae, has become the dominant microsporidian infection in western honey bee colonies. When honey bees ingest Nosema spores, many eventually starve to death because the spores replicate in the stomach and hijack the bee’s nutrition. The risk of Nosema infection can be particularly unsettling to beekeepers because colonies often do not show signs of infection until the colony is severely diminished. This 5-page fact sheet explains how to diagnose and quantify Nosema infection in a honey bee colony. Written by Ashley N. Mortensen, Cameron J. Jack, Meghan McConnell, Liana Teigen, and Jamie Ellis, and published by the Department of Entomology and Nematology, May 2016. ENY-167/IN1123: How to Quantify Nosema Spores Infection Rate in a Honey Bee Colony (ufl.edu)

We developed a procedure for automated confocal microscopy to image the effect of the non-essential yeast gene deletion set on the localisation of the plasma membrane GFP-labelled protein Mrh1p-GFP. To achieve this it was necessary to devise an expression system expressing Redstar2 RFP-fluorescence specifically in the nucleus, mCherry RFP at a lower intensity in the cytoplasm and Mrh1p-GFP in the plasma membrane. This fluorescence labelling scheme utilising specifically designed image analysis scripts allowed automated segmentation of the cells into sub-regions comprising nuclei, cytoplasm and cell-surface. From this high-throughput high content screening approach we were able to determine that gene deletions including emc1Δ, emc2Δ, emc3Δ, emc4Δ, emc5Δ and emc6Δ, caused intracellular mislocalisation at the ER of a plasma membrane protein Mrh1p-GFP. CPY processing patterns were unaffected in these mutants and collectively our data suggest a transport role for the EMC genes within the early secretory pathway. HAC1 is central to the unfolded protein response (UPR) and in its absence, i.e. the absence of UPR, emc1Δ-, emc3Δ-, emc4Δ-, emc5Δ–hac1Δ double mutants were specifically hypersensitive to ER-stress (tunicamycin) lending credence to the usefulness of the high content microscope screening for discovery of functional effects of single mutants.

Recently, we presented a new method of pooling/resampling genome-wide association study (prGWAS) that uncovered new and known loci associated to Alzheimer’s disease. In here, we contrast this method with the Welcome Trust Case Control Consortium (WTCCC) data, a well-known GWAS on seven human complex diseases. Our results suggest that prGWAS can be considered an efficient, specific, and accurate alternative to the conventional GWAS approach at a fraction of the genotyping cost, and provide insights into other potential applications such as next generation sequencing.