Carbohydrate diet and reproductive performance of a fruit fly parasitoid, diachasmimorpha tryoni

Augmentative releases of parasitoid wasps are often used successfully for biological control of fruit flies in programs worldwide. The development of cheaper and more effective augmentative releases of the parasitoid wasp Diachasmimorpha tryoni (Cameron) (Hymenoptera: Braconidae) may allow its use to be expanded to cover Queensland fruit fly, Bactrocera tryoni (Froggatt) (Diptera: Tephritidae), a serious pest of many vegetables and most fruit production in Australia. This demands a fuller understanding of the parasitoid's reproductive biology. In this study, mating status, fecundity, and size of female D. tryoni were determined under laboratory conditions. A range of pre-release diets, 10% concentrations of honey, white sugar, and golden syrup, were also assessed in the laboratory. Mature egg loads and progeny yields of mated and unmated parasitoid females were statistically similar, demonstrating that mating status was not a determinant of parasitoid performance. Female lifespan was not negatively impacted by the act of oviposition, though larger females carried more eggs than smaller individuals, indicating a need to produce large females in mass-rearing facilities to maintain this trait. White sugar gave the highest adult female lifespan, while honey and golden syrup shared similar survivorship curves, all significantly greater compared with water control females. Pre-release feeding of D. tryoni, particularly with white sugar, may enhance the impact of released parasitoids on B. tryoni. These findings are important because honey is currently the standard diet for mass-reared braconids, but white sugar is less than one-third the cost of other foods; however further work is required to assess postrelease performance of the parasitoid

A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies

An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species

Protein profiling of the dimorphic, pathogenic fungus, Penicillium marneffei

<p>Abstract</p> <p>Background</p> <p><it>Penicillium marneffei </it>is a pathogenic fungus that afflicts immunocompromised individuals having lived or traveled in Southeast Asia. This species is unique in that it is the only dimorphic member of the genus. Dimorphism results from a process, termed phase transition, which is regulated by temperature of incubation. At room temperature, the fungus grows filamentously (mould phase), but at body temperature (37°C), a uninucleate yeast form develops that reproduces by fission. Formation of the yeast phase appears to be a requisite for pathogenicity. To date, no genes have been identified in <it>P. marneffei </it>that strictly induce mould-to-yeast phase conversion. In an effort to help identify potential gene products associated with morphogenesis, protein profiles were generated from the yeast and mould phases of <it>P. marneffei</it>.</p> <p>Results</p> <p>Whole cell proteins from the early stages of mould and yeast development in <it>P. marneffei </it>were resolved by two-dimensional gel electrophoresis. Selected proteins were recovered and sequenced by capillary-liquid chromatography-nanospray tandem mass spectrometry. Putative identifications were derived by searching available databases for homologous fungal sequences. Proteins found common to both mould and yeast phases included the signal transduction proteins cyclophilin and a RACK1-like ortholog, as well as those related to general metabolism, energy production, and protection from oxygen radicals. Many of the mould-specific proteins identified possessed similar functions. By comparison, proteins exhibiting increased expression during development of the parasitic yeast phase comprised those involved in heat-shock responses, general metabolism, and cell-wall biosynthesis, as well as a small GTPase that regulates nuclear membrane transport and mitotic processes in fungi. The cognate gene encoding the latter protein, designated <it>RanA</it>, was subsequently cloned and characterized. The <it>P. marneffei </it>RanA protein sequence, which contained the signature motif of Ran-GTPases, exhibited 90% homology to homologous <it>Aspergillus </it>proteins.</p> <p>Conclusion</p> <p>This study clearly demonstrates the utility of proteomic approaches to studying dimorphism in <it>P. marneffei</it>. Moreover, this strategy complements and extends current genetic methodologies directed towards understanding the molecular mechanisms of phase transition. Finally, the documented increased levels of RanA expression suggest that cellular development in this fungus involves additional signaling mechanisms than have been previously described in <it>P. marneffei</it>.</p

Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win–win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)

Developing Genomic Tools for the Management of Threatened Species

Despite a revolution in DNA sequencing and genotyping technologies in the past decade there still exists a deficit in genomic resources for many threatened species. As a result, these species are not always being managed as effectively as possible. Single nucleotide polymorphisms (SNPs) hold great promise for illuminating the genetic characteristics of mammalian populations and monitoring their genetic health. Unfortunately, many techniques for SNP discovery are still beyond the reach of conservation projects. This thesis describes two cost-effective techniques for identifying SNPs in non-model species - whole-genome genotyping using cross-species array data, and reduced representation sequencing using a universal primer resource. I have designed, implemented, and validated strategies that can be utilized for SNP discovery and genotyping in species with no existing genome resources. These tools will facilitate phylogenetics and high-throughput population genetics in non-model species at a reasonable price point. Practical improvements to the conservation genomics toolkit come at a crucial time, as the genetic management of small and vulnerable populations will play an increasingly important role into the future. The strategies outlined here are achievable in the framework of a conservation management project and will hopefully advance real-world outcomes for threatened species

Molecular characterisation of Interleukin-2 in two Australian marsupials (the tammar wallaby, Notamacropus eugenii, and the Tasmanian devil, Sarcophilus harrisii) facilitates the development of marsupial-specific immunological reagents

Interleukin-2 (IL-2) is an important regulator of cellular immunity in mammals. For many years, our inability to identify the expression of this cytokine in marsupials hindered our capacity to progress studies in metatherian immunology. Here, we report the use of molecular techniques to characterise the IL-2 gene for the tammar wallaby (Notamacropus eugenii) and the Tasmanian devil (Sarcophilus harrisii), which allowed the prediction of the structure and probable functions of the IL-2 proteins of these species. Deduced marsupial IL-2 proteins show considerable sequence identity to each other and to common brushtail possum (Trichosurus vulpecula) IL-2 (≥65%) but shared only 35% (tammar wallaby) and 32% (Tasmanian devil) identity with human IL-2. This difference means that reagents used to study IL-2 in human and other eutherians are unlikely to cross-react with marsupials. As a key step in furthering our ability to study cellular immune responses in marsupials and, more specifically, the susceptibility of macropodoid marsupials to intracellular pathogens, a polyclonal antibody was designed for the detection and future investigation of tammar wallaby IL-2 protein expression. The molecular data and polyclonal antibody described herein will support our development of gene probes and immunological reagents that will aid studies of infection and disease in marsupials

Data from: Applying SNP-derived molecular coancestry estimates to captive breeding programs

Captive breeding programs for wildlife species typically rely on pedigrees to inform genetic management. Although pedigree-based breeding strategies are quite effective at retaining long-term genetic variation, management of zoo-based breeding programs continues to be hampered when pedigrees are poorly known. The objective of this study was to evaluate two options for generating single nucleotide polymorphism (SNP) data to resolve unknown relationships within captive breeding programs. We generated SNP data for a zoo-based population of addax (Addax nasomasculatus) using both the Illumina BovineHD BeadChip and double digest restriction site-associated DNA (ddRAD) sequencing. Our results demonstrated that estimates of allele sharing (AS) between pairs of individuals exhibited low variances. Average AS variances were highest when using 50 loci (SNPchipall = 0.00159; ddRADall = 0.0249), but fell below 0.0003 for the SNP chip dataset when sampling ≥250 loci and below 0.0025 for the ddRAD dataset when sampling ≥500 loci. Furthermore, the correlation between the SNPchipall and ddRADall AS datasets was 0.88 (95%CI = 0.84 – 0.91) when subsampling 500 loci. Collectively, our results indicated that both SNP genotyping methods produced sufficient data for accurately estimating relationships, even within an extremely bottlenecked population. Our results also suggested that analytic assumptions historically integrated into the addax pedigree are not adversely impacting long-term pedigree-based management; kinships calculated from the analytic pedigree were significantly correlated (p >>0.001) with AS estimates. Overall, our conclusions are intended to serve as both a proof of concept and a model for applying molecular data to the genetic management of captive breeding programs