Genetic diversity and relatedness in aquaculture and marina populations of the invasive tunicate Didemnum vexillum in the British Isles

Introductions of invasive, non-native species in the marine environment are increasing as human activity within coastal areas rises. Genetic datasets are useful tools to identify source populations, track routes of invasions, and illuminate the role of genetic variation in the establishment and subsequent spread of novel introductions. Here, a microsatellite dataset is used to estimate the genetic diversity and population structure of 7 introduced Didemnum vexillum populations in Britain and Ireland, 4 of which are associated with aquaculture and 3 with marinas. Genetic differentiation observed between these populations indicates human-mediated transport as the main mechanism underlying the population structure of D. vexillum in Britain and Ireland. In addition to elucidating patterns of population structure we found that aquaculture sites showed significantly higher genetic diversity (measured as allelic richness) in comparison to the marina sites. We discuss these findings in relation to the history of each invasion, the complex life history of D. vexillum, and available evidence of the relative invasiveness of these populations. Our results show numerous interesting patterns which highlight further research avenues to elucidate the complex factors underlying the global spread of this successful invader.

Lysine Acetyltransferase p300/CBP Plays an Important Role in Reproduction, Embryogenesis and Longevity of the Pea Aphid Acyrthosiphon pisum

CREB-binding protein (p300/CBP) is a universal transcriptional co-regulator with lysine acetyltransferase activity. Drosophila melanogaster p300/CBP is a well-known regulator of embryogenesis, and recent studies in beetles and cockroaches have revealed the importance of this protein during post-embryonic development and endocrine signaling. In pest insects, p300/CBP may therefore offer a useful target for control methods based on RNA interference (RNAi). We investigated the role of p300/CBP in the pea aphid (Acyrthosiphon pisum), a notorious pest insect used as a laboratory model for the analysis of complex life-history traits. The RNAi-based attenuation of A. pisum p300/CBP significantly reduced the aphid lifespan and number of offspring, as well as shortening the reproductive phase, suggesting the manipulation of this gene contributes to accelerated senescence. Furthermore, injection of p300/CBP dsRNA also reduced the number of viable offspring and increased the number of premature nymphs, which developed in abnormally structured ovaries. Our data confirm the evolutionarily conserved function of p300/CBP during insect embryogenesis and show that the protein has a critical effect on longevity, reproduction and development in A. pisum. The potent effect of p300/CBP silencing indicates that this regulatory protein is an ideal target for RNAi-based aphid control.

Pelagic occurrences of the ice amphipod Apherusa glacialis throughout the Arctic

Apherusa glacialis is a common, sea ice-associated amphipod found throughout the Arctic Ocean and has long been considered permanently associated with the sea ice habitat. However, pelagic occurrences of A. glacialis have also been reported. It was recently suggested that A. glacialis overwinters at depth within the Atlantic-water inflow near Svalbard, to avoid being exported out of the Arctic Ocean through the Fram Strait. This study collated pelagic occurrence records over a 71-year period and found that A. glacialis was consistently found away from its presumed sea ice habitat on a pan-Arctic scale, in different depths and water masses. In the Svalbard region, A. glacialis was found in Atlantic Water both in winter and summer. Additionally, we analyzed A. glacialis size distributions throughout the year, collected mostly from sea ice, in order to elucidate potential life cycle strategies. The majority of young-of-the-year A. glacialis was found in the sea ice habitat during spring, supporting previous findings. Data on size distributions and sex ratios suggest a semelparous lifestyle. A synchronous seasonal vertical migration was not evident, but our data imply a more complex life history than previously assumed. We provide evidence that A. glacialis can no longer be regarded as an autochthonous sympagic species.

Draft Assembly of Phytophthora capsici from Long-Read Sequencing Uncovers Complexity

Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as hosts and fungicides, yet assembling these genomes remains challenging and expensive. Phytophthora capsici is an important, globally distributed plant pathogen that exhibits widespread fungicide resistance and a broad host range. As with other pathogenic oomycetes, P. capsici has a complex life history and a complex genome. Here, we leverage Oxford Nanopore Technologies and existing short-read resources to rapidly generate a low-cost, improved assembly. We generated 10 Gbp from a single MinION flow cell resulting in >1.25 million reads with an N50 of 13 kb. The resulting assembly is 95.2 Mbp in 424 scaffolds with an N50 length of 313 kb. This assembly is approximately 30 Mbp bigger than the current reference genome of 64 Mbp. We confirmed this larger genome size using flow cytometry, with an estimated size of 110 Mbp. BUSCO analysis identified 97.4% complete orthologs (19.2% duplicated). Evolutionary analysis supports a recent whole-genome duplication in this group. Our work provides a blueprint for rapidly integrating benchtop long-read sequencing with existing short-read data, to dramatically improve assembly quality and integrity of complex genomes and offer novel insights into pathogen genome function and evolution.

The illness-death model for family studies

Summary Family studies involve the selection of affected individuals from a disease registry who provide right-truncated ages of disease onset. Coarsened disease histories are then obtained from consenting family members, either through examining medical records, retrospective reporting, or clinical examination. Methods for dealing with such biased sampling schemes are available for continuous, binary, and failure time responses, but methods for more complex life history processes are less developed. We consider a simple joint model for clustered illness-death processes which we formulate to study covariate effects on the marginal intensity for disease onset and to study the within-family dependence in disease onset times. We construct likelihoods and composite likelihoods for family data obtained from biased sampling schemes. In settings where the disease is rare and data are insufficient to fit the model of interest, we show how auxiliary data can augment the composite likelihood to facilitate estimation. We apply the proposed methods to analyze data from a family study of psoriatic arthritis carried out at the University of Toronto Psoriatic Arthritis Registry.

Using an individual-based model to simulate the Gulf of Maine American lobster (Homarus americanus) fishery and evaluate the robustness of current management regulations

Individual-based models (IBMs) can capture complex processes with a flexible probabilistic approach, which makes them useful for studying organisms with complex life history and fishery processes such as the American lobster (Homarus americanus). This research aims to modify and parameterize an individual-based lobster simulator (IBLS) to simulate the American lobster fishery in the Gulf of Maine. To simulate the fishery, the IBLS was tuned to match the seasonal catch and size composition from the 2015 American lobster stock assessment by adjusting the values of coefficients for select parameters. With appropriate coefficients for the initial abundance, recruitment, and seasonal encounter probability levels, the tuned IBLS accurately simulated the historical landings. Given the uncertainty in future American lobster recruitment, the tuned IBLS was then used to evaluate the effectiveness of current management regulations under different levels of recruitment.