Unveiling Crucivirus Diversity by Mining Metagenomic Data.

The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through assembly and mining of metagenomic data.

Flying south: Foraging locations of the Hutton's shearwater () revealed by Time-Depth Recorders and GPS tracking.

The Hutton's shearwater is an endangered seabird endemic to Kaikōura, New Zealand, but the spatial and temporal aspects of its at-sea foraging behavior are not well known.To identify foraging areas and estimate trip durations, we deployed Global Positioning Systems (GPS) devices and Time-Depth Recorders (TDR) on 26 adult Hutton's shearwaters during the chick-rearing period in 2017 and 2018.We found Hutton's shearwaters traveled much further from their breeding grounds at Kaikōura than previously considered, with most individuals foraging in coastal and oceanic areas 125-365 km south and near Banks Peninsula.

Chimerism and population dieback alter genetic inference related to invasion pathways and connectivity of biofouling populations on artificial substrata.

Disentangling pathways by which nonindigenous species expand and spread regionally remains challenging. Molecular ecology tools are often employed to determine the origins and spread of introduced species, but the complexities of some organisms may be reducing the efficacy of these tools. Some colonial species exhibit complexities by way of chimerism and winter colony regression, which may alter the genetic diversity of populations and mask the connectivity occurring among them.

Effects of waterborne cadmium on energy metabolism in the tropical sea cucumber, Stichopus horrens, and a comparison of tissue-specific cadmium accumulation with the temperate sea cucumber Australostichopus mollis.

The sea cucumber Stichopus horrens is an important component of near-shore ecosystems, and in the Kingdom of Tonga it also comprises an important commercial and subsistence fishery. To assess the sensitivity of this species to the toxic trace metal cadmium (Cd), adult S. horrens were exposed for 96h to an environmental (15µgL) or effect (765µgL) concentration of waterborne Cd.

Evolutionary history of ssDNA bacilladnaviruses features horizontal acquisition of the capsid gene from ssRNA nodaviruses.

Bacilladnaviruses have single-stranded (ss) DNA genomes and infect diatoms, a major group of unicellular algae widespread in aquatic habitats. Despite their ecological importance, the provenance and relationships of bacilladnaviruses to other eukaryotic viruses remain unclear. Accordingly, they are currently classified into the 'floating' genus Bacilladnavirus.

Factors influencing the en route survivorship and post-voyage growth of a common ship biofouling organism, Bugula neritina.

The likelihood that viable non-indigenous biofouling species will survive a voyage on a vessel is influenced by a range of factors, including the speed, duration, and route of the voyage and the amount of time the vessel spends in port. In this study, a land-based dynamic flow device was used to test the effect of recruit age, vessel speed and voyage duration on the survivorship and growth of the bryozoan Bugula neritina. In the experiment, one-week-old recruits had a higher likelihood (100%) of surviving voyages than older (one-month-old, 90%) or younger (one-day-old, 79%) recruits, but survival was not influenced by vessel speed (6 and 18 knots) or voyage duration (two and eight days).

Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management.

In this experimental study the patterns in early marine biofouling communities and possible implications for surveillance and environmental management were explored using metabarcoding, viz. 18S ribosomal RNA gene barcoding in combination with high-throughput sequencing. The community structure of eukaryotic assemblages and the patterns of initial succession were assessed from settlement plates deployed in a busy port for one, five and 15 days.

Phylogenetic affinities of the Fregetta storm-petrels are not black and white.

The Fregetta storm-petrels generally are regarded to comprise two species: black-bellied storm-petrels F. tropica (monotypic) breed at Antarctic and sub-Antarctic islands (46-63°S), and white-bellied storm-petrels F. grallaria breed at south temperate islands (28-37°S), with four recognized subspecies.

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

Background: There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously.

Results: Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population.

Diverse small circular DNA viruses circulating amongst estuarine molluscs.

Our understanding of the diversity and abundance of circular replication associated protein (Rep) - encoding single stranded (CRESS) DNA viruses has increased considerably over the last few years due to a combination of modern sequencing technologies and new molecular tools. Studies have used these to identify and recover CRESS DNA viruses from a range of different marine organisms, including copepods, shrimp and molluscs. In our study we identified 79 novel CRESS DNA viruses from three mollusc species (Austrovenus stutchburyi, Paphies subtriangulata and Amphibola crenata) and benthic sediments from the Avon-Heathcote estuary in Christchurch, New Zealand.

Using temporal sampling to improve attribution of source populations for invasive species.

Numerous studies have applied genetic tools to the identification of source populations and transport pathways for invasive species. However, there are many gaps in the knowledge obtained from such studies because comprehensive and meaningful spatial sampling to meet these goals is difficult to achieve. Sampling populations as they arrive at the border should fill the gaps in source population identification, but such an advance has not yet been achieved with genetic data.

Identification of Starling Circovirus in an Estuarine Mollusc (Amphibola crenata) in New Zealand Using Metagenomic Approaches.

Two complete genomes of starling circovirus (StCV) were recovered from Amphibola crenata, an estuarine New Zealand mollusc. This is the first report of StCV outside Europe. The viral genomes were recovered from rolling circle-amplified enriched circular DNA followed by back-to-back primers and specific primer PCR amplification.

Novel ssDNA virus recovered from estuarine Mollusc (Amphibola crenata) whose replication associated protein (Rep) shares similarities with Rep-like sequences of bacterial origin.

Over the past couple of years highly diverse novel ssDNA viruses have been discovered. Here, we present the first ssDNA virus, Gastropod-associated circular ssDNA virus (GaCSV), recovered from a mollusc Amphibola crenata Martyn 1784, which is a deposit feeder that grazes micro-organisms and organic detritus on the surface of tidal mudflats. The GaCSV (2351 nt) genome contains two large bidirectionally transcribed ORFs.

When rediscovery is not enough: taxonomic uncertainty hinders conservation of a critically endangered bird.

In 2003, birds similar to the extinct New Zealand storm-petrel Oceanites maorianus were observed in Hauraki Gulf NZ, raising the possibility of rediscovery after 150 years. O. maorianus has and continues to be surrounded by taxonomic uncertainty, being variously described as a distinct genus, a distinct species, or merely a plumage variant.

Global phylogeography of the widely introduced North West Pacific ascidian Styela clava.

The solitary ascidian Styela clava Herdman, 1882 is considered to be native to Japan, Korea, northern China and the Russian Federation in the NW Pacific, but it has spread globally over the last 80 years and is now established as an introduced species on the east and west coasts of North America, Europe, Australia and New Zealand. In eastern Canada it reaches sufficient density to be a serious pest to aquaculture concerns. We sequenced a fragment of the cytochrome oxidase subunit I mitochondrial gene (COI) from a total of 554 individuals to examine the genetic relationships of 20 S.

Comparative phylogeography of coastal limpets across a marine disjunction in New Zealand.

Cook Strait, which separates the North and South Island of New Zealand, has been a transient, but re-occurring feature of the New Zealand land mass throughout the Pleistocene, maintaining its current width and depth for the past 5000 years. Historic land fragmentation coupled with the complex hydrography of the Greater Cook Strait region has created both biogeographic and phylogeographic disjunctions between the North and South Island in several marine species. Here we use mitochondrial cytochrome b DNA sequences of three endemic intertidal limpets, Cellana ornata, Cellana radians and Cellana flava to assess intraspecific phylogeographic patterns across Cook Strait and to look for interspecific concordance of ecological and evolutionary processes among closely related taxa.