Sharyn J. Goldstien

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. We sequenced 328–359 bp in 85–321 individuals from 8–31 populations spanning the biogeographic range of the three species. Intraspecific phylogeographic analyses show moderate to strong genetic discontinuity among North and South Island populations due to allopatric fragmentation. This pattern was broadly concordant across the three species and the observed divergence among this group of intertidal limpets (0.3–2.0%) is similar to that of previously studied subtidal organisms. For each species, divergence time calculations suggest contemporary North and South Island lineages diverged from their respective most recent common ancestor approximately 200 000 to 300 000 years before present (bp), significantly earlier than previous estimates in other coastal marine taxa that arose from a miscalculation of divergence time.

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. clava populations sampled throughout the introduced and native ranges, in order to investigate invasive population characteristics. The data presented here show a moderate level of genetic diversity throughout the northern hemisphere. The southern hemisphere (particularly New Zealand) displays a greater amount of haplotype and nucleotide diversity in comparison. This species, like many other invasive species, shows a range of genetic diversities among introduced populations independent of the age of incursion. The successful establishment of this species appears to be associated with multiple incursions in many locations, while other locations appear to have experienced rapid expansion from a potentially small population with reduced genetic diversity. These contrasting patterns create difficulties when attempting to manage and mitigate a species that continues to spread among ports and marinas around the world.

Regional connectivity and coastal expansion: differentiating pre-border and post-border vectors for the invasive tunicate Styela clava

The dramatic increase in marine bio‐invasions, particularly of non‐indigenous ascidians, has highlighted the vulnerability of marine ecosystems and the productive sectors that rely on them. A critical issue in managing invasive species is determining the relative roles of ongoing introductions, versus the local movement of propagules from established source populations. Styela clava (Herdman, 1882), the Asian clubbed tunicate, once restricted to the Pacific shores of Asia and Russia, is now abundant throughout the northern and southern hemispheres and has had significant economic impact in at least one site of incursion. In 2005 S. clava was identified in New Zealand. The recent introduction of this species, coupled with its restricted distribution, provided an ideal model to compare and contrast the introduction and expansion process. In this study, the mitochondrial DNA cytochrome oxidase subunit I gene (COI) gene and 11 microsatellite markers were used to test the regional genetic structure and diversity of 318 S. clava individuals from 10 populations within New Zealand. Both markers showed significant differentiation between the northern and southern populations, indicative of minimal pre‐ or post‐border connectivity. Additional statistics further support pre‐ and post‐border differentiation among Port and Harbour populations (i.e. marinas and aquaculture farms). We conclude that New Zealand receives multiple introductions, and that the primary vector for pre‐border incursions and post‐border spread is most likely the extensive influx of recreational vessels that enter northern marinas independent of the Port. This is a timely reminder of the potential for hull‐fouling organisms to expand their range as climates change and open new pathways.

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. The genomes recovered have varying genome architectures, with all encoding at least two major ORFs that have either unidirectional or bidirectional organisation. Analysis of the Reps of the viral genomes showed they are all highly diverse, with only one Rep sequence sharing 65% amino acid identity with the Rep of gastropod-associated circular DNA virus (GaCSV). Our study adds significantly to the wealth of CRESS DNA viruses recovered from freshwater and marine environments and extends our knowledge of the distribution of these viruses.

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

Abstract 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. The metabarcoding results were verified with traditional morphological identification of taxa from selected experimental plates. Metabarcoding analysis identified > 400 taxa at a comparatively low taxonomic level and morphological analysis resulted in the detection of 25 taxa at varying levels of resolution. Despite the differences in resolution, data from both methods were consistent at high taxonomic levels and similar patterns in community shifts were observed. A high percentage of sequences belonging to genera known to contain non-indigenous species (NIS) were detected after exposure for only one day.

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. The smaller ORF (874 nt) has similarities to viral replication-associated protein (Rep) sequences of some bacteria and circoviruses, whereas the larger ORF (955 nt) does not relate to any sequences in public databases and we presume it potentially encodes the capsid protein. Phylogenetic analysis shows that the GaCSV Rep clusters with Rep-like sequences of bacterial origin, highlighting the role of ssDNA viruses in horizontal gene transfer. The occurrence of previously unknown viruses in organisms associated with human pollution is a relatively unexplored field.

Phylogeography of the New Zealand blue duck (Hymenolaimus malacorhynchos): implications for translocation and species recovery

Translocation of individuals among extant populations is an important tool in species conservation that allows managers to supplement dwindling populations and potentially alleviate the deleterious effects of inbreeding. Ideal translocation strategy should consider historical relationships among existing populations to avoid potential disruption of population subdivision and local adaptation. Here, we examine mitochondrial sequence variation in the endangered blue duck Hymenolaimus malacorhynchos, a New Zealand endemic riverine specialist, to facilitate informed decision making in future translocations. Behavioural observations suggest that blue duck dispersal is limited and may result in genetic structure within and between regional populations. We analysed 894 base pairs of mitochondrial control region in 78 adult blue ducks sampled from 11 river catchments across the species’ range (representing four regions in the North Island and three regions in the South Island) and found strong and significant genetic structure both within and among islands. These results, combined with a 2.0% sequence divergence between islands, indicates that North Island and South Island blue ducks should be treated as separate management units. The relationship between genetic differentiation and geographic distance for blue ducks on the South Island conformed to an “isolation by distance” pattern. Overall, we recommend that translocations of blue ducks should not be made between the North and the South Islands and those within each island should be restricted to neighbouring catchments.

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

BackgroundThere has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously.ResultsHybrid-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. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the FST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes.ConclusionsHybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

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. This uncertainty has hindered conservation planning and funding for the species. Here we examine the taxonomic identity of the rediscovered birds and museum specimens using phylogenetic analysis of mitochondrial (1143 bp cytochrome b) and nuclear (890 bp β-fibrinogen) genes. Using cytochrome b sequence amplified from the 150+ year old specimens, we found that the extant and museum O. maorianus were the same taxon (0.01 genetic distance), with both differing from all other storm-petrel taxa. Using both genes, we examined the phylogenetic affinities of O. maorianus to the Oceanitinae and Hydrobatinae storm-petrels finding that O. maorianus was more closely aligned to Fregetta (0.08-0.09) than Oceanites (0.11-0.12), thereby confirming its status as a distinct taxon, not a plumage variant of O. oceanicus. Our analysis verifies that the previously presumed extinct New Zealand storm-petrel has been rediscovered and can now be assigned a conservation priority commensurate with its critically endangered status.

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

ABSTRACT 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.