Placing the Fijian Honeyeaters within the meliphagid radiation: implications for origins and conservation

Understanding the evolutionary relationships of threatened species provides an important framework for making decisions about their conservation. However, unrecognised problems with the underlying phylogenetic analyses may bias the decision-making process. Recent phylogenetic studies have improved our understanding of Meliphagidae, but also indicate discordance between molecular datasets. Here, we examine the causes of this discordance using maximum likelihood tree-building and network analyses of identically sampled datasets for four genetic loci. Our results suggest that while we can be reasonably confident of relationships within species groups, discordance within and between molecular datasets tends to obscure relationships towards the base of the meliphagid tree. This ongoing uncertainty likely reflects differences in the sampling of markers and taxa between previously published analyses. To avoid the problems of conflicting data we used divergence time analyses of only the most densely sampled marker, NADH-ubiquinone oxidoreductase chain 2, to investigate the age and origins of the Fijian Meliphagidae. Our analyses suggest two temporally distinct colonisations of the Fijian archipelago. The large-bodied honeyeaters arrived ,15.6 million years ago, subsequently diversifying and spreading to Tonga and Samoa. In contrast, Myzomela appears to have arrived within the last 5.0 million years. The phylogenetic results therefore imply that conserving the evolutionary diversity of Meliphagidae in Polynesia requires that effort be spread across both the currently recognised taxa and geographical range

Genetic fingerprinting of Fijian kava

DNA analysis of 15 kava cultivars with 20 primer pairs showed no observable difference in the fingerprint pattern. This indicates that while the Fijian kava cultivars have morphological differences, genetically they are very similar. Similar results have been obtained with Hawaiian kava cultivars. This result indicates that when studying diseases such as the dieback disease in kava, a focus on environmental factors may be needed as controlling factors of the diseases

Evidence for the presence of a second species of mongoose in the Fiji Islands

The small Indian Mongoose Herpestes javanicus was introduced in the late nineteenth century into Fiji and is now found throughout the two main islands of Fiji (Viti Levu and Vanua Levu) and on another 11 small outer islands. When trapping mongoose as part of an investigation into the spread of leptospirosis around Suva, six large red-coloured mongoose were also captured. The body measurements (weight, length and hind-foot size) of these red-coloured mongoose were significantly larger than a random sample of the grey-coloured mongoose H. javanicus normally seen. To clarify whether the red-coloured mongoose was a different species or just a different colour morph of H. javanicus, mitochondrial cytochrome B cytb DNA sequences were determined from muscle tissue of four red-coloured individuals. Phylogenetic analyses using cytb sequences show that while the red-coloured mongoose belongs to an Asian clade, it is not H. javanicus or H. edwardsi. Further research is needed to determine the identity and origin of the red-coloured mongoose and to ascertain its prevalence in Fiji

Metagenome profiling identifies potential biocontrol agents for Selaginella kraussiana in New Zealand

Metagenomics can be used to identify potential biocontrol agents for invasive species and was used here to identify candidate species for biocontrol of an invasive club moss in New Zealand. Profiles were obtained for Selaginella kraussiana collected from nine geographically disjunct locations in Northern New Zealand. These profiles were distinct from those obtained for the exotic club moss Selaginella moellendorffii and the native club mosses Lycopodium deuterodensum and Lycopodium volubile also collected in Northern New Zealand. Fungi and bacteria implicated elsewhere in causing plant disease were identified on plants of Selaginella that exhibited signs of necrosis. Most notably, high densities of sequence reads from Xanthomonas translucens and Pseudomonas syringae were associated with some populations of Selaginella but not Lycopodium. Since these bacteria are already in use as biocontrol agents elsewhere, further investigation into their potential as biocontrol of Selaginella in New Zealand is suggested

Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes

The phylogenetic branching order of the green algal groups that gave rise to land plants remains uncertain despite its fundamental importance to understanding plant evolution. Previous studies have demonstrated that land plants evolved from streptophyte algae, but different lineages of streptophytes have been suggested to be the sister group of land plants. To better understand the evolutionary history of land plants and to determine the potential effects of "long-branch attraction" in phylogenetic reconstruction, we analyzed a chloroplast genome data set including three new chloroplast genomes from streptophyte algae: Coleochaetae orbicularis (Coleochaetales), Nitella hookeri (Charales), and Spirogyra communis (Zygnematales). We further applied a site pattern sorting method together with site- and time-heterogeneous models to investigate the branching order among streptophytes and land plants. Our chloroplast phylogenomic analyses support previous hypotheses based on nuclear data in placing Zygnematales alone, or a clade consisting of Coleochaetales plus Zygnematales, as the closest living relatives of land plants

Environmental bio-monitoring with high-throughput sequencing

There is much interest in using high-throughput DNA sequencing methodology to monitor microorganisms, complex plant and animal communities. However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects. Many of these issues have been highlighted by recent microbial studies. Understanding how high-throughput sequencing is best implemented is important for the interpretation of recent results and the success of future applications. Addressing complex biological questions with metagenomics requires the interaction of researchers who bring different skill sets to problem solving. Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving. Educators are in a position to help students, teachers, the public and policy makers interpret the new knowledge that metagenomics brings. To do this, they need to understand, not only the excitement of the science but also the pitfalls and shortcomings of methodology and research designs. We review these issues and some of the research directions that are helping to move the field forward

The evolutionary root of flowering plants

Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse taxon sampling among basal angiosperms. Here, we provide further evidence for concern over substitution model misspecification in analyses of chloroplast DNA sequences. We show that support for Amborella as the sole representative of the most basal angiosperm lineage is founded on sequence site patterns poorly described by time-reversible substitution models. Improving the fit between sequence data and substitution model identifies Trithuria, Nymphaeaceae, and Amborella as surviving relatives of the most basal lineage of flowering plants. This finding indicates that aquatic and herbaceous species dominate the earliest extant lineage of flowering plants

Detection and diversity of pathogenic Vibrio from Fiji

Here we investigate the diversity of pathogenic Vibrio species in marine environments close to Suva, Fiji. We use four distinct yet complementary analyses 13 biochemical testing, phylogenetic analyses, metagenomic analyses and molecular typing 13 to provide some preliminary insights into the diversity of vibrios in this region. Taken together our analyses confirmed the presence of nine Vibrio species, including three of the most important disease-causing vibrios (i.e. V. cholerae, V. parahaemolyticus and V. vulnificus), in Fijian marine environments. Furthermore, since toxigenic V. parahaemolyticus are present on fish for consumption we suggest these bacteria represent a potential public health risk. Our results from Illumina short read sequencing are encouraging in the context of microbial profiling and biomonitoring. They suggest this approach may offer an efficient and costeffective method for studying the dynamics of microbial diversity in marine environments over time