Complete mitochondrial genome of the stoat (Mustela erminea) and New Zealand fur seal (Arctocephalus forsteri) and their significance for mammalian phylogeny

The complete mitochondrial genome of three mustelid species, stoats (Mustela erminea), weasels (Mustela nivalis) and ferrets (Mustela furo), and the New Zealand fur seal (Arctocephalus forsteri) were sequenced using direct mitochondrial DNA extraction and overlapping long PCRs. The usual 37 mammalian mitochondrial genes (13 protein coding genes, 22 t-RNA and 2 r-RNA) were identified in all four mitogenomes. The divergence of stoats from other members of the sub-family Mustelinae was dated 4.5 million years ago. The mitogenomic data were consistent with a bear-like origin of seals

Genomic resources for the spotted ragged-tooth shark Carcharias taurus

Genomic data can be a useful tool in the management and conservation of biodiversity. Here, we report the development of genomic resources for the spotted ragged-tooth shark Carcharias taurus using genome-wide DNA data from Illumina next-generation sequencing. We explored two commonly used genetic marker types: microsatellites and mitochondrial DNA. A total of 4 394 putative microsatellites were identified, of which 10 were tested on 24 individuals and found to have ideal properties for population genetic analyses. Additionally, we reconstructed the first complete mitochondrial genome of a South African spotted ragged-tooth shark, and highlight the most informative gene regions to facilitate future primer design. The data reported here may serve as a resource for future studies and can ultimately be applied in the sustainable conservation and fisheries management of this apex predator.Keywords: genotype, grey nurse shark, Illumina next-generation sequencing, microsatellites, mitogenome, primer design, sand tiger shar

Erratum to: Identifying prey items from New Zealand fur seal (Arctocephalus forsteri) faeces using massive parallel sequencing (Conservation Genet Resour, 10.1007/s12686-016-0560-9)

Unfortunately, in the original publication of the article Table 1 was published erroneously. The corrected Table 1 is given in this erratum. (Table presented.

Mitogenomics data reveal effective population size, historical bottlenecks, and the effects of hunting on New Zealand fur seals (Arctocephalus forsteri)

The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0.012 ± 0.0061). Variation was not constrained geographically. Analyses of mitogenomes support the hypothesis for a population bottleneck approximately 35 generations ago, which coincides with the peak of commercial sealing. Mitogenomic data are consistent with a pre-human effective population size of approximately 30,000 that first declined to around 10,000 (due to the impact of Polynesian colonization, particularly in the first 100 years of their arrival into New Zealand), and then to 100–200 breeding individuals during peak of commercial sealing

A survey of the oral cavity microbiome of New Zealand fur seal pups (Arctocephalus forsteri)

New Zealand fur seals, Arctocephalus forsteri (NZFS hereafter), experienced a catastrophic decline in population size with the onset of commercial sealing in the southern hemisphere, from the 18th to the early 19th century (Lento, Mattlin, Chambers, & Baker, 1994). Despite the remarkable subsequent recovery from the brink of extinction, the future of the species remains uncertain. The extent of the impact of the historical bottleneck on the NZFS's evolutionary potential and their long‐term survival and expansion are yet to be fully understood (Dussex et al., 2016, 2018; Emami‐Khoyi et al., 2016, 2018)

Blood, sweat and tears: a review of non-invasive DNA sampling

The use of DNA data is ubiquitous across animalsciences. DNA may be obtained from an organism for a myriad of reasonsincluding identification and distinction between cryptic species, sex identification, comparisons of different morphocryptic genotypes or assessments of relatedness between organisms prior to a behavioural study. DNA should be obtained while minimizing the impact on the fitness, behaviour or welfare of the subject being tested, as this can bias experimental results and cause long-lasting effects on wild animals. Furthermore, minimizing impact on experimental animals is a key Refinement principle within the '3Rs' framework which aims to ensure that animal welfare during experimentation is optimised. The term 'non-invasive DNA sampling' has been defined to indicate collection methods that do not require capture or cause disturbance to the animal, including any effects on behaviour or fitness. In practice this is not always the case, as the term 'non-invasive' is commonly used in the literature to describe studies where animals are restrained or subjected to aversive procedures. We reviewed the non-invasive DNA sampling literature for the past six years (380 papers published in 2013-2018) and uncovered the existence of a significant gap between the current use of this terminology (i.e. 'non-invasive DNA sampling') and its original definition. We show that 58% of the reviewed papers did not comply with the original definition. We discussthe main experimental and ethical issuessurrounding the potential confusion or misuse of the phrase 'non-invasive DNA sampling' in the current literature and provide potential solutions. In addition, we introduce the terms 'non-disruptive' and 'minimally disruptive' DNA sampling, to indicate methods that eliminate or minimise impacts not on the physical integrity/structure of the animal, but on its behaviour, fitness and welfare, which in the literature reviewed corresponds to the situation for which an accurate term is clearly missing. Furthermore, we outline when these methods are appropriate to use

Oral microbiome metabarcoding in two invasive small mammals from New Zealand

All multicellular organisms host a wide diversity of microorganisms in and on their bodies, which are collectively known as their microbiome. Characterising microbial communities that inhabit different body niches in wild animals is critical to better understand the dynamics of microbiome diversityand its functional significance. The current study is the first to apply massively parallel sequencing of 16S rRNA to characterise the microbial diversity and functional content of oral microbiota in two of New Zealand’s most important invasive mammals, the omnivorous common brushtail possum (Trichosurus vulpecula) and the carnivorous stoat (Mustela erminea). In total, strains of bacteria belonging to 19 different phyla, 27 classes, 52 orders, 103 families, 163 genera and 51 known species were identified from the oral cavities of the study species. Strains of the phyla Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria dominated the core oral microbial diversity in both species, while other taxa were comparatively less abundant. Despite invasive populations typically demonstrating limited genetic variation, intraspecific variation of the core bacterial taxa in the oral microbiota was considerable. This suggests that a complex interaction between genetic, physiological, and environmental factors determines the diversity of the study species’ oral microbiome

Identifying Prey Items from New Zealand Fur Seal (Arctocephalus Forsteri) Faeces Using Massive Parallel Sequencing

The New Zealand fur seal (Arctocephalus forsteri) is one of many pinniped species that has shown a remarkable recovery from the brink of extinction after cessation of commercial sealing during the eighteenth and nineteenth centuries. It is commonly believed that this species competes with recreational and commercial fisheries. We identified prey items using massive parallel sequencing from New Zealand fur seal faecal samples that were collected throughout the species distribution. The data support generalist feeding behaviour for this species. The diet composition showed significant geographical and inter-seasonal variation. As many as 46 species of fish and 18 species of cephalopod were identified from a single colony. The data suggest cartilaginous species (sharks, rays, and skates) constitute an important part of the New Zealand fur seal diet. Approximately 10 % of the species identified in the seal diet were of significant commercial value, which indicates some qualitative food competition between New Zealand fur seals and commercial fisheries in exploiting marine species