Economical genotyping of little blue penguin (Eudyptula minor) clades from feather-based DNA

Determination of clade membership is a crucial requirement for many research questions addressing phylogeography, population structure, mating patterns, speciation, and hybridisation. The little blue penguin (Eudyptula minor) can be separated into two deeply divergent clades. However, assigning clade membership in little blue penguins requires molecular methods. Genetic sequencing can be used to identify clade membership but is expensive. Here, we present an economical alternative to the use of sequencing to determine little blue penguin clade membership. We extracted DNA from feathers using a method that produced reasonable quantities of DNA. We then amplified the D-loop section of the mitochondrial control region from total genomic DNA extracts, using the primers 'C L-tRNAglu' and 'D H-Dbox' followed by digestion with the restriction enzyme AluI. When visualised on a gel, distinctive banding patterns clearly indicated clade membership. We sequenced a subset of our samples and verified the accuracy of this method. The methods we present should facilitate little blue penguin research through a cost-effective approach to clade analysis as well as a successful technique to extract DNA from feathers when blood or tissue samples are not available

Short Note: Report of mummified leopard seal carcass in the southern Dry Valleys, McMurdo Sound, Antarctica.

The wide spread occurrence of mummified seal and penguin carcasses tens of kilometres from the open ocean is an interesting phenomenon occurring in the Antarctic Dry Valleys. Mummified seal carcasses were first reported by Scott’s expedition in 1903 (Scott 1969), and live seals and seal carcasses have since been reported many kilometres from the nearest ice-free ocean. Seal carcasses found in the McMurdo Dry Valleys are predominantly crabeater seals (Lobodon carcinophaga (Hombron & Jacquinot)) with a smaller number of Weddell seals, (Leptonychotes weddellii (Lesson)), also reported. Here we present only the second published report of a leopard seal carcass from the McMurdo Dry Valleys

Latitudinal distribution and mitochondrial DNA (COI) variability of Stereotydeus spp. (Acari: Prostigmata) in Victoria Land and the central Transantarctic Mountains

We examined mitochondrial DNA (COI) variability and distribution of Stereotydeus spp. in Victoria Land and the Transantarctic Mountains, and constructed Neighbour Joining (NJ) and Maximum Likelihood (ML) phylogenetic trees using all publicly available COI sequences for the three Stereotydeus species present (S. belli, S. mollis and S. shoupi). We also included new COI sequences from Miers, Marshall and Garwood valleys in southern Victoria Land (78°S), as well as from the Darwin (79°S) and Beardmore Glacier (83°S) regions. Both NJ and ML methods produced trees which were similar in topology differing only in the placement of the single available S. belli sequence from Cape Hallett (72°S) and a S. mollis haplotype from Miers Valley. Pairwise sequence divergences among species ranged from 9.5–18.1%. NJ and ML grouped S. shoupi from the Beardmore Glacier region as sister to those from the Darwin with pairwise divergences of 8%. These individuals formed a monophyletic clade with high bootstrap support basal to S. mollis and S. belli. Based on these new data, we suggest that the distributional range of S. shoupi extends northward to Darwin Glacier and that a barrier to dispersal for Stereotydeus, and possibly other arthropods, exists immediately to the north of this area

Identifying invertebrate invasions using morphological and molecular analyses: North American Daphnia ‘pulex’ in New Zealand fresh waters

We used a DNA barcoding approach to identify specimens of the Daphnia pulex complex occurring in New Zealand lakes, documenting the establishment of non-indigenous North American Daphnia 'pulex'. Morphological delineation of species in this complex is problematic due to a lack of good morphological traits to distinguish the species, as there is a relatively high degree of morphological stasis within the group through evolutionary time. Accordingly, genetic analyses were used to determine the specific identity and likely geographic origin of this species. Morphologically, individuals most closely resembled Daphnia pulicaria or Daphnia pulex sensu lato, which cannot be separated morphologically. Furthermore, each of these taxa comprises separate species in North America and Europe, despite carrying the same names. We identified individuals using a 658 bp nucleotide portion of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) as North American Daphnia 'pulex', being distinct from European Daphnia pulex sensu stricto and D. pulicaria from Europe or North America. Cellulose allozyme electrophoresis was used to confirm that individuals were not hybrids with D. pulicaria. North American Daphnia 'pulex' in New Zealand were first recorded in New Zealand from South Island lakes that are popular for overseas recreational fishers, indicating a possible source of introduction for this species (e.g. on/in fishing gear). Our study provides an additional example of how genetic techniques can be used for the accurate identification of non-indigenous taxa, particularly when morphological species determination is not possible. The growth of global databases such as GenBank and Barcode of Life Datasystems (BOLD) will further enhance this identification capacity

Testing use of mitochondrial COI sequences for the identification and phylogenetic analysis of New Zealand caddisflies (Trichoptera)

We tested the hypothesis that cytochrome c oxidase subunit 1 (COI) sequences would successfully discriminate recognised species of New Zealand caddisflies. We further examined whether phylogenetic analyses, based on the COI locus, could recover currently recognised superfamilies and suborders. COI sequences were obtained from 105 individuals representing 61 species and all 16 families of Trichoptera known from New Zealand. No sequence sharing was observed between members of different species, and congeneric species showed from 2.3 to 19.5% divergence. Sequence divergence among members of a species was typically low (mean = 0.7%; range 0.0–8.5%), but two species showed intraspecific divergences in excess of 2%. Phylogenetic reconstructions based on COI were largely congruent with previous conclusions based on morphology, although the sequence data did not support placement of the purse-cased caddisflies (Hydroptilidae) within the uncased caddisflies, and, in particular, the Rhyacophiloidea. We conclude that sequence variation in the COI gene locus is an effective tool for the identification of New Zealand caddisfly species, and can provide preliminary phylogenetic inferences. Further research is needed to ascertain the significance of the few instances of high intra-specific divergence and to determine if any instances of sequence sharing will be detected with larger sample sizes

Attention Restraint, Working Memory Capacity, and Mind Wandering: Do Emotional Valence or Intentionality Matter?

Attention restraint appears to mediate the relationship between working memory capacity (WMC) and mind wandering (Kane et al., 2016). Prior work has identifed two dimensions of mind wandering—emotional valence and intentionality. However, less is known about how WMC and attention restraint correlate with these dimensions. Te current study examined the relationship between WMC, attention restraint, and mind wandering by emotional valence and intentionality. A confrmatory factor analysis demonstrated that WMC and attention restraint were strongly correlated, but only attention restraint was related to overall mind wandering, consistent with prior fndings. However, when examining the emotional valence of mind wandering, attention restraint and WMC were related to negatively and positively valenced, but not neutral, mind wandering. Attention restraint was also related to intentional but not unintentional mind wandering. Tese results suggest that WMC and attention restraint predict some, but not all, types of mind wandering

Pest fish detection using environmental DNA – fact sheet

Molecular tools using DNA sequencing can improve pest fish management by ensuring accurate identification of fish, especially larval fish, without the need for specialist taxonomic knowledge. DNA is made of four chemicals; guanine (G), adenine (A), thymine (T), or cytosine (C), joined together as a string (Figure 1). The order of the chemicals is unique to each species and can be used as a DNA "barcode" to identify organisms. It is relatively simple to obtain DNA sequences for a reference gene such as the widely accepted "barcode gene" cytochrome C oxidase subunit 1, and compare the sequence to a voucher specimen sequence in genetic databases such as GenBank and the Barcode of Life database BOLD

Blood tests in primary care:a qualitative study of communication and decision making between doctors and patients

OBJECTIVE: Blood tests are commonly used in primary care as a tool to aid diagnosis, and to offer reassurance and validation for patients. If doctors and patients do not have a shared understanding of the reasons for testing and the meaning of results, these aims may not be fulfilled. Shared decision‐making is widely advocated; yet, most research focusses on treatment decisions rather than diagnostic decisions. The aim of this study was to explore communication and decision‐making around diagnostic blood tests in primary care. METHODS: Qualitative interviews were undertaken with patients and clinicians in UK primary care. Patients were interviewed at the time of blood testing, with a follow‐up interview after they received test results. Interviews with clinicians who requested the tests provided paired data to compare clinicians' and patients' expectations, experiences and understandings of tests. Interviews were analysed thematically using inductive and deductive coding. RESULTS: A total of 80 interviews with 28 patients and 19 doctors were completed. We identified a mismatch in expectations and understanding of tests, which led to downstream consequences including frustration, anxiety and uncertainty for patients. There was no evidence of shared decision‐making in consultations preceding the decision to test. Doctors adopted a paternalistic approach, believing that they were protecting patients from anxiety. CONCLUSION: Patients were not able to develop informed preferences and did not perceive that choice is possible in decisions about testing, because they did not have sufficient information and a shared understanding of tests. A lack of shared understanding at the point of decision‐making led to downstream consequences when test results did not fulfil patients' expectations. Although shared decision‐making is recommended as best practice, it does not reflect the reality of doctors' and patients' accounts of testing; a broader model of shared understanding seems to be more relevant to the complexity of primary care diagnosis. PATIENT OR PUBLIC CONTRIBUTION: A patient and public involvement group comprising five participants with lived experience of blood testing in primary care met regularly during the study. They contributed to the development of the research objectives, planning recruitment methods, reviewing patient information leaflets and topic guides and also contributed to discussion of emerging themes at an early stage in the analysis process

Developmental risk among Aboriginal children living in urban areas in Australia : the Study of Environment on Aboriginal Resilience and Child Health (SEARCH)

Background: Most Australian Aboriginal children are on track with their development, however, the prevalence of children at risk of or with a developmental or behavioural problem is higher than in other children. Aboriginal child development data mostly comes from remote communities, whereas most Aboriginal children live in urban settings. We quantified the proportion of participating children at moderate and high developmental risk as identified by caregivers' concerns, and determined the factors associated with developmental risk among urban Aboriginal communities. Methods: Study methods were co-designed and implemented with four participating urban Aboriginal Community Controlled Health Services in New South Wales, Australia, between 2008 and 2012. Caregiver-reported data on children < 8 years old enrolled in a longitudinal cohort study (Study of Environment on Aboriginal Resilience and Child Health: SEARCH) were collected by interview. The Parents' Evaluation of Developmental Status (PEDS) was used to assess developmental risk through report of caregiver concerns. Odds ratios (OR) were calculated using multinomial logistic regression to investigate risk factors and develop a risk prediction model. Results: Of 725 children in SEARCH with PEDS data (69% of eligible), 405 (56%) were male, and 336 (46%) were aged between 4.5 and 8 years. Using PEDS, 32% were at high, 28% moderate, and 40% low/no developmental risk. Compared with low/no risk, factors associated with high developmental risk in a mutually-adjusted model, with additional adjustment for study site, were male sex (OR 2.42, 95% confidence intervals 1.62-3.61), being older (4.5 to < 8 years versus < 3 years old, 3.80, 2.21-6.54), prior history of ear infection (1.95, 1.21-3.15), having lived in 4 or more houses versus one house (4.13, 2.04-8.35), foster care versus living with a parent (5.45, 2.32-12.78), and having a caregiver with psychological distress (2.40, 1.37-4.20). Conclusion: In SEARCH, 40% of urban Aboriginal children younger than 8 years were at no or low developmental risk. Several factors associated with higher developmental risk were modifiable. Aboriginal community-driven programs to improve detection of developmental problems and facilitate early intervention are needed