Insights into Platypus Population Structure and History from Whole-Genome Sequencing.

The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10-9/bp/generation (95% CI 4.1 × 10-9-1.2 × 10-8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.

Correction to: Sonographic evaluation of uncommonly assessed upper extremity peripheral nerves: anatomy, technique, and clinical syndromes.

The original version of this article unfortunately contained mistake. Fig. 13a (Anatomy of the Ulnar Digital nerve of the Thumb) as originally published erroneously depicts the ulnar digital nerve of the thumb as a branch of the ulnar nerve.

Sonographic evaluation of uncommonly assessed upper extremity peripheral nerves: anatomy, technique, and clinical syndromes.

Targeted ultrasound of the median, ulnar, and radial nerves is a well-established technique for suspected upper extremity peripheral neuropathy. However, sonographic imaging of the brachial plexus and smaller peripheral nerve branches is more technically difficult and the anatomy is less familiar to many radiologists. As imaging techniques improve, many clinicians refer patients for imaging of previously less-familiar structures. In addition, some patients may present with injuries that could involve local neurovascular structures. Finally, patients presenting with isolated peripheral neuropathies may be referred for perineural injections with local anesthetic for diagnostic purposes, or steroid for therapeutic reasons. This requires sonologists to have a firm understanding of the courses of these nerves and the surrounding anatomic landmarks that can be used to accurately identify and characterize them. We discuss clinical syndromes referable to specific peripheral nerve branches in the upper extremity, the relevant anatomy, and sonographic technique.

Fragmentation by major dams and implications for the future viability of platypus populations.

The evolutionarily unique platypus (Ornithorhynchus anatinus) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation (FST) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers; FST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, FST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.

The platypus: evolutionary history, biology, and an uncertain future.

The platypus (Ornithorhynchus anatinus) is one of the world's most evolutionarily distinct mammals, one of five extant species of egg-laying mammals, and the only living species within the family Ornithorhynchidae. Modern platypuses are endemic to eastern mainland Australia, Tasmania, and adjacent King Island, with a small introduced population on Kangaroo Island, South Australia, and are widely distributed in permanent river systems from tropical to alpine environments. Accumulating knowledge and technological advancements have provided insights into many aspects of its evolutionary history and biology but have also raised concern about significant knowledge gaps surrounding distribution, population sizes, and trends. The platypus' distribution coincides with many of Australia's major threatening processes, including highly regulated and disrupted rivers, intensive habitat destruction, and fragmentation, and they were extensively hunted for their fur until the early 20th century. Emerging evidence of local population declines and extinctions identifies that ecological thresholds have been crossed in some populations and, if threats are not addressed, the species will continue to decline. In 2016, the IUCN Red Listing for the platypus was elevated to "Near Threatened," but the platypus remains unlisted on threatened species schedules of any Australian state, apart from South Australia, or nationally. In this synthesis, we review the evolutionary history, genetics, biology, and ecology of this extraordinary mammal and highlight prevailing threats. We also outline future research directions and challenges that need to be met to help conserve the species.

Use of implanted acoustic tags to assess platypus movement behaviour across spatial and temporal scales.

The platypus (Ornithorhynchus anatinus) is an evolutionarily distinct mammal, endemic to Australian freshwaters. Many aspects of its ecology and life-history, including detailed understanding of movements, are poorly known, hampered by its cryptic and mainly nocturnal habits and small numbers. We effectively trialled intraperitoneal implanted acoustic transmitters in nine platypuses in the Severn River (NSW), Australia, as a potential approach for studying movements in this challenging species. We tracked platypus movements over six months, at fine and broad spatial scales, using an array of acoustic sensors. Over six months (March-August 2016), four of five adult platypuses (two females\three males) maintained localized movements (average monthly maximums 0.37 km ± 0.03 sd), while one adult, one sub-adult, and one juvenile (males) moved further: average monthly maxima 1.2 km ± 2.0 sd, 0.9 km ± 0.6 sd, 4.5 km ± 5.9 sd, respectively. The longest recorded movement was by a male adult, covering 11.1 km in three days and travelling a maximum distance of about 13 km between records. Only one implanted animal was not detected immediately after release, indicative of transmission failure rather than an adverse event. High cumulative daily movements (daily 1.9 km ± 0.8 sd) indicated high metabolic requirements, with implications for previous estimates of platypus abundances and carrying capacities, essential for effective conservation. This novel approach offers new avenues to investigate relating to mating, nesting, and intraspecific competition behaviours and their temporal and spatial variation.

Life history and dynamics of a platypus (Ornithorhynchus anatinus) population: four decades of mark-recapture surveys.

Knowledge of the life-history and population dynamics of Australia's iconic and evolutionarily distinct platypus (Ornithorhynchus anatinus) remains poor. We marked-recaptured 812 unique platypuses (total 1,622 captures), over four decades (1973-2014) in the Shoalhaven River, Australia. Strong sex-age differences were observed in life-history, including morphology and longevity. Apparent survival of adult females (Φ = 0.76) were higher than adult males (Φ = 0.57), as in juveniles: females Φ = 0.27, males Φ = 0.13. Females were highly likely to remain in the same pool (adult: P = 0.85, juvenile: P = 0.88), while residency rates were lower for males (adult: P = 0.74, juvenile: P = 0.46). We combined survival, movement and life-histories to develop population viability models and test the impact of a range of life-history parameters. While using estimated apparent survival produced unviable populations (mean population growth rate r = -0.23, extinction within 20 years), considering residency rates to adjust survival estimates, indicated more stable populations (r = 0.004, p = 0.04 of 100-year extinction). Further sensitivity analyses highlighted adult female survival and overall success of dispersal as most affecting viability. Findings provide robust life-history and viability estimates for a difficult study species. These could support developing large-scale population dynamics models required to underpin a much needed national risk assessment for the platypus, already declining in parts of its current distribution.

Role of intrathyroidal calcifications detected on ultrasound as a marker of malignancy.

OBJECTIVES: Clinically palpable thyroid nodules are present in between 4% and 7% of the population, with only a small percentage of those harboring malignancy. Thus, it is important to find a cost-effective way to determine which nodules are more likely to be malignant. The purpose of this study was to evaluate the use of intrathyroidal calcifications detected on ultrasound as a risk factor for malignancy. STUDY DESIGN: Retrospective chart review. METHODS: One hundred fifty-nine patients with thyroid disease were included in this study. Patients were selected from a thyroid ultrasound (TUS) database. Charts were then reviewed, and only those patients who had a preoperative TUS and underwent surgery for tissue diagnosis were included. RESULTS: Of the 159 patients, 66 (41.5%) were diagnosed with cancer. Of those with malignancy, 52 (78.8%) had calcifications noted on TUS. Ninety-three of the patients were diagnosed with benign pathology. Of those 93 patients, 36 (38.7%) had TUS findings consistent with calcifications, whereas 57 (61.3%) did not. Statistical analysis using a chi-square test showed a strong association between cancer status and calcification, with P <.001. In our study, calcifications on TUS had a sensitivity of 78.8% and a specificity of 61.3%, with an odds ratio of 5.88. CONCLUSION: The presence of calcifications detected on TUS should alert the physician for the possibility of malignancy, and further work-up should be pursued. This information may be used to improve the sensitivity of other diagnostic tests such as fine needle aspiration biopsies. Given the relatively low sensitivity and specificity of the test, its use alone as a marker of malignancy is limited, but it may be used in combination with other known risk factors and tests to decide on the most appropriate treatment plan.

Awareness and enforcement of guidelines for publishing industry-sponsored medical research among publication professionals: the Global Publication Survey.

OBJECTIVE: To gather information about current practices and implementation of publication guidelines among publication professionals working in or for the pharmaceutical industry. DESIGN/SETTING: Web-based survey publicised via email and social media to members of the International Society for Medical Publication Professionals (ISMPP) and other organisations from November 2012 to February 2013. PARTICIPANTS: 469 individuals involved in publishing industry-sponsored research in peer-reviewed journals, mainly working in pharmaceutical or device companies ('industry', n=144), communication agencies ('agency', n=238), contract research organisations (CRO, n=15) or as freelancers (n=34). Most respondents (78%) had worked on medical publications for ≥5 years and 62% had a PhD/MD. RESULTS: Over 90% of industry, agency and CRO respondents routinely refer to Good Publication Practice (GPP2) and the International Committee of Medical Journal Editors' Uniform Requirements. Most respondents (78% industry, 79% agency) received mandatory training on ethical publication practices. Over 90% of respondents' companies had publication guidelines or policies and required medical writing support to be acknowledged in publications (96% industry, 99% agency). Many industry respondents used publication management tools to monitor compliance with company guidelines and about half (46%) stated that their company had formal publication audits. Fewer agencies audited adherence to guidelines but 20% of agency respondents reported audits of employees and 6% audits of freelancers. Of concern, 37% of agency respondents reported requests from authors or sponsors that they believed were unethical, although 93% of these requests were withdrawn after respondents explained the need for compliance with guidelines. Most respondents' departments (63% industry, 58% agency, 60% CRO) had been involved in publishing studies with negative or inconclusive results. CONCLUSIONS: Within this sample, most publication professionals working in or for industry were aware of, and applying, major publication guidelines. However, the survey also identified specific areas where education and promotion of guidelines are needed to ensure ethical publication practices.

Monotreme lactation protein is highly expressed in monotreme milk and provides antimicrobial protection.

Monotremes (platypus and echidna) are the descendants of the oldest ancestor of all extant mammals distinguished from other mammals by mode of reproduction. Monotremes lay eggs following a short gestation period and after an even briefer incubation period, altricial hatchlings are nourished over a long lactation period with milk secreted by nipple-less mammary patches located on the female's abdomen. Milk is the sole source of nutrition and immune protection for the developing young until weaning. Using transcriptome and mass spectrometry analysis of milk cells and milk proteins, respectively, a novel Monotreme Lactation Protein (MLP) was identified as a major secreted protein in milk. We show that platypus and short-beaked echidna MLP genes show significant homology and are unique to monotremes. The MLP transcript was shown to be expressed in a variety of tissues; however, highest expression was observed in milk cells and was expressed constitutively from early to late lactation. Analysis of recombinant MLP showed that it is an N-linked glycosylated protein and biophysical studies predicted that MLP is an amphipathic, α-helical protein, a typical feature of antimicrobial proteins. Functional analysis revealed MLP antibacterial activity against both opportunistic pathogenic Staphylococcus aureus and commensal Enterococcus faecalis bacteria but showed no effect on Escherichia coli, Pseudomonas aeruginosa, Staphylococcus epidermidis, and Salmonella enterica. Our data suggest that MLP is an evolutionarily ancient component of milk-mediated innate immunity absent in other mammals. We propose that MLP evolved specifically in the monotreme lineage supporting the evolution of lactation in these species to provide bacterial protection, at a time when mammals lacked nipples.

Ten polymorphic microsatellite DNA markers for the platypus, Ornithorhynchus anatinus.

We identified and optimized 10 microsatellite loci for the platypus, Ornithorhynchus anatinus (Monotremata: Ornithorhynchidae), and screened 21 individuals from the southern tablelands area of New South Wales, Australia. Each polymorphic locus possessed between two and 12 alleles with observed heterozygosities between 0.118 and 0.950. The intent of this effort was to provide informative loci for studies on the population genetics of this species.