Boom-bust population dynamics drive rapid genetic change

Increasing environmental threats and more extreme environmental perturbations place species at risk of population declines, with associated loss of genetic diversity and evolutionary potential. While theory shows that rapid population declines can cause loss of genetic diversity, populations in some environments, like Australia's arid zone, are repeatedly subject to major population fluctuations yet persist and appear able to maintain genetic diversity. Here, we use repeated population sampling over 13 y and genotype-by-sequencing of 1903 individuals to investigate the genetic consequences of repeated population fluctuations in two small mammals in the Australian arid zone. The sandy inland mouse (Pseudomys hermannsburgensis) experiences marked boom-bust population dynamics in response to the highly variable desert environment. We show that heterozygosity levels declined, and population differentiation (FST) increased, during bust periods when populations became small and isolated, but that heterozygosity was rapidly restored during episodic population booms. In contrast, the lesser hairy-footed dunnart (Sminthopsis youngsoni), a desert marsupial that maintains relatively stable population sizes, showed no linear declines in heterozygosity. These results reveal two contrasting ways in which genetic diversity is maintained in highly variable environments. In one species, diversity is conserved through the maintenance of stable population sizes across time. In the other species, diversity is conserved through rapid genetic mixing during population booms that restores heterozygosity lost during population busts.

slimr: An R package for tailor-made integrations of data in population genomic simulations over space and time

Software for realistically simulating complex population genomic processes is revolutionizing our understanding of evolutionary processes, and providing novel opportunities for integrating empirical data with simulations. However, the integration between standalone simulation software and R is currently not well developed. Here, we present slimr, an R package designed to create a seamless link between standalone software SLiM >3.0, one of the most powerful population genomic simulation frameworks, and the R development environment, with its powerful data manipulation and analysis tools. We show how slimr facilitates smooth integration between genetic data, ecological data and simulation in a single environment. The package enables pipelines that begin with data reading, cleaning and manipulation, proceed to constructing empirically based parameters and initial conditions for simulations, then to running numerical simulations and finally to retrieving simulation results in a format suitable for comparisons with empirical data - aided by advanced analysis and visualization tools provided by R. We demonstrate the use of slimr with an example from our own work on the landscape population genomics of desert mammals, highlighting the advantage of having a single integrated tool for both data analysis and simulation. slimr makes the powerful simulation ability of SLiM directly accessible to R users, allowing integrated simulation projects that incorporate empirical data without the need to switch between software environments. This should provide more opportunities for evolutionary biologists and ecologists to use realistic simulations to better understand the interplay between ecological and evolutionary processes.

The genetic signature left by the range expansion of red foxes in Australia is detectable after more than 80 years of population stability

Reconstructing biological invasions from historical sources can provide insights into how they occur but are difficult to do when invasions are poorly documented. Genetic signatures left by invaders can also offer insights into invasion routes, points of origin and general biology but often present conclusions that are contradictory to expectations. Here, we test the ability of continental-wide microsatellite genotype data from 29 loci and 3122 samples to reconstruct the well-documented invasion of red foxes Vulpes vulpes from the United Kingdom into Australia over 150 years ago, an invasion that has led to the extinction of many native species. Our analysis reveals several key signals of invasion evident in Australian foxes. They display lower levels of diversity than foxes sampled from the UK, exhibit clines in diversity from the point of introduction (south-east Australia) to the edge of their range, and show strong evidence of allele surfing in westerly and north-easterly directions. These characteristics are consistent with a single point of origin followed by rapid expansion in westerly and north-easterly directions as suggested by historical records. We also find little genetic structure in foxes across Australia with only the vast Nullarbor Plains and Great Victoria Desert region presenting a detectable barrier to their dispersal. As such, no mainland region within the current range of foxes can be considered genetically isolated and therefore appropriate for localised eradication efforts. Overall, our analyses demonstrate the ability of comprehensive population genetic studies to reconstruct invasion histories even after more than 80 years since colonisation was stabilised.

Swinging back from the brink? Polygamous mating strategies revealed for an iconic threatened freshwater fish

Catastrophic fish death events are increasing in frequency and severity globally. A series of major recent fish deaths in the semi-arid lower Darling-Baaka river system (LDBR) of Australia are emblematic of these issues with tens of millions of native fish perishing. In 2018-2019 there was a major death event for Australia's largest freshwater fish, Murray cod (Maccullochella peelii). To aid the recovery and guide restoration activities of local Murray cod populations, it is essential to gather information on the mating strategies and effective population size following the fish death event. After the fish deaths, we collected larvae during the 2020 and 2021 breeding seasons and used single nucleotide polymorphisms (SNPs) to provide insight mating strategies and to estimate effective population size. Larvae were detected in both years along the entire length of the LDBR. Sixteen percent of the inferred breeding individuals were found to contribute to multiple pairings, confirming a complex and polygamous mating system. A high frequency of polygamy was evident both within and between years with 100 % polygamy identified among parents that produced offspring in both 2020 and 2021 and 95 % polygamy identified among parents involved in multiple spawning events within years. Post-larval Murray cod samples collected between 2016 and 2021 were co-analysed to further inform kinship patterns. Again, monogamy was rare with no confirmed cases of the same male-female pair contributing to multiple breeding events within or between seasons. Effective population size based on Murray cod collected after the fish death event was estimated at 721.6 (CI 471-1486), though this has likely declined following a subsequent catastrophic fish death event in the LDBR in March 2023. Our data provide insight into the variability of Murray cod mating strategies, and we anticipate that this knowledge will assist in planning conservation actions to ultimately help recover a species in crisis.

Episodic population fragmentation and gene flow reveal a trade-off between heterozygosity and allelic richness

In episodic environments like deserts, populations of some animal species exhibit irregular fluctuations such that populations are alternately large and connected or small and isolated. Such dynamics are typically driven by periodic resource pulses due, for example, to large but infrequent rainfall events. The repeated population bottlenecks resulting from fragmentation should lower genetic diversity over time, yet species undergoing these fluctuations appear to maintain high levels of genetic diversity. To resolve this apparent paradox, we simulated a metapopulation of constant size undergoing repeat episodes of fragmentation and change in gene flow to mimic outcomes experienced by mammals in an Australian desert. We show that episodic fragmentation and gene flow have contrasting effects on two measures of genetic diversity: heterozygosity and allelic richness. Specifically, fragmentation into many, small subpopulations, coupled with periods of infrequent gene flow, preserves allelic richness at the expense of heterozygosity. In contrast, fragmentation into a few, large subpopulations maintains heterozygosity at the expense of allelic richness. The strength of the trade-off between heterozygosity and allelic richness depends on the amount of gene flow and the frequency of gene flow events. Our results imply that the type of genetic diversity maintained among species living in strongly fluctuating environments will depend on the way populations fragment, with our results highlighting different mechanisms for maintaining allelic richness and heterozygosity in small, fragmented populations.

Quality indicators in intensive care medicine for Germany - fourth edition 2022

The measurement of quality indicators supports quality improvement initiatives. The German Interdisciplinary Society of Intensive Care Medicine (DIVI) has published quality indicators for intensive care medicine for the fourth time now. After a scheduled evaluation after three years, changes in several indicators were made. Other indicators were not changed or only minimally. The focus remained strongly on relevant treatment processes like management of analgesia and sedation, mechanical ventilation and weaning, and infections in the ICU. Another focus was communication inside the ICU. The number of 10 indicators remained the same. The development method was more structured and transparency was increased by adding new features like evidence levels or author contribution and potential conflicts of interest. These quality indicators should be used in the peer review in intensive care, a method endorsed by the DIVI. Other forms of measurement and evaluation are also reasonable, for example in quality management. This fourth edition of the quality indicators will be updated in the future to reflect the recently published recommendations on the structure of intensive care units by the DIVI.

Climate warming drives a temperate-zone lizard to its upper thermal limits, restricting activity, and increasing energetic costs

Lizards are considered vulnerable to climate change because many operate near their thermal maxima. Exposure to higher temperatures could reduce activity of these animals by forcing them to shelter in thermal refugia for prolonged periods to avoid exceeding lethal limits. While rising temperatures should reduce activity in tropical species, the situation is less clear for temperate-zone species where activity can be constrained by both low and high temperatures. Here, we measure the effects of natural variation in environmental temperatures on activity in a temperate grassland lizard and show that it is operating near its upper thermal limit in summer even when sheltering in thermal refuges. As air temperatures increased above 32 °C, lizard activity declined markedly as individuals sought refuge in cool microhabitats while still incurring substantial metabolic costs. We estimate that warming over the last two decades has required these lizards to increase their energy intake up to 40% to offset metabolic losses caused by rising temperatures. Our results show that recent increases in temperature are sufficient to exceed the thermal and metabolic limits of temperate-zone grassland lizards. Extended periods of high temperatures could place natural populations of ectotherms under significantly increased environmental stress and contribute to population declines and extinction.

Polyandry and non-random fertilisation maintain long-term genetic diversity in an isolated island population of adders (Vipera berus)

Conservation genetic theory suggests that small and isolated populations should be subject to reduced genetic diversity i.e., heterozygosity and allelic diversity. Our 34 years study of an isolated island population of adders (Vipera berus) in southern Sweden challenges this notion. Despite a lack of gene flow and a yearly mean estimated reproductive adult population size of only 65 adult adders (range 12-171), the population maintains high levels of heterozygosity and allelic diversity similar to that observed in two mainland populations. Even a 14-year major "bottleneck" i.e., a reduction in adult adder numbers, encompassing at least four adder generations, did not result in any reduction in the island adders' heterozygosity and allelic diversity. Female adders are polyandrous, and fertilisation is non-random, which our empirical data and modelling suggest are underpinning the maintenance of the population's high level of heterozygosity. Our empirical results and subsequent modelling suggest that the positive genetic effects of polyandry in combination with non-random fertilisation, often overlooked in conservation genetic analyses, deserve greater consideration when predicting long-term survival of small and isolated populations.

Real-world effectiveness of anti-interleukin-23 antibodies in chronic plaque-type psoriasis of patients from the Austrian Psoriasis Registry (PsoRA)

With the introduction of the latest class of biologic drugs targeting interleukin (IL)-23p19, three new, highly effective drugs can be used for the treatment of chronic plaque psoriasis. However, poorer skin improvement as well as higher rates of serious adverse events have been reported for patients under real-world conditions (outside clinical trials). This accounts especially for patients who have already been treated with biologic drugs. We therefore aimed to determine effectiveness and safety of IL-23p19 inhibitors in real-world patients by analysing data from the Psoriasis Registry Austria (PsoRA) in this observational, retrospective, multicentre cohort study. Data for 197 patients (52.3% biologic-non-naïve), who were treated with anti-IL-23p19 antibodies (127 guselkumab, 55 risankizumab and 15 tildrakizumab) for at least 3 months, were eligible for analysis. In general, biologic-non-naïve patients displayed a less favourable response to anti-IL-23 treatment as compared to biologic-naïve patients. However, after correction for previous biologic exposure, few differences in PASI improvement were detected among biologic-naïve and -non-naïve patients treated with different IL-23p19 inhibitors. This indicates that treatment effectiveness is not related to the class of the previously administered therapy in biologic-non-naïve patients. Therefore, IL-23p19 inhibitors represent a promising treatment alternative for patients who have not responded to previous biologics. However, as with other biologic agents (including IL-17 inhibitors), we did not observe an entirely satisfactory treatment response (i.e. PASI < 3 and/or PASI 75) to anti-IL-23 treatment in one out of four to five patients. Adverse events (mainly non-severe infections) were observed in 23 (11.7%) patients with no major differences regarding the administered IL-23 inhibitor or previous biologic exposure.

Reproductive Strategies and Population Genetic Structure in Two Dryland River Floodplain Plants, Marsilea drummondii and Eleocharis acuta

Aquatic plants share a range of convergent reproductive strategies, such as the ability to reproduce both sexually and asexually through vegetative growth. In dryland river systems, floodplain inundation is infrequent and irregular, and wetlands consist of discrete and unstable habitat patches. In these systems, life history strategies such as long-distance dispersal, seed longevity, self-fertilisation, and reproduction from vegetative propagules are important strategies that allow plants to persist. Using two aquatic plants, Marsilea drummondii and Eleocharis acuta, we investigated the proportions of sexual and asexual reproduction and self-fertilisation by employing next-generation sequencing approaches, and we used this information to understand the population genetic structure of a large inland floodplain in western New South Wales (NSW), Australia. Asexual vegetative reproduction and self-fertilisation were more common in M. drummondii, but both species used sexual reproduction as the main mode of reproduction. This resulted in a highly differentiated genetic structure between wetlands and a similar genetic structure within wetlands. The similarity in genetic structure was influenced by the wetland in the two species, highlighting the influence of the floodplain landscape and hydrology on structuring population genetic structure. The high levels of genetic variation among wetlands and the low variation within wetlands suggests that dispersal and pollination occur within close proximity and that gene flow is restricted. This suggests a reliance on locally sourced (persistent) seed, rather than asexual (clonal) reproduction or recolonisation via dispersal, for the population maintenance of plants in dryland rivers. This highlights the importance of floodplain inundation to promote seed germination, establishment, and reproduction in dryland regions.

Large-sample-size assessment of socioeconomic predictors of community-level resource management occurrence

Community-level resource management efforts are cornerstones in ensuring sustainable use of natural resources. Yet, understanding how community characteristics influence management practices remains contested. With a sample size of ≥725 communities, we assessed the effects of key community (i.e., socioeconomic) characteristics (human population size and density, market integration, and modernization) on the probability of occurrence of fisheries management practices, including gear, species, and spatial restrictions. The study was based in Solomon Islands, a Pacific Island country with a population that is highly dependent on coastal fisheries. People primarily dwell in small communities adjacent to the coastline dispersed across 6 island provinces and numerous smaller islands. We used nationally collected data in binomial logistic regression models to examine the likelihood of management occurrence, given socioeconomic context of communities. In contrast to prevailing views, we identified a positive and statistically significant association between both human population size and market integration and all 3 management practices. Human population density, however, had a statistically significant negative association and modernization a varied and limited association with occurrence of all management practices. Our method offers a way to remotely predict the occurrence of resource management practices based on key socioeconomic characteristics. It could be used to improve understanding of why some communities conduct natural resource management activities when statistical patterns suggest they are not likely to and thus improve understanding of how some communities of people beat the odds despite limited market access and high population density.

Solving the puzzle of mercury fate and emissions by coal-fired power plants: The potential of hydrodynamic-atmospheric modelling

There is currently a significant gap in knowledge about the emission and deposition of mercury (Hg) from coal-fired power plants in Australia. To fill this gap, we propose a novel method that combines several sources of information (stratigraphic data, hydrodynamic modelling and atmospheric modelling), to identify the sources and fates of Hg emitted from coal-fired power plants. The stratigraphic record from Lake Macquarie (Australia) shows that mercury deposition increased up to 7-times since the 1950s, which is when coal-fired power plants were commissioned in the catchment. The stratigraphy also shows a decrease in Hg deposition with power plant retrofits. Using results from multiple models (statistical modelling, hydrodynamic modelling, particle density modelling and atmospheric emissions modelling), we found that ash dams contribute little Hg to Lake Macquarie. Instead, most of the Hg contamination in the lake is a result of atmospheric emissions from the power plants, and these power plants are also depositing Hg in the urban areas to the west of the lake. Our results demonstrate that the multi-proxy approach demonstrated in the paper can be used to provide clues as to the source of Hg, so that appropriate mitigation strategies and regulatory frameworks can be implemented.

Plotting for change: an analytical framework to aid decisions on which lineages are candidate species in phylogenomic species discovery

A recent study argued that coalescent-based models of species delimitation mostly delineate population structure, not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here, we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable or uninformative. For de novo genomic studies of species boundaries, we propose six steps: (1) visualize genetic affinities among individuals to identify both discrete and admixed genetic groups from first principles and to hold aside individuals involved in contemporary admixture for independent consideration; (2) apply phylogenetic techniques to identify lineages; (3) assess diagnosability of those lineages as potential candidate species; (4) interpret the diagnosable lineages in a geographical context (sympatry, parapatry, allopatry); (5) assess significance of difference or trends in the context of sampling intensity; and (6) adopt a holistic approach to available evidence to inform decisions on species status in the difficult cases of allopatry. We adopt this approach to distinguish candidate species from within-species lineages for a widespread species complex of Australian freshwater fishes (Retropinna spp.). Our framework addresses two cornerstone issues in systematics that are often not discussed explicitly in genomic species discovery: diagnosability and how to determine it, and what criteria should be used to decide whether diagnosable lineages are conspecific or represent different species.

Biologic drug survival rates in the era of anti-interleukin-17 antibodies: a time-period-adjusted registry analysis

Background

Drug survival rates reflect efficacy and safety and may be influenced by the availability of alternative treatment options. Little is known about time‐dependent drug survival in psoriasis and the effect of increasing numbers of biologic treatment options.

Objectives

To determine whether drug survival is influenced by the availability of treatment options and by factors such as gender, psoriatic arthritis or previous biologic treatment.

Methods

This observational, retrospective, multicentre cohort study analysed data from patients registered in the Austrian Psoriasis Registry (PsoRA) who were treated with biologics between 1 January 2015 and 30 November 2019.

Results

A total of 1572 patients who received 1848 treatment cycles were included in this analysis. The highest long‐term Psoriasis Area and Severity Index improvement was observed after treatment with ixekizumab, followed by ustekinumab and secukinumab, adalimumab and etanercept. Overall, ustekinumab surpassed all other biologics in drug survival up to 48 months. However, when adjusted for biologic naïvety, its superiority vanished and drug survival rates were similar for ixekizumab (91·6%), secukinumab (90·2%) and ustekinumab (92·8%), all of them superior to adalimumab (76·5%) and etanercept (71·9%) at 12 months and beyond. Besides biologic non‐naïvety (2·10, P < 0·001), the introduction of a new drug such as secukinumab or ixekizumab (relative hazard ratio 1·6, P = 0·001) and female gender (1·50, P = 0·019) increased the risk of treatment discontinuation overall, whereas psoriatic arthritis did not (1·12, P = 0·21).

Conclusions

The time‐dependent availability of drugs should be considered when analysing and comparing drug survival. Previous biologic exposure significantly influences drug survival. Women are more likely to stop treatment.

What is already known about this topic?

Female gender and previous biologic exposure have been discussed as predictors for decreased drug survival in patients with psoriasis, but it remains unknown whether a time‐dependent increased availability of treatment options alters biologic drug survival.

What does this study add?

The increased availability of alternative biologic treatments over time leads to an elevated risk for treatment discontinuation overall; therefore, drug survival analysis has to be time adjusted.

Moreover, the study reveals that the impact of previous biologic treatment on drug survival is tremendous and confirms worse drug survival in female patients.

Linked Comment: Gniadecki. Br J Dermatol 2021; 184:996–997.

Low-threshold SARS-CoV-2 testing facility for hospital staff: Prevention of COVID-19 outbreaks?

BACKGROUND

The ongoing global SARS-CoV-2 pandemic has caused over 4.7 million infections greatly challenging healthcare workers (HCW) and medical institutions worldwide. The SARS-CoV-2 pandemic has shown to significantly impact mental and physical health of HCW. Thus, implementation of testing facilities supporting HCW are urgently needed.

METHODS

A low-threshold SARS-CoV-2 testing facility was introduced at the University Hospital Bonn, Germany, in March 2020. Irrespective of clinical symptoms employees were offered a voluntary and free SARS-CoV-2 test. Furthermore, employees returning from SARS-CoV-2 risk regions and employees after risk contact with SARS-CoV-2 infected patients or employees were tested for SARS-CoV-2 infection. Pharyngeal swabs were taken and reverse transcription polymerase chain reaction for detection of SARS-CoV-2 was performed, test results being available within 24 h. Profession, symptoms and reason for SARS-CoV-2 testing of employees were recorded.

RESULTS

Between 9th March and April 30, 2020, a total of 1510 employees were tested for SARS-CoV-2 infection. 1185 employees took advantage of the low-threshold testing facility. One percent (n = 11) were tested positive for SARS-CoV-2 infection, 18% being asymptomatic, 36% showing mild and 36% moderate/severe symptoms (missing 10%). Furthermore, of 56 employees returning from SARS-CoV-2 risk regions, 18% (10/56) were tested SARS-CoV-2 positive. After risk contact tracking by the hospital hygiene 6 patient-to-employee transmissions were identified in 163 employees with contact to 55 SARS-CoV-2 positive patients.

CONCLUSION

In the absence of easily accessible public SARS-CoV-2 testing facilities low-threshold SARS-CoV-2 testing facilities in hospitals with rapid testing resources help to identify SARS-CoV-2 infected employees with absent or mild symptoms, thus stopping the spread of infection in vulnerable hospital environments. High levels of professional infection prevention training and implementation of specialized wards as well as a perfectly working hospital hygiene network identifying and tracking risk contacts are of great importance in a pandemic setting.

AB1303-HPR TIME UNTIL DIAGNOSIS IN RHEUMATOLOGICAL PRACTICE: RESULTS FROM A CROSS-SECTIONAL MIDDLE-EUROPEAN COHORT COMPARED TO DATA FROM A SYSTEMATIC LITERATURE REVIEW

Background:

The time from first symptom to diagnosis (= diagnostic delay) is considered as key factor for better outcome in many chronic inflammatory rheumatic diseases, especially for rheumatoid arthritis (RA) and vasculitides like giant cell arteritis (GCA). A longer diagnostic delay may cause pain, reduced functionality, reduced life-quality and increased morbidity, as well as structural damages of the organs linked with higher mortality. This retrospective study assessed the diagnostic delay in consecutive Middle-European outpatients and compared results with those of a systematic literature review (SLR).

Objectives:

To compare disease-specific diagnostic delays of consecutive rheumatic patients with international data from a systematic literature review.

Methods:

Charts of a single-centre cohort with consecutively recruited patients were retrospectively reviewed for patients’ and diseases’ characteristics at a Middle-European university outpatient clinic for rheumatology. A SLR was performed according to PRISMA guidelines.

Results:

The average mean ± SD time from first symptom to established diagnosis was 7.9 ± 11.7 (0.02-56.7) years. Spondyloarthritis patients showed the longest diagnostic delay with 13.1 ± 14.2 (0.1-56.7) years, whereas polymyalgia rheumatica-patients had the shortest diagnostic delay with 1.5 ± 0.4 (0.3-18.0) months. In the SLR, most data for diagnostic delays are comparable to the Innsbruck cohort, but the diagnostic delay for psoriatic arthritis in Innsbruck is longer than in the Danish DANBIO registry (p<0.001). Independent risk factors for prolonged diagnostic delays could not be identified.

Conclusion:

For this Middle-European area, initiatives are justified especially to shorten diagnostic delays of SpA and PsA.

References:

[1]O’Dell JR. Treating rheumatoid arthritis early: A window of opportunity? Arthritis Rheum. 2002;46:283–5.

[2]Seo MR, Baek HL, Yoon HH, Ryu HJ, Choi HJ, Baek HJ, et al. Delayed diagnosis is linked to worse outcomes and unfavourable treatment responses in patients with axial spondyloarthritis. Clin Rheumatol. 2015;34:1397–405.

[3]Diagnostic delay of more than 6 months contributes to poor radiographic and functional outcome in psoriatic arthritis. Ann Rheum Dis. 2015;74:1045–50.

[4]Dejaco C, Brouwer E, Mason JC, Buttgereit F, Matteson EL, Dasgupta B. Giant cell arteritis and polymyalgia rheumatica: current challenges and opportunities. Nat Rev Rheumatol. Nature Publishing Group; 2017;13:578–92.

Acknowledgments:

We acknowledge and thank all patients who could be recruited to the SolutionX project. Ethical vote was obtained by the local ethics committee of the Medical University of Innsbruck (AN2017-0041 370/4.18).

Disclosure of Interests:

Rick Mc-Cutchan: None declared, Sarah Maier: None declared, Valentin Winkler: None declared, Bernhard Gruber: None declared, Michael Schirmer Grant/research support from: total <3000.- €, Speakers bureau: total <3000.- €

Taxonomy and conservation of grassland earless dragons: new species and an assessment of the first possible extinction of a reptile on mainland Australia

Taxonomic research is of fundamental importance in conservation management of threatened species, providing an understanding of species diversity on which management plans are based. The grassland earless dragon lizards (Agamidae: Tympanocryptis) of southeastern Australia have long been of conservation concern but there have been ongoing taxonomic uncertainties. We provide a comprehensive taxonomic review of this group, integrating multiple lines of evidence, including phylogeography (mtDNA), phylogenomics (SNPs), external morphology and micro X-ray CT scans. Based on these data we assign the lectotype of T. lineata to the Canberra region, restrict the distribution of T. pinguicolla to Victoria and name two new species: T. osbornei sp. nov. (Cooma) and T. mccartneyi sp. nov. (Bathurst). Our results have significant conservation implications. Of particular concern is T. pinguicolla, with the last confident sighting in 1969, raising the possibility of the first extinction of a reptile on mainland Australia. However, our results are equivocal as to whether T. pinguicolla is extant or extinct, emphasizing the immediate imperative for continued surveys to locate any remaining populations of T. pinguicolla. We also highlight the need for a full revision of conservation management plans for all the grassland earless dragons.

Trophic transfer of metals in a seagrass food web: Bioaccumulation of essential and non-essential metals

Metal concentrations are reported for a seagrass ecosystem receiving industrial inputs. δ¹³C and δ¹⁵N isotope ratios were used to establish trophic links. Copper concentrations (dry mass) ranged from <0.01 μg/g in fish species to 570 μg/g (μ = 49 ± SD = 90 μg/g) in the oyster Saccostrea glomerata. Zinc concentrations ranged from 0.6 μg/g in the seagrass Zostera capricorni to 10,800 μg/g in the mud oyster Ostrea angasi (μ = 434 ± 1390 μg/g). Cadmium concentrations ranged from <0.01 μg/g in fish species to 268 μg/g in Ostrea angasi (μ = 6 ± 25 μg/g). Lead concentrations ranged from <0.01 μg/g for most fish species to 20 μg/g in polychaetes (μ = 2 ± 3 μg/g). Biomagnification of metals did not occur. Organisms that fed on particulate organic matter and benthic microalgae had higher metal concentrations than those that fed on detritus. Species physiology also played an important role in the bioaccumulation of metals.

Confirmation of little eagle (Hieraaetus morphnoides) migration by satellite telemetry

The post-breeding migration of an adult male little eagle (Hieraaetus morphnoides) was followed from south-eastern Australia to the Northern Territory using a GPS satellite transmitter. The bird bred in open woodland habitat on the edge of the city of Canberra, Australian Capital Territory (ACT), before it flew more than 3300km in 18 days, to winter in an area of eucalypt savannah in the Northern Territory. It remained there for 59 days, within a range of ~30km2, after which the last signal was transmitted. The bird was subsequently resighted back in its ACT territory at the end of winter, thus completing a return migration. This is the first confirmation of post-breeding migration for the species.

Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups

Identifying geographical areas with the greatest representation of the tree of life is an important goal for the management and conservation of biodiversity. While there are methods available for using a single phylogenetic tree to assess spatial patterns of biodiversity, there has been limited exploration of how separate phylogenies from multiple taxonomic groups can be used jointly to map diversity and endemism. Here, we demonstrate how to apply different phylogenetic approaches to assess biodiversity across multiple taxonomic groups. We map spatial patterns of phylogenetic diversity/endemism to identify concordant areas with the greatest representation of biodiversity across multiple taxa and demonstrate the approach by applying it to the Murray–Darling basin region of southeastern Australia. The areas with significant centers of phylogenetic diversity and endemism were distributed differently for the five taxonomic groups studied (plant genera, fish, tree frogs, acacias, and eucalypts); no strong shared patterns across all five groups emerged. However, congruence was apparent between some groups in some parts of the basin. The northern region of the basin emerges from the analysis as a priority area for future conservation initiatives focused on eucalypts and tree frogs. The southern region is particularly important for conservation of the evolutionary heritage of plants and fishes.

Non-Invasive Genetic Mark-Recapture as a Means to Study Population Sizes and Marking Behaviour of the Elusive Eurasian Otter (Lutra lutra)

Quantifying population status is a key objective in many ecological studies, but is often difficult to achieve for cryptic or elusive species. Here, non-invasive genetic capture-mark-recapture (CMR) methods have become a very important tool to estimate population parameters, such as population size and sex ratio. The Eurasian otter (Lutra lutra) is such an elusive species of management concern and is increasingly studied using faecal-based genetic sampling. For unbiased sex ratios or population size estimates, the marking behaviour of otters has to be taken into account. Using 2132 otter faeces of a wild otter population in Upper Lusatia (Saxony, Germany) collected over six years (2006-2012), we studied the marking behaviour and applied closed population CMR models accounting for genetic misidentification to estimate population sizes and sex ratios. We detected a sex difference in the marking behaviour of otters with jelly samples being more often defecated by males and placed actively exposed on frequently used marking sites. Since jelly samples are of higher DNA quality, it is important to not only concentrate on this kind of samples or marking sites and to invest in sufficiently high numbers of repetitions of non-jelly samples to ensure an unbiased sex ratio. Furthermore, otters seemed to increase marking intensity due to the handling of their spraints, hence accounting for this behavioural response could be important. We provided the first precise population size estimate with confidence intervals for Upper Lusatia (for 2012: N = 20 ± 2.1, 95% CI = 16-25) and showed that spraint densities are not a reliable index for abundances. We further demonstrated that when minks live in sympatry with otters and have comparably high densities, a non-negligible number of supposed otter samples are actually of mink origin. This could severely bias results of otter monitoring if samples are not genetically identified.

Modeling food web structure and selenium biomagnification in Lake Macquarie, New South Wales, Australia, using stable carbon and nitrogen isotopes

As a consequence of coal-fired power station operations, elevated selenium concentrations have been reported in the sediments and biota of Lake Macquarie (New South Wales, Australia). In the present study, an ecosystem-scale model has been applied to determine how selenium in a seagrass food web is processed from sediments and water through diet to predators, using stable isotopes (δ(13) C and δ(15) N) to establish the trophic position of organisms. Trophic position, habitat, and feeding zone were examined as possible factors influencing selenium bioaccumulation. Selenium concentrations ranged from 0.2 μg/g dry weight in macroalgae species to 12.9 μg/g in the carnivorous fish Gerres subfasciatus. A mean magnification factor of 1.39 per trophic level showed that selenium is biomagnifying in the seagrass food web. Habitat and feeding zone influenced selenium concentrations in invertebrates, whereas feeding zone was the only significant factor influencing selenium concentrations in fish. The sediment-water partitioning coefficient (Kd ) of 4180 showed that partitioning of selenium entering the lake to particulate organic material (POM) is occurring, and consequently availability to food webs from POM is high. Trophic transfer factors (invertebrate = 1.9; fish = 1.2) were similar to those reported for other water bodies, showing that input source is not the main determinant of the magnitude of selenium bioaccumulation in a food web, but rather the initial partitioning of selenium into bioavailable POM. Environ Toxicol Chem 2015;34:608-617. © 2014 SETAC.

landgenreport: a new r function to simplify landscape genetic analysis using resistance surface layers

We describe functions recently added to the r package popgenreport that can be used to perform a landscape genetic analysis (LGA) based on landscape resistance surfaces, which aims to detect the effect of landscape features on gene flow. These functions for the first time implement a LGA in a single framework. Although the approach has been shown to be a valuable tool to study gene flow in landscapes, it has not been widely used to date, despite the type of data being widely available. In part, this is likely due to the necessity to use several software packages to perform landscape genetic analyses. To apply LGA functions, two types of data sets are required: a data set with spatially referenced and genotyped individuals, and a resistance layer representing the effect of the landscape. The function outputs three pairwise distance matrices from these data: a genetic distance matrix, a cost distance matrix and a Euclidean distance matrix. Statistical tests are performed to test whether the cost matrix contributes to the understanding of the observed population structure. A full report on the analysis and outputs in the form of plots and tables of all intermediate steps of the LGA is produced. It is possible to customize the LGA to allow for different cost path approaches and measures of genetic distances. The package is written in the r language and is available through the Comprehensive r Archive. Comprehensive tutorials and information on how to install and use the package are provided at the authors' website (www.popgenreport.org).

History of metal contamination in Lake Illawarra, NSW, Australia

Lake Illawarra has a long history of sediment contamination, particularly by metals, as a result of past and current industrial operations and land uses within the catchment. In this study, we examined the history of metal contamination in sediments using metal analysis and (210)Pb and (137)Cs dating. The distributions of copper, zinc, arsenic, selenium, cadmium and lead concentrations within sediment cores were in agreement with historical events in the lake, and indicated that metal contamination had been occurring since the start of industrial activities in Port Kembla in the late 1800 s. Most metal contamination, however, has occurred since the 1960s. Sedimentation rates were found to be 0.2 cm year(-1) in Griffins Bay and 0.3 cm year(-1) in the centre of the lake. Inputs from creeks bringing metals from Port Kembla in the northeast of the lake and a copper slag emplacement from a former copper refinery on the Windang Peninsula were the main sources of metal inputs to Lake Illawarra. The metals of highest concern were zinc and copper, which exceeded the Australian and New Zealand sediment quality guideline values at some sites. Results showed that while historical contamination persists, current management practices have resulted in reduced metal concentrations in surface sediments in the depositional zones in the centre of the lake.

Creating new evolutionary pathways through bioinvasion: the population genetics of brushtail possums in New Zealand

Rapid increases in global trade and human movement have created novel mixtures of organisms bringing with them the potential to rapidly accelerate the evolution of new forms. The common brushtail possum (Trichosurus vulpecula), introduced into New Zealand from Australia in the 19th century, is one such species having been sourced from multiple populations in its native range. Here, we combine microsatellite DNA- and GIS-based spatial data to show that T. vulpecula originating from at least two different Australian locations exhibit a population structure that is commensurate with their introduction history and which cannot be explained by landscape features alone. Most importantly, we identify a hybrid zone between the two subspecies which appears to function as a barrier to dispersal. When combined with previous genetic, morphological and captive studies, our data suggest that assortative mating between the two subspecies may operate at a behavioural or species recognition level rather than through fertilization, genetic incompatibility or developmental inhibition. Nevertheless, hybridization between the two subspecies of possum clearly occurs, creating the opportunity for novel genetic combinations that would not occur in their natural ranges and which is especially likely given that multiple contact zones occur in New Zealand. This discovery has implications for wildlife management in New Zealand because multiple contact zones are likely to influence the dispersal patterns of possums and because differential susceptibility to baiting with sodium fluoroacetate between possums of different origins may promote novel genetic forms.

A novel flow-based assay reveals discrepancies in ADAMTS-13 inhibitor assessment as compared with a conventional clinical static assay

BACKGROUND

Several static Bethesda-type assays are routinely used to determine ADAMTS-13-neutralizing autoantibodies in acquired thrombotic thrombocytopenic purpura (TTP), but the inhibitory activity of these antibodies has not been thoroughly evaluated under the more physiologic condition of flow.

OBJECTIVES

We investigated whether ADAMTS-13 inhibitor assessment with the FRETS-VWF73 assay is predictive for evaluation under flow.

METHODS

Anti-ADAMTS-13 autoantibodies were purified from patients with acquired TTP by chromatography involving an ADAMTS-13 affinity matrix and/or protein G. ADAMTS-13 activity was measured with the FRETS-VWF73 assay and a novel flow assay determining the ADAMTS-13-mediated decrease in platelet aggregate surface coverage, caused by perfusion of a suspension containing platelets, erythrocytes and von Willebrand factor (VWF) over a surface coated with extracellular matrix components. The neutralizing activities of ADAMTS-13 inhibitors were compared under static conditions and under flow by use of the two assays.

RESULTS

The suitability of the flow-based ADAMTS-13 activity assay for quantification of ADAMTS-13 inhibitors could be demonstrated by reversibility of the ADAMTS-13-dependent decrease in surface coverage upon addition of goat ADAMTS-13 antiserum. Testing the neutralizing activity of purified autoantibodies from six patients in the flow assay according to their FRETS-VWF73-based inhibitor titers gave rise to vastly different inhibitory effects, indicating a discrepancy in inhibitor assessment between static and flow conditions.

CONCLUSIONS

Anti-ADAMTS-13 autoantibodies may show inhibitory properties in vivo that are not consistent with the ADAMTS-13 inhibitor levels determined in routine static assays, possibly because certain epitopes are selectively exposed under shear. Consequently, the course of disease and treatment efficacy may vary among TTP patients, despite common inhibitor titers.

Recent history of sediment metal contamination in Lake Macquarie, Australia, and an assessment of ash handling procedure effectiveness in mitigating metal contamination from coal-fired power stations

This study assessed historical changes in metal concentrations in sediments of southern Lake Macquarie resulting from the activities of coal-fired power stations, using a multi-proxy approach which combines (210)Pb, (137)Cs and metal concentrations in sediment cores. Metal concentrations in the lake were on average, Zn: 67 mg/kg, Cu: 15 mg/kg, As: 8 mg/kg, Se: 2mg/kg, Cd: 1.5 mg/kg, Pb: 8 mg/kg with a maximum of Zn: 280 mg/kg, Cu: 80 mg/kg, As: 21 mg/kg, Se: 5 mg/kg, Cd: 4 mg/kg, Pb: 48 mg/kg. The ratios of measured concentrations in sediment cores to their sediment guidelines were Cd 1.8, As 1.0, Cu 0.5, Pb 0.2 and Zn 0.2, with the highest concern being for cadmium. Of special interest was assessment of the effects of changes in ash handling procedures by the Vales Point power station on the metal concentrations in the sediments. Comparing sediment layers before and after ash handling procedures were implemented, zinc concentrations have decreased 10%, arsenic 37%, selenium 20%, cadmium 38% and lead 14%. An analysis of contaminant depth profiles showed that, after implementation of new ash handling procedures in 1995, selenium and cadmium, the main contaminants in Australian black coal had decreased significantly in this estuary.

Metal mobilization from soils by phytosiderophores - experiment and equilibrium modeling

AIMS

To test if multi-surface models can provide a soil-specific prediction of metal mobilization by phytosiderophores (PS) based on the characteristics of individual soils.

METHODS

Mechanistic multi-surface chemical equilibrium modeling was applied for obtaining soil-specific predictions of metal and PS speciation upon interaction of the PS 2'-deoxymugineic acid (DMA) with 6 soils differing in availability of Fe and other metals. Results from multi-surface modeling were compared with empirical data from soil interaction experiments.

RESULTS

For soils in which equilibrium was reached during the interaction experiment, multi-surface models could well predict PS equilibrium speciation. However, in uncontaminated calcareous soils, equilibrium was not reached within a week, and experimental and modeled DMA speciation differed considerably. In soils with circum-neutral pH, on which Fe deficiency is likely to occur, no substantial Fe mobilization by DMA was predicted. However, in all but the contaminated soils, Fe mobilization by DMA was observed experimentally. Cu and Ni were the quantitatively most important metals competing with Fe for complexation and mobilization by DMA.

CONCLUSION

Thermodynamics are unable to explain the role of PS as Fe carrier in calcareous soils, and the kinetic aspects of metal mobilization by PS need to be closer examined in order to understand the mechanisms underlying strategy II Fe acquisition.