Native-born Research Articles

Expansion of a retrovirus lineage in the koala genome

Retroviruses have left their legacy in host genomes over millions of years as endogenous retroviruses (ERVs), and their structure, diversity, and prevalence provide insights into the historical dynamics of retrovirus-host interactions. In bioinformatic analyses of koala (Phascolarctos cinereus) whole-genome sequences, we identify a recently expanded ERV lineage (phaCin-β) that is related to the New World squirrel monkey retrovirus. This ERV expansion shares many parallels with the ongoing koala retrovirus (KoRV) invasion of the koala genome, including highly similar and mostly intact sequences, and polymorphic ERV loci in the sampled koala population. The recent phaCin-β ERV colonization of the koala genome appears to predate the current KoRV invasion, but polymorphic ERVs and divergence comparisons between these two lineages predict a currently uncharacterized, possibly still extant, phaCin-β retrovirus. The genomics approach to ERV-guided discovery of novel retroviruses in host species provides a strong incentive to search for phaCin-β retroviruses in the Australasian fauna.

Comparative Study of Brain Size Ontogeny: Marsupials and Placental Mammals.

Simple SummaryThis study examined brain/body ontogenetic growth in marsupials and compared it with placental mammals. While marsupials display morphology and cerebral organization diverse from placentals, their neocortical arrangement and cellular composition is unclear. Unfortunately, knowledge of marsupial ontogenetic brain/body size allometry is limited. Since marsupial brain structure and volume differ when compared with those of placentals, marsupials are considered to possess simple behavioural patterns. This is misleading, since even at a basic observation, Australian marsupials display many of the same mental capacities as other mammals. Consequently, the study findings support further investigation into the intellectual abilities of marsupials.There exists a negative allometry between vertebrate brain size and body size. It has been well studied among placental mammals but less is known regarding marsupials. Consequently, this study explores brain/body ontogenetic growth in marsupials and compares it with placental mammals. Pouch young samples of 43 koalas (Phascolarctos cinereus), 28 possums (Trichosurus vulpecula), and 36 tammar wallabies (Macropus eugenii) preserved in a solution of 10% buffered formalin, as well as fresh juveniles and adults of 43 koalas and 40 possums, were studied. Their brain size/body size allometry was compared to that among humans, rhesus monkeys, dogs, cats, rats, guinea pigs, rabbits, wild pigs, and mice. Two patterns of allometric curves were found: a logarithmic one (marsupials, rabbits, wild pigs, and guinea pigs) and a logistic one (the rest of mammals).

Genetic erosion detected in a specialist mammal living in a fast‐developing environment

AbstractFragmentation of habitat is a major threat across a wide range of taxa. Subsequent effects include reduced population sizes and isolation of populations. Both can have detrimental consequences for populations as they increase the risk of genetic erosion. While it is critical to prevent and, if required, reverse genetic erosion, we often lack adequate data to assess whether and how much genetic erosion has occurred. Here, we present a genetic monitoring study where we investigated changes in genetic diversity and genetic patterns in a threatened, specialist mammal, the koala (Phascolarctos cinereus). Our study population inhabits an increasingly fragmented landscape and has experienced a sharp decline in population size within the past three decades. We used 1038 single nucleotide polymorphic loci (SNPs) to compare measures of genetic diversity between samples collected in 2018 and in 2006 (two generations prior) and investigated simultaneous changes in the environment. We found a decline in both heterozygosity and effective population size (Ne), and an increase in sub‐structuring, average relatedness, and inbreeding (FIS) alongside an increasingly threatening and more fragmented environment. Given the extent of genetic erosion in only two generations, we urge consideration for the implementation of mitigation measures for this population and for threatened populations in similar conditions. Our study further emphasizes the importance of effective management of at‐risk populations including monitoring of genetic erosion.

Koala retrovirus load and non-A subtypes are associated with secondary disease among wild northern koalas.

Koala Retrovirus (KoRV) has been associated with neoplasia in the vulnerable koala (Phascolarctos cinereus). However, there are conflicting findings regarding its association with secondary disease. We undertook a large-scale assessment of how the different KoRV subtypes and viral load are associated with Chlamydia pecorum infection and a range of disease pathologies in 151 wild koalas admitted for care to Currumbin Wildlife Hospital, Australia. Viral load (KoRV pol copies per ml of plasma) was the best predictor of more disease pathologies than any other KoRV variable. The predicted probability of a koala having disease symptoms increased from 25% to over 85% across the observed range of KoRV load, while the predicted probability of C. pecorum infection increased from 40% to over 80%. We found a negative correlation between the proportion of env deep sequencing reads that were endogenous KoRV-A and total KoRV load. This is consistent with suppression of endogenous KoRV-A, while the exogenous KoRV subtypes obtain high infection levels. Additionally, we reveal evidence that the exogenous subtypes are directly associated with secondary disease, with the proportion of reads that were the endogenous KoRV-A sequence a negative predictor of overall disease probability after the effect of KoRV load was accounted for. Further, koalas that were positive for KoRV-D or KoRV-D/F were more likely to have urogenital C. pecorum infection or low body condition score, respectively, irrespective of KoRV load. By contrast, our findings do not support previous findings that KoRV-B in particular is associated with Chlamydial disease. Based on these findings we suggest that koala research and conservation programs should target understanding what drives individual differences in KoRV load and limiting exogenous subtype diversity within populations, rather than seeking to eliminate any particular subtype.

Birthright Granted and Revoked: The Effects of Irish Citizenship Policy on Migrant Fertility

I examine Ireland's experiment with birthright citizenship between 1999 and 2004. Critics argue that birthright citizenship may induce higher migrant fertility and threaten national identity. I find that migrants arriving during birthright citizenship had lower fertility rates than those arriving before the policy was implemented and after it was revoked. These migrants were better educated and more likely to be employed, suggesting that birthright citizenship made Ireland a more attractive destination for high-skill migrants. I find evidence that non-UK migrants already in Ireland before 1999 increased fertility in response to birthright citizenship, though their fertility was still below that of natives.

A novel alphaherpesvirus and concurrent respiratory cryptococcosis in a captive koala (Phascolarctos cinereus).

A novel alphaherpesvirus was detected in a captive adult, lactating, female koala (Phascolarctos cinereus) admitted to James Cook University Veterinary Emergency Teaching & Clinical Hospital in March 2019, showing signs of anorexia and severe respiratory disease. Postmortem examination revealed gross pathology indicative of pneumonia. Histopathology demonstrated a chronic interstitial pneumonia, multifocal necrotising adrenalitis and hepatitis. Intranuclear inclusion bodies were detected by light microscopy in the respiratory epithelium of the bronchi, bronchioles, alveoli, and hepatocytes, biliary epithelium and adrenal gland associated with foci of necrosis. Cryptococcus gattii was isolated from fresh lung on necropsy, positively identified by PCR, and detected histologically by light microscopy, only in the lung tissue. A universal viral family‐level PCR indicated that the virus was a member of the Herpesviruses. Sequence analysis in comparison to other known and published herpesviruses, indicated the virus was a novel alphaherpesvirus, with 97% nucleotide identity to macropodid alphaherpesvirus 1. We provisionally name the novel virus phascolarctid alphaherpesvirus 3 (PhaHV‐3). Further research is needed to determine the distribution of this novel alphaherpesvirus in koala populations and establish associations with disease in this host species.

Field Testing Satellite-Derived Vegetation Health Indices for a Koala Habitat Managers Toolkit

A Central Queensland University (CQU) partnership with the Queensland Government National Park management agency has developed a koala (Phascolarctos cinereus) habitat managers’ toolkit for vegetation health assessment. Private and public landholders use the field-based toolkit to assess habitat suitability or monitor conservation outcomes for the koala—an iconic Australian arboreal herbivorous marsupial. The toolkit was upgraded recently with instructions to process European Space Agency (ESA) Sentinel-2 multispectral satellite-derived selected vegetation maps for areal vegetation health trend monitoring. A field campaign sought to validate the relatively coarse spatial resolution derived indices (photosynthetic health, leaf area index and leaf water content) to verify their suitability for the habitat management decision-support toolkit. Other user requirement-driven criteria for including remote sensing in the toolkit were imagery and associated processing software costs and ease of map production for habitat managers without cost-effective access to spatial science skills. Despite moderate-to-low field and image vegetation proxy correlations, discussing the results with stakeholders indicates that, at a landscape scale, the use of cost-free, suitable temporal resolution, 10-m spatial resolution imagery is satisfactory when aligned with the design outcomes of a habitat health toolkit.

Future-proofing the koala: Synergising genomic and environmental data for effective species management.

Climatic and evolutionary processes are inextricably linked to conservation. Avoiding extinction in rapidly changing environments often depends upon a species' capacity to adapt in the face of extreme selective pressures. Here, we employed exon capture and high-throughput next-generation sequencing to investigate the mechanisms underlying population structure and adaptive genetic variation in the koala (Phascolarctos cinereus), an iconic Australian marsupial that represents a unique conservation challenge because it is not uniformly threatened across its range. An examination of 250specimens representing 91 wild source locations revealed that five major genetic clusters currently exist on a continental scale. The initial divergence of these clusters appears to have been concordant with the Mid-Brunhes Transition (~430 to 300kya), a major climatic reorganisation that increased the amplitude of Pleistocene glacial-interglacial cycles. While signatures of polygenic selection and environmental adaptation were detected, strong evidence for repeated, climate-associated range contractions and demographic bottleneck events suggests that geographically isolated refugia may have played a more significant role in the survival of the koala through the Pleistocene glaciation than in situ adaptation. Consequently, the conservation of genome-wide genetic variation must be aligned with the protection of core koala habitat to increase the resilience of vulnerable populations to accelerating anthropogenic threats. Finally, we propose that the five major genetic clusters identified in this study should be accounted for in future koala conservation efforts (e.g., guiding translocations), as existing management divisions in the states of Queensland and New South Wales do not reflect historic or contemporary population structure.

Modelling Genetic Benefits and Financial Costs of Integrating Biobanking into the Captive Management of Koalas.

Simple SummaryManaged wildlife breeding faces high costs and genetic diversity challenges associated with caring for small populations. Biobanking (freezing of sex cells and tissues for use in assisted breeding) and associated reproductive technologies could help alleviate these issues in koala captive management by enhancing retention of genetic diversity in captive-bred animals and lowering program costs through reductions in the size of the required live captive colonies. Australia’s zoos and wildlife hospitals provide rare opportunities to refine and cost-effectively integrate these tools into conservation outcomes for koalas due to extensive already-existing infrastructure, technical expertise, and captive animals.Zoo and wildlife hospital networks are set to become a vital component of Australia’s contemporary efforts to conserve the iconic and imperiled koala (Phascolarctos cinereus). Managed breeding programs held across zoo-based networks typically face high economic costs and can be at risk of adverse genetic effects typical of unavoidably small captive colonies. Emerging evidence suggests that biobanking and associated assisted reproductive technologies could address these economic and genetic challenges. We present a modelled scenario, supported by detailed costings, where these technologies are optimized and could be integrated into conservation breeding programs of koalas across the established zoo and wildlife hospital network. Genetic and economic modelling comparing closed captive koala populations suggest that supplementing them with cryopreserved founder sperm using artificial insemination or intracytoplasmic sperm injection could substantially reduce inbreeding, lower the required colony sizes of conservation breeding programs, and greatly reduce program costs. Ambitious genetic retention targets (maintaining 90%, 95% and 99% of source population heterozygosity for 100 years) could be possible within realistic cost frameworks, with output koalas suited for wild release. Integrating biobanking into the zoo and wildlife hospital network presents a cost-effective and financially feasible model for the uptake of these tools due to the technical and research expertise, captive koala colonies, and ex situ facilities that already exist across these networks.

A Possible Link between the Environment and Cryptococcus gattii Nasal Colonisation in Koalas (Phascolarctos cinereus) in the Liverpool Plains, New South Wales.

Cryptococcosis caused by yeasts of the Cryptococcus gattii species complex is an increasingly important mycological disease in humans and other mammals. In Australia, cases of C. gattii-related cryptococcosis are more prevalent in the koala (Phascolarctos cinereus) compared to humans and other animals, likely due to the close association that both C. gattii and koalas have with Eucalyptus species. This provides a cogent opportunity to investigate the epidemiology of spontaneous C. gattii infections in a free-living mammalian host, thereby offering insights into similar infections in humans. This study aimed to establish a link between nasal colonisation by C. gattii in free-ranging koalas and the tree hollows of Eucalyptus species, the key environmental source of the pathogen. We (i) detected and genotyped C. gattii from nine out of 169 free-ranging koalas and representative tree hollows within their home range in the Liverpool Plains, New South Wales, and (ii) examined potential environmental predictors of nasal colonisation in koalas and the presence of C. gattii in tree hollows. Phylogenetic analyses based on multi-locus sequence typing (MLST) revealed that the koalas were most likely colonised by the most abundant C. gattii genotypes found in the Eucalyptus species, or closely related genotypes. Importantly, the likelihood of the presence of C. gattii in tree hollows was correlated with increasing hollow size.

Режимы гражданства в странах Евросоюза и включение населения мигрантского происхождения в политическое сообщество

The article is devoted to the analysis of differences in the approaches of European Union member states to the inclusion of migrants into the political community by granting them citizenship. These differences are operationalized through the category of “citizenship regimes”. The article distingui shes three types of citizenship regimes — liberal, restrictive, and mixed. Whether a particular regime can be categorized into one of these citizenship regime types is determined on the basis of three indicators: (1) application/nonapplication of birthright citizenship (jus soli), (2) the presence of the institution of dual (multiple) citizenship, and (3) the relative simplicity/complexity of the naturalization procedure. At the same time, due to the lack of the comprehensive statistical data, which would allow assessing all possible components of this procedure, in order to evaluate the degree of the simplicity/complexity of the procedure, the authors focus on such a parameter as the minimum time period of residence in the country required to apply for citizenship. Having considered the evolution of the legal systems of the EU states, the authors reveal important differences in the approaches to the naturalization of migrants along the axis between the “old” countries of the European Union, on the one hand, and new members of the United Europe from the former socialist countries, on the other. While the “old” EU members tend to gradually liberalize citizenship regimes, the new ones are leaning towards a restrictive model, which manifests itself both in the difficult conditions of naturalization and rejection of the birthright citizenship law. The convergence of the positions of these two groups of countries on this issue is not visible.

Case series: Computed tomography (CT) demonstrates lacrimal canal involvement in koalas (Phascolarctos cinereus) with maxillary incisor dental disease.

Dental disease is common in wild and captive koalas. Effective treatments are limited and dental disease may not be recognised until it is quite severe. We describe the appearance of varying severities of dental disease on computed tomography (CT) images in a case series of six koalas. This case series demonstrates the use of CT to detect both mild and severe dental disease in koalas. The study also documents the normal CT appearance of the nasolacrimal duct in the koala. The only clinical abnormality in koalas with the mildest dental disease was ocular discharge. Computed tomography findings associated with ocular discharge were periapical lysis of first maxillary incisors, lacrimal canal remodelling and subsequent nasolacrimal duct obstruction. Dental disease should be a differential diagnosis for ocular discharge in koalas and CT examination enables visualisation of early stages of dental disease.

Democracy as Fetish, by Ralph Cintron, University Park: Penn State University Press

Democracy as Fetish, by Ralph Cintron, University Park: Penn State University Press

Until Justice Be Done: America's First Civil Rights Movement, from the Revolution to Reconstruction

Until Justice Be Done: America's First Civil Rights Movement, from the Revolution to Reconstruction

Differentiation from above and below: Evolving immigration policy and the integration dilemma in Singapore

Singapore is known for differentiating highly skilled and low-skilled migrants by regulating their social rights, employment, and pathways to permanent residency and citizenship. Since 2009, the city-state has made further differentiation between highly skilled migrants and natives, that is, native-born citizens. Existing studies on migrant differentiation mostly adopt a state-centric perspective. We argue that differentiation is also driven by forces from below. We introduce the concept of differential fairness to capture natives’ justification for differentiation between themselves and migrants, particularly the highly skilled. Drawing on survey data and in-depth interviews with natives and Chinese and Indian migrants, we show that natives demand for preferential policies to protect their interests. We further reveal that the measures of differentiation have created an integration dilemma, in which natives and migrants hold divergent views on fairness and expectations of migrant integration.

Imprisonment and Citizenship in Senegal, 1917–1946: The Case of the Originaires

This paper examines the incarceration of the Originaires in colonial Senegal to illuminate how imprisonment had shaped or altered their French citizenship rights in prisons. Among the prison population in colonial Senegal were some Originaires, the residents of the Four Communes who were granted French citizenship rights as early as 1833, a status that remained ambiguous until 1916 when a new law made them full-pledged French citizens. But the colonial government restrictions on access to full French citizenship rights in the Four Communes compelled the Originaires to mobilize to defend those rights. Their struggle found a breeding ground in the colonial prisons where some Originaire prisoners made two types of claims: to equality with European prisoners based on notions of birthright citizenship and cultural claims to being a different category of prisoners that deserved differential treatment compared to “natives.” By building their requests for equal admission to the European regime around the violation of their citizenship rights, this study will demonstrate that Originaire prisoners made arguments that tied their claims-making specifically to race and status without losing sight of the cultural differences between themselves and “native” prisoners, all in the context of a racially segregated prison world.

Fire severity and its local extent are key to assessing impacts of Australian mega‐fires on koala (Phascolarctos cinereus) density

AbstractAimMega‐fires are predicted to increase with climate change. Australia experienced the largest ever documented forest fires in 2019–2020, but the response of most taxa remains poorly known. We used acoustic arrays to estimate impact of the mega‐fires on the density of an iconic marsupial.LocationNorth‐east New South Wales, Australia.Time periodPre‐fire density estimated in 2018–2019 and post‐fire density in 2019–2020.Major taxa studiedKoala, Phascolarctos cinereus.MethodsWe estimated male density before and after fires using large acoustic arrays and spatial count models. Acoustic arrays sampled three timber production forests with a gradient in fire severity and three unburnt controls in national parks.ResultsKoalas were temporarily extirpated where high fire severity dominated the landscape, but some localized recovery was evident after 1 year. Where moderate severity fire dominated, density was reduced by about 50% within 1 year, but koalas were widespread throughout the burnt area. In our third area dominated by low severity fire, no impact was detected as pre‐ and post‐fire uncertainty intervals overlapped. Control sites surveyed at similar times showed little change in density between years. There was no relationship between pyrodiversity and koala density. Within arrays broadly dominated by moderate or high severity fire, density 1 year after fire was lower in burnt patches of both low and high severity fire. Regionally, 9.8% of landscape samples (2 km × 2 km) in koala habitat were dominated by high fire severity, while a further 6.1% were dominated by moderate fire severity, suggesting c. 13% decline in koala density.Main conclusionsA substantial impact of high severity fire was confirmed. Severe impacts were localized across the landscape, recovery had begun within a year and resilience was evident where low severity fire dominated. However, more frequent fires in the future will compound koala losses.

Chlamydiosis and Cystic Dilatation of the Ovarian Bursa in Female Koalas (Phascolarctos cinereus): Novel Insights into the Pathogenesis and Mechanisms of Formation

Chlamydiosis and Cystic Dilatation of the Ovarian Bursa in Female Koalas (Phascolarctos cinereus): Novel Insights into the Pathogenesis and Mechanisms of Formation

How microbiomes can help inform conservation: landscape characterisation of gut microbiota helps shed light on additional population structure in a specialist folivore

BackgroundThe koala (Phascolarctos cinereus), an iconic yet endangered specialised folivore experiencing widespread decline across Australia, is the focus of many conservation programs. Whilst animal translocation and progressive conservation strategies such as faecal inoculations may be required to bring this species back from the brink of extinction, insight into the variation of host-associated gut microbiota and the factors that shape this variation are fundamental for their success. Despite this, very little is known about the landscape variability and factors affecting koala gut microbial community dynamics. We used large scale field surveys to evaluate the variation and diversity of koala gut microbiotas and compared these diversity patterns to those detected using a population genetics approach. Scat samples were collected from five locations across South East Queensland with microbiota analysed using 16S rRNA gene amplicon sequencing.ResultsAcross the landscape koala gut microbial profiles showed large variability, with location having a large effect on bacterial community composition and bacterial diversity. Certain bacteria were found to be significantly differentially abundant amongst locations; koalas from Noosa showed a depletion in two bacterial orders (Gastranaerophilales and Bacteroidales) which have been shown to provide beneficial properties to their host. Koala gut microbial patterns were also not found to mirror population genetic patterns, a molecular tool often used to design conservation initiatives.ConclusionsOur data shows that koala gut microbiotas are extremely variable across the landscape, displaying complex micro- and macro- spatial variation. By detecting locations which lack certain bacteria we identified koala populations that may be under threat from future microbial imbalance or dysbiosis. Additionally, the mismatching of gut microbiota and host population genetic patterns exposed important population structure that has previously gone undetected across South East Queensland. Overall, this baseline data highlights the importance of integrating microbiota research into conservation biology in order to guide successful conservation programs such as species translocation and the implementation of faecal inoculations.

The New Deal for New Americans: Immigration Status and Mental Health

Extreme circumstances immigrants experience causes them to have a higher risk for mental health problems. It gets even more severe for refugees than host populations and other migrant groups. Thus, in this paper, mental health disparities between native-born citizens and refugees in the US will be investigated by considering social policies. Firstly, immigration status in the US will be investigated in terms of its relation to mental health. Then, mental health will be examined, and the focus will be on anxiety disorders and depression as these are the two common disorders among refugees. In the following section, Social-Ecological Model will be used as a framework to explain the relationship between immigration status and mental health. The Refugee Act of 1980 and The New Deal for New Americans Act will be used to understand the current political climate in terms of the refugee situation in the US, and we will examine how this has an impact on refugees' mental health. This paper will be concluded after mentioning the obstacles and the recommendations.