The genetic consequences of demography and disturbance in small mammal populations

Social, demographic and ecological processes shape patterns of genetic diversity. These patterns can therefore reveal insights into the biology of species and the response of populations to disturbance. During my PhD, I used a combination of computer simulations, molecular techniques and field-based experiments to explore how biological and ecological processes shape populations and their underlying genetic diversity. Dispersal and mating systems have long been known to shape population-level patterns of genetic structure. However, few studies focus on how these processes shape spatial genetic patterns within populations. Using the agile antechinus (Antechinus agilis) as a model, I carried out computer simulations to investigate how dispersal and mating behaviour shape fine-scale genetic structure (over the scale of metres) across autosomal, mitochondrial and Y chromosome markers. While dispersal was the major driver of fine-scale genetic structure, variation in mating behaviour also created differences in the level of structure detected at uniparentally inherited markers. Thus, comparing sex-specific patterns across markers with differing modes of inheritance can help elucidate demographic processes occurring within populations. In addition to microsatellite, mitochondrial and Y chromosome markers, high throughput sequencing data is becoming increasingly accessible for ecological research. However, decisions about marker choice, bioinformatic pipelines and filtering can be overwhelming for experts and non-experts alike. Through my empirical research focusing on a native Australian rodent, the pale field-rat (Rattus tunneyi), in the Kimberley region of Western Australia, I explored how marker choice and bioinformatic methods influence biological conclusions. Genetic analyses revealed low levels of genetic structure across this disturbance-prone landscape. While population-level estimates of genetic structure were fairly robust, measures of heterozygosity and diversity differed among marker types and filtering criteria. This demonstrates the importance of understanding how methodological decisions can impact biological inference from genetic data. The pale field-rat is one of many small mammals declining across northern Australia. This is due, in part, to the interaction between altered fire regimes and other key threats. To better understand this decline, I investigated habitat preferences, fire response and post-fire population recovery using a replicated fire experiment and capture-mark-recapture study. Mixed modelling showed that capture rate was negatively correlated with the extent of experimental fire, and that pale field-rat habitat preferences did not change in the post-fire landscape. However, all populations completely recovered one year after fire. The fire experiment suggested that spatial recovery processes differed according to the size and spatial pattern of fires. To test these different recovery hypotheses, I used parentage and genetic spatial autocorrelation analysis to explore patterns of relatedness before and after fire. This indicated that post-fire recovery after patchy fires was driven by in situ survivors from within unburnt refuges, compared to recolonisation after thorough fires. Furthermore, changes in female dispersal strategies appeared to be driving these different recovery patterns. These results suggest that fire management should aim to maximise the patchiness of burns and limit their extent in order to facilitate recovery of small mammals in this system. My thesis demonstrates that the combined use of computer simulations, direct field research and genetic analyses can reveal novel insights into the demographic processes occurring within populations and the response of populations to disturbance. I discuss how these insights add to our understanding of mammal declines in northern Australia and can be used to inform fire management

The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers

For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens—hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual‐level simulations to investigate the effects of dispersal and mating system on fine‐scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine‐scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex‐biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine‐scale genetic structure.This study was part of a PhD project by R.E.S. carried out with the support of an Australian Postgraduate Award Scholarship. S.C.B. was supported by an Australian Research Council Future Fellowship (FT130100043)

Do schools and alcohol mix? Australian parents\u27 perspectives

© 2020, Emerald Publishing Limited. Purpose: Alcohol use by adults at school events and alcohol promotion through school fundraising activities is common, but little is known about secondary school parents\u27 attitudes towards these practices. Parental attitudes may influence principals\u27 decision-making on this topic, particularly in jurisdictions where education department guidance is limited. This study explored parents\u27 attitudes towards the consumption or promotion of alcohol in schools or at school events. Design/methodology/approach: Parents (n = 298) from five non-government secondary schools in Western Australia completed an online survey and provided responses relating to the promotion and availability of alcohol through their child\u27s school. Findings: This sample of parents were evenly divided in support of alcohol consumption or support of schools as alcohol-free zones. Parents reporting higher alcohol consumption were more supportive of alcohol promotion and use through schools, and those with higher education supported use of alcohol for school fundraising. Almost 20% of parents were neutral on several measures indicating they could be swayed by social pressure. Engaging parents is an ongoing challenge for school principals and alcohol may play a part in engagement activities. The results from this small, exploratory study suggest even engaged parents may have very differing views on alcohol use in schools. Practical implications: Education departments are encouraged to explore these issues carefully and introduce changes incrementally to assist decision-making and minimise potential parent disengagement. Originality/value: This paper addresses a knowledge gap about parents\u27 attitudes towards alcohol in secondary schools. These findings can support those involved in the development of school alcohol policies

Nanoscale protein architecture of the kidney glomerular basement membrane

In multicellular organisms, proteins of the extracellular matrix (ECM) play structural and functional roles in essentially all organs, so understanding ECM protein organization in health and disease remains an important goal. Here, we used sub-diffraction resolution stochastic optical reconstruction microscopy (STORM) to resolve the in situ molecular organization of proteins within the kidney glomerular basement membrane (GBM), an essential mediator of glomerular ultrafiltration. Using multichannel STORM and STORM-electron microscopy correlation, we constructed a molecular reference frame that revealed a laminar organization of ECM proteins within the GBM. Separate analyses of domains near the N- and C-termini of agrin, laminin, and collagen IV in mouse and human GBM revealed a highly oriented macromolecular organization. Our analysis also revealed disruptions in this GBM architecture in a mouse model of Alport syndrome. These results provide the first nanoscopic glimpse into the organization of a complex ECM. DOI: http://dx.doi.org/10.7554/eLife.01149.00

Dysregulation of the haem-haemopexin axis is associated with severe malaria in a case-control study of Ugandan children.

BACKGROUND: Malaria is associated with haemolysis and the release of plasma haem. Plasma haem can cause endothelial injury and organ dysfunction, and is normally scavenged by haemopexin to limit toxicity. It was hypothesized that dysregulation of the haem-haemopexin pathway contributes to severe and fatal malaria infections. METHODS: Plasma levels of haemin (oxidized haem), haemopexin, haptoglobin, and haemoglobin were quantified in a case-control study of Ugandan children with Plasmodium falciparum malaria. Levels at presentation were compared in children with uncomplicated malaria (UM; n = 29), severe malarial anaemia (SMA; n = 27) or cerebral malaria (CM; n = 31), and evaluated for utility in predicting fatal (n = 19) vs non-fatal (n = 39) outcomes in severe disease. A causal role for haemopexin was assessed in a pre-clinical model of experimental cerebral malaria (ECM), following disruption of mouse haemopexin gene (hpx). Analysis was done using Kruskall Wallis tests, Mann-Whitney tests, log-rank tests for survival, and repeated measures ANOVA. RESULTS: In Ugandan children presenting with P. falciparum malaria, haemin levels were higher and haemopexin levels were lower in SMA and CM compared to children with UM (haemin, p \u3c 0.01; haemopexin, p \u3c 0.0001). Among all cases of severe malaria, elevated levels of haemin and cell-free haemoglobin at presentation were associated with subsequent mortality (p \u3c 0.05). Compared to ECM-resistant BALB/c mice, susceptible C57BL/6 mice had lower circulating levels of haemopexin (p \u3c 0.01), and targeted deletion of the haemopexin gene, hpx, resulted in increased mortality compared to their wild type littermates (p \u3c 0.05). CONCLUSIONS: These data indicate that plasma levels of haemin and haemopexin measured at presentation correlate with malaria severity and levels of haemin and cell-free haemoglobin predict outcome in paediatric severe malaria. Mechanistic studies in the ECM model support a causal role for the haem-haemopexin axis in ECM pathobiology

Low-calorie diets for people with isolated impaired fasting glucose

Standard lifestyle interventions prove ineffective in preventing type 2 diabetes among individuals with isolated impaired fasting glucose, a highly prevalent prediabetes phenotype globally. Here, we propose low-calorie diets as a promising strategy for diabetes prevention in this high-risk population

Measuring the effect of wing tears on flight in common pipistrelle bats (Pipistrellus pipistrellus)

Bat wings are susceptible to tearing. Many bats are admitted to care with wing tears and their flight is subjectively measured prior to release. This study presents a new method to objectively measure the effect of bat wing tears on the flight of common pipistrelle bats, Pipistrellus pipistrellus. Bats were filmed and their wing movements and body positions tracked using freely available software. Results found that bats with bilateral tears moved their wings with smaller movements, and with more wing beats per second. Bats with wing tears tended to tilt their whole body towards the healthier wing - which is the wing with no or smaller wing tears. Differences in wing movements and body positioning suggest that flight might be affected in bats with wing tears, and future work should assess whether foraging and survival are also affected in these animals

Cost-effectiveness of a lifestyle intervention in high-risk individuals for diabetes in a low- and middle-income setting:Trial-based analysis of the Kerala Diabetes Prevention Program

BACKGROUND: Data on the cost-effectiveness of lifestyle-based diabetes prevention programs are mostly from high-income countries, which cannot be extrapolated to low- and middle-income countries. We performed a trial-based cost-effectiveness analysis of a lifestyle intervention targeted at preventing diabetes in India. METHODS: The Kerala Diabetes Prevention Program was a cluster-randomized controlled trial of 1007 individuals conducted in 60 polling areas (electoral divisions) in Kerala state. Participants (30-60 years) were those with a high diabetes risk score and without diabetes on an oral glucose tolerance test. The intervention group received a 12-month peer-support lifestyle intervention involving 15 group sessions delivered in community settings by trained lay peer leaders. There were also linked community activities to sustain behavior change. The control group received a booklet on lifestyle change. Costs were estimated from the health system and societal perspectives, with 2018 as the reference year. Effectiveness was measured in terms of the number of diabetes cases prevented and quality-adjusted life years (QALYs). Three times India's gross domestic product per capita (US$6108) was used as the cost-effectiveness threshold. The analyses were conducted with a 2-year time horizon. Costs and effects were discounted at 3$2.0 (intervention group: US$303.6; control group: US$301.6), incremental societal cost of US$6.2 (intervention group: US$367.8; control group: US$361.5), absolute risk reduction of 2.1$95.2, and the cost per QALY gained was US$50.0. From a societal perspective, the corresponding figures were US$295.1 and US$155.0. For the number of diabetes cases prevented, the probability for the intervention to be cost-effective was 84.0% and 83.1% from the health system and societal perspectives, respectively. The corresponding figures for QALY gained were 99.1% and 97.8%. The results were robust to discounting and sensitivity analyses. CONCLUSIONS: A community-based peer-support lifestyle intervention was cost-effective in individuals at high risk of developing diabetes in India over 2 years. TRIAL REGISTRATION: The trial was registered with Australia and New Zealand Clinical Trials Registry ( ACTRN12611000262909 ). Registered 10 March 2011

PL-016 Endurance training, muscle fibre type composition and the maximal capacity for fat oxidation

Objective A greater capacity for fat oxidation in endurance trained athletes is linked to greater utilisation of intramuscular lipid (IMCL). IMCL breakdown occurs only in type I muscle fibres yet little is known about the fibre type specific abundance of lipid regulatory proteins. We explored the impact of endurance training on the maximal rate fat oxidation, muscle fibre type and muscle fibre type specific abundance of proteins regulating IMCL metabolism. Methods Endurance trained (n=7, 28 ± 3 years, VO2max62.6 ± 1.6 ml·min-1·kg-1) and untrained (n=8, 25 ± 1 years, VO2max44.9 ± 1.9 ml·min-1·kg-1) males performed an incremental exercise test to determine maximal fat oxidation rate. Muscle fibre type composition and fibre type-specific IMCL content was assessed with immunofluorescence microscopy and protein abundance was analysed with immunoblotting on pooled single muscle fibres and whole muscle. Results Endurance trained individuals displayed a higher peak fat oxidation rate (0.49 ± 0.05 vs. 0.20 ± 0.03 g·min-1, P<0.05), which correlated with type I fibre percentage (R = 0.83, P < 0.01) and VO2max (R = 0.78, P < 0.01). Type I muscle fibres from endurance trained individuals had a greater abundance of ATGL. In whole muscle, the endurance trained group had greater abundance of PLIN2, PLIN5 and ATGL compared to the untrained group (P < 0.05). Furthermore, autophagy flux measured as LC3-II/I ratio was higher in type I muscle fibres and LC3-II/I, lysosomal markers (LAMP2) and chaperone-mediated autophagy markers (LAMP2A) were all higher in whole muscle of endurance trained individuals (P < 0.05). Conclusions These results demonstrate that the maximal rate of fat oxidation is related to the proportion of type I muscle fibres. Furthermore, IMCL storage and the abundance of key proteins regulating lipid metabolism is fibre type specific and greater in endurance trained individuals. Muscle fibre type composition should be considered when investigating the regulation of IMCL utilisation and markers of autophagy

Factors affecting the survival of harbor (Phoca vitulina) and gray seal (Halichoerus grypus) juveniles admitted for rehabilitation in the UK and Ireland

The UK shores are home to approximately 40% of the world's population of gray seals (Halichoerus grypus) and 40% of Europe's harbor seals (Phoca vitulina). Stranded juvenile seals of both species are frequently rescued and admitted for rehabilitation. This study investigates the causes of P. vitulina and H. grypus admittance to rehabilitation centers in the UK and Ireland and identifies factors that can affect juvenile seal survival. Rehabilitation records for 1,435 P. vitulina and 2,691 H. grypus were used from five rehabilitation centers from 1988 through 2020. The most common nonexclusive reasons for seal admission to rehabilitation centers included malnourishment (37%), injuries (37%), maternal abandonment (15%), lethargy (12%), and parasite infections (8%). A mixed effects logistic regression model showed that H. grypus had 4.55 times higher survival odds than P. vitulina and that the odds of survival to release multiplied by 1.07 for every kilogram over their age-predicted weight. This weight-dependent survival could be attributed to the importance of fat in thermoregulation, hydration, and buoyancy during foraging. We recommend that seal rehabilitators pay special attention to the weight of admitted juvenile seals during triage and treatment to enhance their odds of survival and consequent release to the wild