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 250 specimens 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 300 kya), 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.

Dermatological conditions of farmed Crocodilians: A review of pathogenic agents and their proposed impact on skin quality.

The control of pathogens that target crocodilian skin is essential to the long-term success and sustainability of intensive farming operations worldwide. To understand the impact these pathogens may have on the skin, a brief overview of skin histology is given. A review of the known viral, bacterial, fungal and helminth taxa associated with skin conditions in commercially significant crocodilian species is presented. Best management practices are discussed, with an emphasis on addressing extrinsic factors that influence transmission and pathogenicity. It is argued that, in the past, reduced immune function arising from inadequate thermal regulation was the leading cause of skin disease in captive crocodilians. Consequently, innovations such as temperature control, coupled with the adoption of more stringent hygiene standards, have greatly reduced the prevalence of many infectious skin conditions in intensively farmed populations. However, despite improvements in animal husbandry and disease management, viral pathogens such as West Nile virus, herpesvirus and poxvirus continue to afflict crocodilians in modern captive production systems.

Unmasking the complexity of species identification in Australasian flying-foxes.

Pteropus (flying-foxes) are a speciose group of non-echolocating large bats, with five extant Australian species and 24 additional species distributed amongst the Pacific Islands. In 2015, an injured flying-fox with unusual facial markings was found in Sydney, Australia, following severe and widespread storms. Based on an initial assessment, the individual belonged to Pteropus but could not be readily identified to species. As a consequence, four hypotheses for its identification/origin were posited: the specimen represented (1) an undescribed Australian species; or (2) a morphological variant of a recognised Australian species; or (3) a hybrid individual; or (4) a vagrant from the nearby Southwest Pacific Islands. We used a combination of morphological and both mitochondrial- and nuclear DNA-based identification methods to assess these hypotheses. Based on the results, we propose that this morphologically unique Pteropus most likely represents an unusual P. alecto (black flying-fox) potentially resulting from introgression from another Pteropus species. Unexpectedly, this individual, and the addition of reference sequence data from newly vouchered specimens, revealed a previously unreported P. alecto mitochondrial DNA lineage. This lineage was distinct from currently available haplotypes. It also suggests long-term hybridisation commonly occurs between P. alecto and P. conspicillatus (spectacled flying-fox). This highlights the importance of extensive reference data, and the inclusion of multiple vouchered specimens for each species to encompass both intraspecific and interspecific variation to provide accurate and robust species identification. Moreover, our additional reference data further demonstrates the complexity of Pteropus species relationships, including hybridisation, and potential intraspecific biogeographical structure that may impact on their management and conservation.

Evaluation of next generation sequencing for the analysis of Eimeria communities in wildlife.

Next-generation sequencing (NGS) techniques are well-established for studying bacterial communities but not yet for microbial eukaryotes. Parasite communities remain poorly studied, due in part to the lack of reliable and accessible molecular methods to analyse eukaryotic communities. We aimed to develop and evaluate a methodology to analyse communities of the protozoan parasite Eimeria from populations of the Australian marsupial Petrogale penicillata (brush-tailed rock-wallaby) using NGS. An oocyst purification method for small sample sizes and polymerase chain reaction (PCR) protocol for the 18S rRNA locus targeting Eimeria was developed and optimised prior to sequencing on the Illumina MiSeq platform. A data analysis approach was developed by modifying methods from bacterial metagenomics and utilising existing Eimeria sequences in GenBank. Operational taxonomic unit (OTU) assignment at a high similarity threshold (97%) was more accurate at assigning Eimeria contigs into Eimeria OTUs but at a lower threshold (95%) there was greater resolution between OTU consensus sequences. The assessment of two amplification PCR methods prior to Illumina MiSeq, single and nested PCR, determined that single PCR was more sensitive to Eimeria as more Eimeria OTUs were detected in single amplicons. We have developed a simple and cost-effective approach to a data analysis pipeline for community analysis of eukaryotic organisms using Eimeria communities as a model. The pipeline provides a basis for evaluation using other eukaryotic organisms and potential for diverse community analysis studies.

Preexercise carbohydrate feeding and high-intensity exercise capacity: effects of timing of intake and carbohydrate concentration.

The present study aimed to investigate the influence of timing of preexercise carbohydrate feeding (Part A) and carbohydrate concentration (Part B) on short-duration high-intensity exercise capacity. In Part A, 17 males, and in Part B 10 males, performed a peak power output (PPO) test, two familiarization trials at 90% of PPO, and 4 (for Part A) or 3 (for Part B) experimental trials involving exercise capacity tests at 90% PPO. In Part A, the 4 trials were conducted following ingestion of a 6.4% carbohydrate/electrolyte sports drink ingested 30 (C30) or 120 (C120) minutes before exercise, or a flavor-matched placebo administered either 30 (P30) or 120 (P120) minutes before exercise. In Part B, the 3 trials were performed 30 min after ingestion of 0%, 2% or 12% carbohydrate solutions. All trials were performed in a double-blind cross-over design following and overnight fast. Dietary intake and activity in the 2 days before trials was recorded and replicated on each visit. Glucose, lactate, heart rate, and mood/arousal were recorded at intervals during the trials. In Part A, C30 produced the greatest exercise capacity (mean ± SD; 9.0 ± 1.9 min, p < .01) compared with all other trials (7.7 ± 1.5 min P30, 8.0 ± 1.7 min P120, 7.9 ± 1.9 min C120). In Part B, exercise capacity (min) following ingestion of the 2% solution (9.2 ± 2.1) compared with 0% (8.2 ± 0.7) and 12% (8.0 ± 1.3) solutions approached significance (p = .09). This study provides new evidence to suggest that timing of carbohydrate intake is important in short duration high-intensity exercise tasks, but a concentration effect requires further exploration.

Fluid balance and sodium losses during indoor tennis match play.

This study assessed fluid balance, sodium losses, and effort intensity during indoor tennis match play (17 ± 2 °C, 42% ± 9% relative humidity) over a mean match duration of 68.1 ± 12.8 min in 16 male tennis players. Ad libitum fluid intake was recorded throughout the match. Sweat loss from change in nude body mass; sweat electrolyte content from patches applied to the forearm, calf, and thigh, and back of each player; and electrolyte balance derived from sweat, urine, and daily food-intake analysis were measured. Effort intensity was assessed from on-court heart rate compared with data obtained during a maximal treadmill test. Sweat rate (M ± SD) was 1.1 ± 0.4 L/hr, and fluid-ingestion rate was 1.0 ± 0.6 L/hr (replacing 93% ± 47% of fluid lost), resulting in only a small mean loss in body mass of 0.15% ± 0.74%. Large interindividual variabilities in sweat rate (range 0.3-2.0 L/hr) and fluid intake (range 0.31-2.52 L/hr) were noted. Whole-body sweat sodium concentration was 38 ± 12 mmol/L, and total sodium losses during match play were 1.1 ± 0.4 g (range 0.5-1.8 g). Daily sodium intake was 2.8 ± 1.1 g. Indoor match play largely consisted of low-intensity exercise below ventilatory threshold (mean match heart rate was 138 ± 24 beats/min). This study shows that in moderate indoor temperature conditions players ingest sufficient fluid to replace sweat losses. However, the wide range in data obtained highlights the need for individualized fluid-replacement guidance.