Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus): a dietary-specialist species distributed across heterogeneous environments.

The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for current taxonomic classification of three koala subspecies, with only a single evolutionary significant unit supported. Furthermore, ~70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (i.e., Blue Mountains region; AvHecorr=0.20, PL% = 68.6). Broad-scale population differentiation is primarily driven by an isolation by distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala's ability to maintain gene flow and adapt across divergent environments as long as the required food source is available.

Daylight saving time can decrease the frequency of wildlife-vehicle collisions.

Daylight saving time (DST) could reduce collisions with wildlife by changing the timing of commuter traffic relative to the behaviour of nocturnal animals. To test this idea, we tracked wild koalas (Phascolarctos cinereus) in southeast Queensland, where koalas have declined by 80% in the last 20 years, and compared their movements with traffic patterns along roads where they are often killed. Using a simple model, we found that DST could decrease collisions with koalas by 8% on weekdays and 11% at weekends, simply by shifting the timing of traffic relative to darkness. Wildlife conservation and road safety should become part of the debate on DST.

Molecular studies on European equine isolates of Leptospira interrogans serovars Bratislava and Muenchen.

Strains of Leptospira interrogans belonging to two very closely related serovars ­ Bratislava and Muenchen ­ are known to cause widespread infection of the horse population in many parts of the world. Conventional serological typing of isolates has been unable to differentiate between wildlife, pig, dog and possibly horse maintained isolates and therefore has been unable to provide further insight into their diversity and the relationship between them. Twenty-one such European isolates of serovar Bratislava and Muenchen were examined by restriction endonuclease analysis and multiple-locus variable-number tandem repeat analysis in an attempt to elucidate their epidemiology. The restriction pattern types were identified and fell into one of four REA designed pattern types, B1, B2a, M1, M2a. Nine strains from Northern Ireland and two from Germany belonged to B2a, which is a ubiquitous strain being originally isolated from a large number of wild and domestic animal species in the UK. Five strains were identified as B1 and they came from Portugal, The Netherlands, Germany and Northern Ireland; three strains isolated in Germany belong to M1; two strains belonged to M2a. Genotypes B1 and M1 have, with the exception of one hedgehog isolate, been recovered only from horses and it may indicate their adaptation to this species.

Animal leptospirosis.

Leptospirosis is a global disease of animals, which can have a major economic impact on livestock industries and is an important zoonosis. The current knowledge base is heavily biased towards the developed agricultural economies. The disease situation in the developing economies presents a major challenge as humans and animals frequently live in close association. The severity of disease varies with the infecting serovar and the affected species, but there are many common aspects across the species; for example, the acute phase of infection is mostly sub-clinical and the greatest economic losses arise from chronic infection causing reproductive wastage. The principles of, and tests for, diagnosis, treatment, control and surveillance are applicable across the species.

A 5-year Chlamydia vaccination programme could reverse disease-related koala population decline: predictions from a mathematical model using field data.

BACKGROUND: Many koala populations around Australia are in serious decline, with a substantial component of this decline in some Southeast Queensland populations attributed to the impact of Chlamydia. A Chlamydia vaccine for koalas is in development and has shown promise in early trials. This study contributes to implementation preparedness by simulating vaccination strategies designed to reverse population decline and by identifying which age and sex category it would be most effective to target. METHODS: We used field data to inform the development and parameterisation of an individual-based stochastic simulation model of a koala population endemic with Chlamydia. The model took into account transmission, morbidity and mortality caused by Chlamydia infections. We calibrated the model to characteristics of typical Southeast Queensland koala populations. As there is uncertainty about the effectiveness of the vaccine in real-world settings, a variety of potential vaccine efficacies, half-lives and dosing schedules were simulated. RESULTS: Assuming other threats remain constant, it is expected that current population declines could be reversed in around 5-6 years if female koalas aged 1-2 years are targeted, average vaccine protective efficacy is 75%, and vaccine coverage is around 10% per year. At lower vaccine efficacies the immunological effects of boosting become important: at 45% vaccine efficacy population decline is predicted to reverse in 6 years under optimistic boosting assumptions but in 9 years under pessimistic boosting assumptions. Terminating a successful vaccination programme at 5 years would lead to a rise in Chlamydia prevalence towards pre-vaccination levels. CONCLUSION: For a range of vaccine efficacy levels it is projected that population decline due to endemic Chlamydia can be reversed under realistic dosing schedules, potentially in just 5 years. However, a vaccination programme might need to continue indefinitely in order to maintain Chlamydia prevalence at a sufficiently low level for population growth to continue.

Altodouro, a new Leptospira serovar of the Pomona serogroup isolated from rodents in northern Portugal.

A Leptospira strain (designated RIM 139) was isolated from the kidney of a house-mouse, Mus musculus, in Trás-os-Montes e Alto Douro region of northern Portugal. The isolate showed typical leptospiral motility and morphology under dark-field microscopy and was pathogenic for hamsters. Species determination was carried out on basis of PCR products generated by species-specific primers and by sequencing of the secY gene. Putative serogroup typing was performed using the microscopic agglutination test (MAT) with a panel of rabbit anti-Leptospira sera representative of the major pathogenic serogroups. Serovar identification was carried out by a combination of monoclonal antibodies and cross-agglutinin absorption test (CAAT). The novel nature of the strain was confirmed by restriction endonuclease analysis (REA). Results showed that RIM 139 represents a new serovar. The name Altodouro is proposed for this new serovar. Speciation findings - PCR analysis of the ompL1 gene and sequencing of the secY gene - indicated that it belonged to Leptospira kirschneri as did amplification with G1/G2 and B64-I/B64-II the primer sets.

Fat-soluble vitamin and mineral comparisons between zoo-based and free-ranging koalas (Phascolarctos cinereus).

As part of a health investigation on koalas at San Diego Zoo, serum samples were analyzed from 18 free-ranging and 22 zoo-based koalas, Phascolarctos cinereus. Serum concentrations of calcium, chloride, cobalt, copper, iron, magnesium, manganese, molybdenum, phosphorus, potassium, selenium, sodium, zinc, and vitamins A, E, and 25(OH)D3 were quantified. Calcium, chloride, molybdenum, selenium, and vitamin E concentrations were significantly higher in zoo-based koalas than in free-ranging koalas, whereas magnesium, manganese, phosphorus, and zinc concentrations were significantly higher in the free-ranging koalas. No significant differences were found between genders. The results from this study will help to establish a starting point for determining target circulating nutrient concentrations in koalas.

Estimating the active space of male koala bellows: propagation of cues to size and identity in a Eucalyptus forest.

Examining how increasing distance affects the information content of vocal signals is fundamental for determining the active space of a given species' vocal communication system. In the current study we played back male koala bellows in a Eucalyptus forest to determine the extent that individual classification of male koala bellows becomes less accurate over distance, and also to quantify how individually distinctive acoustic features of bellows and size-related information degrade over distance. Our results show that the formant frequencies of bellows derived from Linear Predictive Coding can be used to classify calls to male koalas over distances of 1-50 m. Further analysis revealed that the upper formant frequencies and formant frequency spacing were the most stable acoustic features of male bellows as they propagated through the Eucalyptus canopy. Taken together these findings suggest that koalas could recognise known individuals at distances of up to 50 m and indicate that they should attend to variation in the upper formant frequencies and formant frequency spacing when assessing the identity of callers. Furthermore, since the formant frequency spacing is also a cue to male body size in this species and its variation over distance remained very low compared to documented inter-individual variation, we suggest that male koalas would still be reliably classified as small, medium or large by receivers at distances of up to 150 m.

Perception of size-related formant information in male koalas (Phascolarctos cinereus).

Advances in bioacoustics allow us to study the perceptual and functional relevance of individual acoustic parameters. Here, we use re-synthesised male koala bellows and a habituation-dishabituation paradigm to test the hypothesis that male koalas are sensitive to shifts in formant frequencies corresponding to the natural variation in body size between a large and small adult male. We found that males habituated to bellows, in which the formants had been shifted to simulate a large or small male displayed a significant increase in behavioural response (dishabituation) when they were presented with bellows simulating the alternate size variant. The rehabituation control, in which the behavioural response levels returned to that of the last playbacks of the habituation phase, indicates that this was not a chance increase in response levels. Our results provide clear evidence that male koalas perceive and attend to size-related formant information in their own species-specific vocalisations and suggest that formant perception is a widespread ability shared by marsupials and placental mammals, and perhaps by vertebrates more widely.

Cues to body size in the formant spacing of male koala (Phascolarctos cinereus) bellows: honesty in an exaggerated trait.

Determining the information content of vocal signals and understanding morphological modifications of vocal anatomy are key steps towards revealing the selection pressures acting on a given species' vocal communication system. Here, we used a combination of acoustic and anatomical data to investigate whether male koala bellows provide reliable information on the caller's body size, and to confirm whether male koalas have a permanently descended larynx. Our results indicate that the spectral prominences of male koala bellows are formants (vocal tract resonances), and show that larger males have lower formant spacing. In contrast, no relationship between body size and the fundamental frequency was found. Anatomical investigations revealed that male koalas have a permanently descended larynx: the first example of this in a marsupial. Furthermore, we found a deeply anchored sternothyroid muscle that could allow male koalas to retract their larynx into the thorax. While this would explain the low formant spacing of the exhalation and initial inhalation phases of male bellows, further research will be required to reveal the anatomical basis for the formant spacing of the later inhalation phases, which is predictive of vocal tract lengths of around 50 cm (nearly the length of an adult koala's body). Taken together, these findings show that the formant spacing of male koala bellows has the potential to provide receivers with reliable information on the caller's body size, and reveal that vocal adaptations allowing callers to exaggerate (or maximise) the acoustic impression of their size have evolved independently in marsupials and placental mammals.

Perception of male caller identity in Koalas (Phascolarctos cinereus): acoustic analysis and playback experiments.

The ability to signal individual identity using vocal signals and distinguish between conspecifics based on vocal cues is important in several mammal species. Furthermore, it can be important for receivers to differentiate between callers in reproductive contexts. In this study, we used acoustic analyses to determine whether male koala bellows are individually distinctive and to investigate the relative importance of different acoustic features for coding individuality. We then used a habituation-discrimination paradigm to investigate whether koalas discriminate between the bellow vocalisations of different male callers. Our results show that male koala bellows are highly individualized, and indicate that cues related to vocal tract filtering contribute the most to vocal identity. In addition, we found that male and female koalas habituated to the bellows of a specific male showed a significant dishabituation when they were presented with bellows from a novel male. The significant reduction in behavioural response to a final rehabituation playback shows this was not a chance rebound in response levels. Our findings indicate that male koala bellows are highly individually distinctive and that the identity of male callers is functionally relevant to male and female koalas during the breeding season. We go on to discuss the biological relevance of signalling identity in this species' sexual communication and the potential practical implications of our findings for acoustic monitoring of male population levels.

Multilocus sequence typing method for identification and genotypic classification of pathogenic Leptospira species.

BACKGROUND: Leptospira are the parasitic bacterial organisms associated with a broad range of mammalian hosts and are responsible for severe cases of human Leptospirosis. The epidemiology of leptospirosis is complex and dynamic. Multiple serovars have been identified, each adapted to one or more animal hosts. Adaptation is a dynamic process that changes the spatial and temporal distribution of serovars and clinical manifestations in different hosts. Serotyping based on repertoire of surface antigens is an ambiguous and artificial system of classification of leptospiral agents. Molecular typing methods for the identification of pathogenic leptospires up to individual genome species level have been highly sought after since the decipherment of whole genome sequences. Only a few resources exist for microbial genotypic data based on individual techniques such as Multiple Locus Sequence Typing (MLST), but unfortunately no such databases are existent for leptospires. RESULTS: We for the first time report development of a robust MLST method for genotyping of Leptospira. Genotyping based on DNA sequence identity of 4 housekeeping genes and 2 candidate genes was analyzed in a set of 120 strains including 41 reference strains representing different geographical areas and from different sources. Of the six selected genes, adk, icdA and secY were significantly more variable whereas the LipL32 and LipL41 coding genes and the rrs2 gene were moderately variable. The phylogenetic tree clustered the isolates according to the genome-based species. CONCLUSION: The main advantages of MLST over other typing methods for leptospires include reproducibility, robustness, consistency and portability. The genetic relatedness of the leptospires can be better studied by the MLST approach and can be used for molecular epidemiological and evolutionary studies and population genetics.