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Lassa fever is of public health concern in West Africa due to its endemic nature. Housing conditions have been revealed to be important sites for primary transmission. This study assessed environmental and housing conditions of a low-income community for factors that could contribute to the transmission of Lassa fever. The study employed a cross-sectional design with a field component. Observational checklist and an interviewer-administered questionnaire were used to assess environmental conditions and respondents’ hygiene knowledge and practices respectively. Rodent traps were also placed in selected households. Data collected were analysed using SPSS Version20. 40% of the respondents had poor housing conditions, 80% had good hygiene practice while 20% had poor knowledge. Respondents with good housing condition were 1.9 times more likely to have good hygiene practice compared to houses with poor housing condition (OR= 1.941, p= 0.009). Rodents trapped from the households were Rattus rattus (43.2%), Rattus fuscipes (38.6%) and Rattus norvegicus (18.2%). Houses with most rats trapped had the poorest housing conditions and hygiene practices. The results suggest that households in the community are susceptible to the transmission of Lassa fever. Therefore, effective awareness campaigns on the transmission of Lassa fever and good hygiene and sanitation practice should be encouraged in and around the home.

The native rat lungworm (Angiostrongylus mackerrasae) and the invasive rat lungworm (Angiostrongylus cantonensis) occur in eastern Australia. The species identity of A. mackerrasae remained unquestioned until relatively recently, when compilation of mtDNA data indicated that A. mackerrasae sensu Aghazadeh et al. (2015b) clusters within A. cantonensis based on their mitochondrial genomes (mtDNA). To re-evaluate the species identity of A. mackerrasae, we sought material that would be morphologically conspecific with A. mackerrasae. We combined morphological and molecular approaches to confirm or refute the specific status of A. mackerrasae. Nematodes conspecific with A. mackerrasae from Rattus fuscipes and Rattus rattus were collected in Queensland, Australia. Morphologically identified A. mackerrasae voucher specimens were characterized using amplification of cox1 followed by the generation of reference complete mtDNA. The morphologically distinct A. cantonensis, A. mackerrasae and A. malaysiensis are genetically distinguishable forming a monophyletic mtDNA lineage. We conclude that A. mackerrasae sensu Aghazadeh et al. (2015b) is a misidentified specimen of A. cantonensis. The availability of the mtDNA genome of A. mackerrasae enables its unequivocal genetic identification and differentiation from other Angiostrongylus species.

Australia has about six species of native Rattus and about ten species of Antechinus. The three species, Rattus fuscipes (the Australian bush rat), Antechinus stuartii, and A. swainsonii, are representative of forest-dwelling small mammals. The first is an omnivorous rodent.

Cryptosporidium viatorum is a globally distributed pathogenic species of Cryptosporidium that has only ever been recorded from humans, until now. For the first time, we molecularly characterised a novel subtype of C. viatorum (subtype XVbA2G1) from the endemic Australian swamp rat (Rattus lutreolus) using the small subunit of nuclear ribosomal RNA (SSU) gene and then subtyped it using the 60-kilodalton glycoprotein (gp60) gene. In total, faecal samples from 21 swamp rats (three were positive for C. viatorum), three broad toothed rats (Mastacomys fuscus) and two bush rats (Rattus fuscipes) were tested for Cryptosporidium. The long-term, isolated nature of the swamp rat population in Melbourne's drinking water catchment system (where public access is prohibited), the lack of C. viatorum from other mammals and birds living within the vicinity of this system and its genetic distinctiveness in both the SSU and gp60 gene sequences from other species of Cryptosporidium collectively suggest that C. viatorum might be endemic to native rats in Australia. The current state of knowledge of epidemiological surveys of Cryptosporidium of rats and the zoonotic potential are further discussed in light of the finding of C. viatorum. Long-term studies, with the capacity to repetitively sample a variety of hosts in multiple localities, in different seasons and years, will allow for greater insight into the epidemiological patterns and zoonotic potential of rare Cryptosporidium species such as C. viatorum., Graphical abstract Image 1, Highlights • First detection of Cryptosporidium viatorum (XVbA2G1) in a non-human host. • Found in native Australian swamp rat Rattus leutreolus. • Appraisal of current state of knowledge of Cryptosporidium in rats. • Cognisance of epidemiology and zoonotic potential through long-term monitoring.

Invasive animal species are a major factor in the extinction and endangerment of native species worldwide. Longterm monitoring reveals some mammal recoveries have not been sustained in the presence of a broad-scale threat abatement program aimed at reducing the impact of the introduced Vulpes vulpes (red fox)-a top-order predator and key threat to many native species in Australia. Over 51,000 records of 19 terrestrial mammal species reported from a range of survey methods (pitfall traps, Elliott box traps, wire cage traps, spotlighting, sand plots, and nest boxes) across the Upper Warren region of southwestern Australia were used to investigate population changes over 41 years (1974-2014). Since the mid-1990s, populations of at least 7 native mammal species or genera have successively declined at similarly rapid rates and magnitudes (80-100%): Sminthopsis spp., Rattus fuscipes, Phascogale tapoatafa, Isoodon obesulus, Pseudocheirus occidentalis, Bettongia penicillata, and Notamacropus irma. R. fuscipes has not been recorded in the region since 2005 and may have become locally extinct. The other species that have declined remain at risk of becoming locally extinct. Three species have increased since 2000: Trichosurus vulpecula, Dasyurus geoffroii, and Notamacropus eugenii. The Upper Warren region in which this community disassembly has occurred is one of the principal sites for the conservation of many threatened mammal species and is within Australia's global biodiversity hotspot. We discuss the critical importance of long-term monitoring and the need to identify the causes of population change to inform how conservation and management activities can best be focussed. Predation by the introduced Felis catus (cat) is hypothesized as the most likely common or primary cause behind many of the recent declines in the Upper Warren. The integrated reduction of both cats and foxes, conducted within an experimental framework, is the most direct and definitive action to test this and deliver the greatest practical conservation outcomes.

Fauna surveys were conducted near the coastal village of Vincentia on the south coast of New South Wales from 2000 to 2014 in response to a proposal to extend a golf course. The surveys consisted of trapping ground-dwelling mammals along six, 200 m long transects and targeted surveys for the Eastern Bristlebird Dasyornis brachypterus and Ground Parrot Pezoporus wallicus. Eight native species of ground-dwelling mammal were trapped including the White-footed Dunnart Sminthopsis leucopus, Eastern Chestnut Mouse Pseudomys gracilicaudatus and Eastern Pygmy Possum Cercartetus nanus, species currently listed on the Threatened Species Conservation Act (1995) and the New Holland Mouse Pseudomys novaehollandiae listed as vulnerable under the Environment Protection and Biodiversity Conservation Act (1999). The most abundant mammals trapped were the Bush Rat Rattus fuscipes and the Brown Antechinus A. stuartii accounting for 67% and 14% of all Elliott trap captures, respectively. The survey provided the firs...

Vector-borne haemoprotozoans comprise a diverse group of eukaryote single-celled organisms transmitted by haematophagous (blood-feeding) invertebrates. They can cause debilitating diseases that impact wildlife, livestock, companion animals and humans. Recent research has shown that Australian wildlife host a diverse range of haemoprotozoan species; however, to date this work has primarily been confined to a few host species or isolated populations in rural habitats. There has been little investigation into the presence of these blood parasites in wildlife inhabiting urban and peri-urban areas. In this study, blood and tissue samples and ticks were collected from wildlife in New South Wales and Western Australia. Extracted DNA samples were screened with pan-specific molecular assays to determine the presence of haemoprotozoans using amplicon metabarcoding and Sanger sequencing approaches. In addition, light microscopy was performed on blood films. Eight haemoprotozoans were identified in the present study, which included species of Babesia, Hepatozoon, Theileria and Trypanosoma. Blood samples were collected from 134 animals; 70 black rats (Rattus), 18 common brush-tailed possums (Trichosurus vulpecula), two bush rats (Rattus fuscipes), 22 chuditch (Dasyurus geoffroii), 20 long-nosed bandicoots (Perameles nasuta), one quenda (Isoodon fusciventer) and one swamp rat (Rattus lutreolus). Molecular screening of DNA extracted from blood samples identified 52.2% (95% CI: 43.8–60.5%) of individuals were positive for at least one haemoprotozoan species, with 19.4% (95% CI: 13.4–26.7%) positive for more than one species. The present study provides the first sequences of Theileria cf. peramelis from black rats and long-nosed bandicoots. Babesia lohae was identified from brush-tailed possums. Two Hepatozoon genotypes were identified from black rats and bush rats. Black rats showed the highest haemoprotozoan diversity, with five species identified. No known human pathogens that have been described in the northern hemisphere were identified in the present study, and future work is required to understand the zoonotic potential of these microbes in Australia. This work represents the first large-scale body of research using molecular tools to investigate haemoprotozoans in animals at the urban-wildland interface. Further research is needed to investigate potential consequences of infection in wildlife, particularly effects of pathogen spillover from invasive black rats to native wildlife.

Australian temperate forests support a high diversity of truffle-like fungi, and a rich assortment of mammals that feed upon them. We sampled seasonal diets of four sympatric mammals (two rodents, two marsupials) in an eastern Australian wet sclerophyll forest and identified all dietary fungi. Fifty-two different spore types were found in diets, most of which were from truffle-like fungi. All mammals consumed fungi, but occurrence of fungi and the variety of taxa in the diets peaked in winter and spring. Bush rats (Rattus fuscipes) were significantly more mycophagous than other mammals sampled in terms of proportion of scats containing fungi, number of taxa per sample, and overall diversity of dietary fungi. Most fungal taxa were eaten only occasionally, but a few truffle-like taxa dominated diets and appear to be staple food for the small mammal community. Our work supports the view that mycophagous mammals are important for maintenance of ecosystem health through their spore dispersal abilities.

ContextPredation by feral cats (Felis catus) threatens a range of vertebrate species across Australia, and cat-free islands increasingly act as safe havens for biodiversity. A feral cat eradication program has begun on Kangaroo Island (4405km2) in South Australia, and poison baiting is likely to be one of the main methods used. Aims Here, we trial a non-toxic version of a cat bait, ‘Eradicat’, on western Kangaroo Island, to examine its potential impact on non-target species. MethodsNon-toxic baits containing the biomarker Rhodamine B were deployed across four sites in early August and late November in 2018, with bait take and consumption assessed both by remote cameras and by the presence of Rhodamine B in mammalian whisker samples taken post-baiting. Key resultsCats encountered baits on very few occasions and took a bait on only one occasion in August (60% of all baits laid was taken by either the common brushtail possum (Trichosurus vulpecula), bush rat (Rattus fuscipes) or Australian raven (Corvus coronoides). In November, Rosenberg’s goanna (Varanus rosenbergi) and southern brown bandicoot (south-eastern subspecies; Isoodon obesulus obesulus), listed nationally as Endangered, also took baits (3% and 1% respectively). The Kangaroo Island dunnart (Sminthopsis fuliginosus aitkeni), listed nationally as endangered, approached a bait on only one occasion, but did not consume it. Evidence of bait consumption was visible in the whiskers of captured common brushtail possums (100% of post-baiting captured individuals in August, 80% in November), bush rats (59% in August and 50% in November), house mice (Mus musculus) (45% in November) and western pygmy-possums (Cercartetus concinnus) (33% in November). ConclusionsAlthough feral cat baiting has the potential to significantly benefit wildlife on Kangaroo Island, impacts on non-target species (particularly the bush rat and common brushtail possum) may be high. ImplicationsAlternative cat baits, such as those containing a toxin to which native species have a higher tolerance or that are less readily consumed by native wildlife, will be more appropriate.

Resource selection by animals influences individual fitness, the abundance of local populations, and the distribution of species. Further, the degree to which individuals select particular resources can be altered by numerous factors including competition, predation, and both natural- and human-induced environmental change. Understanding the influence of such factors on the way animals use resources can guide species conservation and management in changing environments. In this study, we investigated the effects of a prescribed fire on small-scale (microhabitat) resource selection, abundance, body condition, and movement pathways of a native Australian rodent, the bush rat ( Rattus fuscipes ). Using a before-after, control-impact design, we gathered data from 60 individuals fitted with spool and line tracking devices. In unburnt forest, selection of resources by bush rats was positively related to rushes, logs and complex habitat, and negatively related to ferns and litter. Fire caused selection for spreading grass, rushes, and complex habitat to increase relative to an unburnt control location. At the burnt location after the fire, rats selected patches of unburnt vegetation, and no rats were caught at a trapping site where most of the understory had been burnt. The fire also reduced bush rat abundance and body condition and caused movement pathways to become more convoluted. After the fire, some individuals moved through burnt areas but the majority of movements occurred within unburnt patches. The effects of fire on bush rat resource selection, movement, body condition, and abundance were likely driven by several linked factors including limited access to shelter and food due to the loss of understory vegetation and heightened levels of perceived predation risk. Our findings suggest the influence of prescribed fire on small mammals will depend on the resulting mosaic of burnt and unburnt patches and how well this corresponds to the resource requirements of particular species.

We provide hematologic (n = 34) and biochemical (n = 30) blood values for wild-caught Australian bush rats (Rattus fuscipes). Hematology values have similar range limits compared with other rat species. Biochemistry values for glucose, alanine transaminase, aspartate aminotransferase, and creatine kinase have higher maximum ranges compared with other rats.

718. Australian Bush Rat Rattus fuscipes French: Rat de brousse / German: Australische SchwarzfulRratte / Spanish: Rata peluda de Australia Other common names: Allied Rat, Bush Rat; Western Swamp Rat (fuscipes), Southern Bush Rat (assimilis) Taxonomy. Mus fuscipes Waterhouse, 1839, “Australia, King George’s Sound.” Restricted by J. M. Taylor and B. E. Horner in 1973 to “ ‘Little Grove’ on Princess Royal Harbour, approx. 4 mi [= 6 km] south of Mount Melville, Albany, Western Australia, Australia.” Rattus fuscipes is sister to all other Australian Rattus except R. leucopus, which is basal to this clade. Each of the recognized subspecies is morphologically and genetically distinct; although they can interbreed, they might may represent distinct species (especially coracius) with further research. Rattus f. assimilis might represent multiple subspecies. Four subspecies recognized, but subspecific taxonomy requires reassessment. Subspecies and Distribution. R.c.fuscipesWaterhouse,1839—SWWesternAustraliaaswellasvariousoffshoreIs. R.c.asstmilisGould,1858—EVictoriaandSEQueenslandandsomeoffshoreIs. R.c.coraciusThomas,1923—NEQueensland,includingHinchinbrook I. R. c. greyi Gray, 1841 — SE South Australia and SW Victoria as well as various offshore Is including Kangaroo I. Descriptive notes. Head-body 100-205 mm, tail 100-195 mm, ear 18-25 mm, hindfoot 30-40 mm; weight 50-225 g. The Australian Bush Rat is medium-sized and highly variable, with males larger than females. Pelage is soft and dense, with coarser black guard hairs throughout. Dorsum is gray-brown to reddish brown and blends into ventral pelage. Hairs are gray and translucent basally. Some island populations have lighter and redder dorsum, while populations in more humid regions are darker. Venter is light gray to buffy cream. Feet are light colored on mainland and dusky on Kangaroo Island and in western Australia. Ears are rounded, sparsely haired, and similar in color to dorsum; vibrissae are relatively short. Tail is ¢.100% of head-body length, nearly naked, and variably in color, ranging from brown to gray to blackish occasionally. Skull is elongated and relatively flat. Subspecies assimilis and coracius are larger; grey: and fuscipes are c.10-20% shorter and 30-40% lighter. In winter at high elevations and southern regions, body fat increases, weight decreases, and fur becomes more dense. Subspecies coracius tends to be more reddish brown dorsally and white ventrally, has lighter feet, and commonly has white blaze between ears; fuscipes generally is browner dorsally and gray ventrally, has darker feet, and lacks blaze between ears. Many species of cestodes (e.g. Bertiella, Choanotaenia, and Taenia), nematodes (e.g. Angiostrongylus, Contracaecum, Dipetalonema, Gongylonema, Paraustrostrongylus, Syphacia, and Trichosomoides), trematodes (e.g. Brachylecithum and Neodiplostomum), chiggers (e.g. Ascoschoengastia, Schoutedenichia, and Trombicula), ticks (e.g. Ixodes and Haemaphysalis), lice (Hoplopleura), fleas (e.g. Acanthopsylla, Bibikovana, Stephanocircus, and Xenopsylla), protozoans (e.g. Haemobartonella, Toxoplasma, and Trypanosoma), bacteria (e.g. Brucella, Leptospira, and Streptobacillus), and a staphylinid beetle (Myotyphlus) have been recorded from the Australian Bush Rat—the most of any Australian rodent. There are five pairs of mammae: two pectoral and three abdominal (specimens from northern New South Wales have only one pectoral pair). Chromosomal complement is 2n = 38, FN = 60. Habitat. Subalpine woodland, coastal scrub, coastal heath, eucalyptus forest, and tropical moist forest from sea level to elevations of 2210 m. Northern populations of Australian Bush Rats are found in more forested habitats, and southern populations are confined to drier regions. They rely on dense understory for shelter and cover from predators while foraging at night. Food and Feeding. The Australian Bush Rat is selectively omnivorous, being highly insectivorous and herbivorous. In winter, diets mostly contain fungi, fibrous stems, leaves, and specific grasses and lilies. In summer, diet mostly contains insects, fruit, and seeds. The species is highly dependent on fungal mycorrhizae and leaf litter insects, which makes them highly susceptible to bush fires that can almost completely eliminate these foods for extended periods of time. Food is hoarded, and waterlogged items are occasionally retrieved, most commonly in times of food depravation. Breeding. Australian Bush Rats reproduce year-round, but breeding is rare in winter, especially in southern parts of the distribution. Estrous cycles range from 4-5 (assimalis, with proestrus of 10-14 hours) to 5-3 (coracius, with proestrus of 24 hours). Postpartum estrus occurs c.41 hours after birth and lasts less than 24 hours. Females give birth by tucking their hindfeet under their body, tail to one side and forefeet used for support, and licking each young as it comes out. A male might be present during births, and in one instance, he helped with cleaning young and ate placenta, which is normally done by the female. Postpartum females are aggressive and can kill the male during postpartum heat. Gestation lasts 22-24 days (mean 22-8) and can be extended to 28-32 days by delayed implantation during lactation. Litters have 1-7 young in captivity and 1-8 young in the wild (mean four and five, respectively). Ovulation rates are higher in fuscipes and grey: (6-4-8-4) and lower in assimilis and coracius (4-9-5-4), with corresponding larger and smaller litter sizes. Young are born with eyes closed, pink and hairless, weighing c.4 g, and ¢.56 mm long. They have hair at c.12 days and walk at c.15 days; eyes do not open until 20 days old. They are probably weaned a little after opening their eyes at c.20-25 days. They become completely independentafter 4-5 weeks and are capable of reproducing in the wild at c.4 months; some individuals born in spring can breed before winter. Subadults disperse after they become able to. Males generally disperse much farther (762 m) than females (213 m) in Victoria, but in Queensland, they both reportedly traveled 365 m. They usually live ¢.12 months in the wild but up to 16 months in captivity. Activity patterns. The Australian Bush Rat is nocturnal, generally foraging and moving around at night. Their peak activity pattern is bimodal, just after sunset and just before sunrise, although this can change with weather conditions. In Queensland, males moved (average c.183 m) around at night further than females (127 m). Movement of males during major breeding months was significantly farther than ofjuveniles and females. During fires, Australian Bush Rats are known to hide in their burrows, and after fires, they hide in ash because there is no vegetation for cover. Exploratory activity increases in summer. The Australian Bush Rat is terrestrial, although it will occasionally climb trees to reach food. Nests are made in burrows, and individuals will take refuge in hollow logs and rock crevices. Pathways connect various burrows, but they usually are inconspicuous except where vegetation is thick. Nest consists of main tunnel that descends 30-45 cm below the surface to nest chamber c.15 cm in diameter and lined with grass and other fibrous vegetation. Movements, Home range and Social organization. Australian Bush Rats occur at densities of ¢.10 ind/ha, and highest densities occur in tropical forests. Females expand or retain their home ranges in spring; males vastly expand their home ranges or disperse. Female home ranges thus do not overlap, but male home ranges overlap multiple adjacent female home ranges. Australian Bush Rats can be rather aggressive toward conspecifics and are not gregarious. They make various sounds accompanying aggressive displays and non-aggressive behaviors, which include squeals, ultrasonic pipping, ultrasonic whistle, and coughing. On silent encounters, individuals might sniff each other, occasionally stretching their bodies. Copulation always occurs at night, is generally accompanied by allogrooming, and can occur (not always with ejaculation) even when a female is not in heat. Because their life span is short, near complete die offs of breeding individuals of the previous year can occur. During fires, populations decrease, and food availability also affects population size. Status and Conservation. Classified as Least Concern on The IUCN Red List. The Australian Bush Rat has a relatively wide distribution and is common through most ofits distribution. It occurs in many protected areas. It is highly sensitive to habitat destruction, alteration, and degradation and is probably threatened by logging and mismanaged fire regimes and bushfires. It is considered an economic pest in cane fields. Bibliography. Lindenmayer et al. (2005), Menkhorst & Knight (2010), Menkhorst et al. (2016), Musser & Carleton (2005), Peakall et al. (2006), Rowe et al. (2011), Stewart (1979), Taylor & Calaby (1988a), Taylor & Horner (1973), Tory et al. (1997), Van Dyck & Strahan (2008), Warneke (1971), Wood (1971)., Published as part of Don E. Wilson, Russell A. Mittermeier & Thomas E. Lacher, Jr, 2017, Muridae, pp. 536-884 in Handbook of the Mammals of the World – Volume 7 Rodents II, Barcelona :Lynx Edicions on pages 848-849, DOI: 10.5281/zenodo.6887260

The black-tailed dusky antechinus (Antechinus arktos) is an endangered, small carnivorous marsupial endemic to Australia, which occurs at low population density along with abundant sympatric populations of other small mammals: Antechinus stuartii, Rattus fuscipes and Melomys cervinipes. Using A. arktos as a model species, we aimed to evaluate the effectiveness of infrared digital camera traps for detecting and differentiating small mammals and to comment on the broad applicability of this methodology. We also sought to understand how the detection probabilities of our target species varied over time and characterize their activity patterns. We installed 11 infrared cameras at one of only three known sites where A. arktos occurs for five consecutive deployments. Cameras were fixed to wooden stakes and oriented vertically, 35 cm above ground, directly facing bait containers. Using this method, we successfully recorded and identified individuals from all four species of small mammal known previously in the area from live trapping, including A. arktos. This validates the effectiveness of the infrared camera type and orientation for small mammal studies. Periods of activity for all species were highly coincident, showing a strong peak in activity during the same two-hour period immediately following sunset. A. arktos, A. stuartii and M. cervinipes also displayed a strong negative linear relationship between detection probability and days since deployment. This is an important finding for camera trapping generally, indicating that routine camera deployment lengths (of one-to-two weeks) between baiting events may be too long when targeting some small mammals.

This study investigated the presence of rabies and rabies-related lyssaviruses in the brain, liver and spleen of some wild animal species (rodents, shrews and civet cats) slaughtered for human consumption in Enugu State, Southeastern Nigeria. Attempts were made to establish possible exposure potential of humans to rabies and rabies-related lyssaviruses through handling, processing, selling, buying and consumption of these wild animals and establish the species of the viral isolates if any. A total of four hundred and eighty four 329) wild animals were sampled for rabies and rabies-related lyssaviruses using florescent antibody technique (FAT), cell culture test for the isolation and Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) for detection of lyssavirus nucleic acid. The animals sampled include eighty nine land squirrels (Xerus erythropus), seventy African giant rats (Cricetomysgambians), one hundred and one black rats eighty bush rats (Rattus fuscipes), seventy two shrews and seventy civet cats (Civetticitis civetta). The animals were collected fresh from hunters or markets, restaurants and bars where they are slaughtered and consumed as delicacy in the study area. There was no lyssavirus isolated from the three hundred and forty rodent samples (brain, liver, spleen) examined. Similarly, there was no lyssavirus isolated from the seventy civet cat samples (liver, spleen, brain). And samples (liver, spleen, brain) from seventy two shrews. The results of this study suggest that rodents and civet cats slaughtered for human consumption in Enugu State, Nigeria are free of rabies and rabies-related lyssaviruses. Therefore, there is no exposure potential to rabies or rabies-related lyssaviruses in those involved in the hunting, handling, processing, selling, buying and consumption of bush meat of these animal species. Also, the shrews and some other rodents such as black rats (Rattus rattus) were noted to be free of rabies and rabies-related lyssaviruses in the study area.

Australia has a range of native and introduced large herbivores that could affect the abundance of small mammals through direct and indirect effects. Here we study the relationship between occurrence of the introduced rusa deer (Rusa timorensis) and the native swamp wallaby (Wallabia bicolor), and the abundance of four species of native small mammals in coastal heath vegetation with varying fire history.The abundance of two species, the brown antechinus (Antechinus stuartii) and bush rat (Rattus fuscipes), was related to occurrence of large herbivores and was dependent also on fire history. Abundance of swamp rats (R. lutreolus) and New Holland mice (Pseudomys novaehollandiae) was not related to the occurrence of any of the large herbivores, and did not depend on fire history. At sites burned within the last 9 years, captures of brown antechinus were negatively related to both deer and wallaby occurrence, and captures of bush rats were negatively related to deer occurrence. However, at sites that burned more than 15 years ago, captures of brown antechinus and bush rats were not related to large herbivore occurrence. Overall there was either no relationship, or a negative one, between small mammals and the large herbivores.This mensurative study has demonstrated relationships between deer and wallabies and small mammals, with fire as an additional important factor. From the results of the current study we put forward a series of hypotheses that need to be tested by future experiments.

In some regions, extensive habitat clearance and fragmentation have largely restricted remnant vegetation to linear strips, often bordering roads and railway lines. Such areas may be important for the persistence of native wildlife but there is a paucity of research on their biodiversity value. This study in south-eastern South Australia compared the diversity and abundance of small, terrestrial animals in remnant vegetation, roadsides and farmland. Pitfall and Elliott trapping at 30 sites resulted in a total of 1,024 captures of 28 amphibian, reptile and mammal species, with 819 captures of six mammal species. Overall species diversity was highest in remnant sites and lowest in farm sites. Although low capture rates for reptiles and amphibians precluded statistical testing of individual species, many were caught in both remnant and roadside sites, but rarely at farm sites. Mammal captures consisted of four native (Cercartetus concinnus and C. lepidus, Pseudomys apodemoides and Rattus fuscipes) and two introduced (Mus musculus and Rattus rattus) species. Mus musculus was the most commonly caught species and was significantly more abundant in roadside than remnant vegetation. Abundance was negatively correlated with habitat quality and, at a finer scale, positively associated with percentage cover of exotic grasses. C. concinnus was also commonly captured; however, the absence of a difference in capture rates between remnant and roadside sites suggests that roadside vegetation provides important habitat. The abundance of C. concinnus was positively associated with percentage canopy cover. The current results highlight the conservation value of roadside vegetation and suggest that such areas should be both retained and appropriately managed.

Despite an apparent increase in cases of angiostrongyliasis in humans and animals in Australia, the epidemiology of infection with the two species of Angiostrongylus that co-exist in this country, namely A. cantonensis and A. mackerrasae, is poorly understood. This knowledge gap is particularly important with respect to Angiostrongylus mackerrasae, a species evidently native to Australia, as its ability to cause disease in humans is unknown. Likewise, there is little information on the roles of native and introduced species of rodents and molluscs as hosts of Angiostrongylus species in Australia. This thesis focuses on the gaps in the knowledge about the epidemiology of two species in southeast Queensland, highlighting the hotspots for transmission of the parasite in urban Brisbane. A comprehensive survey of rats belonging to the species Rattus rattus, Rattus norvegicus and Rattus fuscipes was conducted. The prevalence of infection with Angiostrongylus spp. was 16.5% in Rattus spp. trapped in urban Brisbane and surrounds which is much higher than estimates of earlier studies. This highlights the possible risk of zoonotic infection in children, dogs and wildlife in this region and indicates the necessity for public awareness as well as more detailed epidemiological studies on this parasite in eastern Australia. Of the two Australian species, Angiostrongylus mackerrasae appears to be adapted to life in the native bush rat, Rattus fuscipes. This species evidently has an identical life cycle to that of Angiostrongylus cantonensis. A. mackerrasae may have greater potential to infect non-rodent hosts as it has been found as adult form in the lungs, as has been recorded for an individual flying fox. This raises concerns as to the potential of this native angiostrongylid to infect domestic animals and humans. To date, data on the taxonomy, epidemiology and population genetics of A. mackerrasae are poor or unknown. Here, we describe the mitochondrial (mt) genome of A. mackerrasae with the aim of addressing some of these knowledge gaps. The complete mitochondrial (mt) genome of A. mackerrasae was amplified from a single morphologically identified adult worm, by long-PCR in two overlapping amplicons (8 kb and 10 kb). The amplicons were sequenced using the MiSeq Illumina platform and annotated using an in-house pipeline. Amino acid sequences inferred from individual protein coding genes of the mt genomes were concatenated and then subjected to phylogenetic analysis using Bayesian inference. The mt genome of A. mackerrasae is 13,640 bp in size and contains 12 protein coding genes (cox1-3, nad1-6, nad4L, atp6 and cob), and two ribosomal RNA (rRNA) and 22 transfer RNA (tRNA) genes. The mt genome of A. mackerrasae has similar characteristics to those of other Angiostrongylus species which is explained in detail in chapter 3. Phylogenic comparisons reveal that A. mackerrasae is closely related to A. cantonensis and the two sibling species may have recently diverged compared with all other species in the genus with a highly specific host selection. This mt genome will provide a source of genetic markers for explorations of the epidemiology, biology and population genetics of A. mackerrasae. The potential pathogenicity of A. mackerrasae for human and animals was also investigated in this PhD and the results reveal that A. mackerrasae causes severe eosinophilic meningitis in mice and guinea pigs and can potentially cause similar neurological disease in human and animals. It was also revealed that mice immune response is less responsive to A. cantonensis comparing to the similar species A. mackerrasae, as A. cantonensis live for a longer time in meninges of the accidental host and this can help the parasite causing a more patent infection in human and animals. The data of this project raises the possibility that cerebral meningitis remains a potential problem in South Eastern Queensland, particularly as people encroach onto forested areas. Angiostrongylus mackerassae appears to be a species that diverged from A. cantonensis after invasion of the Australian mainland. This species may have greater pathogenesis both in definitive and accidental hosts.

The decline of large coevolved frugivorous species within fragmented habitats can have an effect on ecological processes, for example, seed dispersal and germination. It is therefore necessary for more resilient species to ensure essential processes are maintained within the system. This study investigates the influence of two rodent species, Melomys cervinipes (Fawn-footed Melomys) and Rattus fuscipes (Bush Rat), on the germination process of rainforest fruits. Both species are endemic to north Queensland rainforest and commonly found in fragmented habitats in high densities. We found in 85% of fruit species tested, rodent feeding increased seed germination rate by a factor of 3.5. Our results suggest that rodents can play a significant role in enhancing germination rates of fruits in the tropical rainforest of far north Queensland.

Fleas are important arthropod vectors for a variety of diseases in veterinary and human medicine, and bacteria belonging to the genus Bartonella are among the organisms most commonly transmitted by these ectoparasites. Recently, a number of novel Bartonella species and novel species candidates have been reported in marsupial fleas in Australia. In the present study the genetic diversity of marsupial fleas was investigated; 10 species of fleas were collected from seven different marsupial and placental mammal hosts in Western Australia including woylies (Bettongia penicillata), western barred bandicoots (Perameles bougainville), mardos (Antechinus flavipes), bush rats (Rattus fuscipes), red foxes (Vulpes vulpes), feral cats (Felis catus) and rabbits (Oryctolagus cuniculus). PCR and sequence analysis of the cytochrome oxidase subunit I (COI) and the 18S rRNA genes from these fleas was performed. Concatenated phylogenetic analysis of the COI and 18S rRNA genes revealed a close genetic relationship between marsupial fleas, with Pygiopsylla hilli from woylies, Pygiopsylla tunneyi from western barred bandicoots and Acanthopsylla jordani from mardos, forming a separate cluster from fleas collected from the placental mammals in the same geographical area. The clustering of Bartonella species with their marsupial flea hosts suggests co-evolution of marsupial hosts, marsupial fleas and Bartonella species in Australia.

Summary 1. The ecology of endotherms is driven by their great energetic need for thermoregulation, which renders mammals and birds particularly vulnerable to environmental temperature and resource fluctuations. Important outstanding questions are whether populations are specialized to their particular climate, and to what extent gene × environment interactions determine thermal responses. 2. Here, we show that phylogenetic relatedness and climate interact to determine metabolic capacities, body temperature and morphology in a wild rat (Rattus fuscipes). 3. Mitochondrial metabolic capacities are greater in warm climate populations, indicating that these responses are not the result of cold adaptation. However, glycolytic capacities, fur thickness and capacity for nonshivering thermogenesis are greater in cool climate populations. In populations from cooler climates, body temperatures are lower, but more variable. Together, these changes lead to substantial energy savings in cool climate populations, although all traits are constrained by phylogenetic relatedness. 4. We demonstrate for the first time that gene × environment interactions determine thermal responses in wild mammal populations, and we suggest that physiological variability among populations may render the species more resilient to climate change because it increases whole-species performance breadth. Climate envelope modelling is therefore insufficient to predict the future impact of climate change.

Residency status of individuals in populations may be an important determinant of the outcomes of interspecific competition between native and introduced species. We examined direct behavioral interactions between two similarly sized rodents, the alien Rattus rattus and native Rattus fuscipes when they were respective residents and intruders in a small enclosure. Resident individuals were dominant in their behaviors toward intruders irrespective of the species that was resident. In contrast, interactive behaviors between conspecifics were often neutral or amicable, supporting suggestions that R. rattus and R. fuscipes are social animals. We then tested whether rodent species use heterospecific odors to avoid aggressive competitive interactions and partition space in the field. Neither R. fuscipes nor R. rattus responded to traps scented with the odors of male or female heterospecifics. If R. fuscipes does not recognize the odor of introduced R. rattus, then odors will not be cues to the presence or territorial space of competing heterospecifics. Rather, findings from both enclosure and field trials suggest that direct aggressive interactions between individual R. rattus and R. fuscipes probably facilitate segregation of space between these two species in wild populations, where resident animals may typically be the winners and exclude heterospecific intruders. These findings have implications for the invasion success of introduced rodents such as R. rattus into intact forests, where native populations may have competitive advantage because of their residency status.

Two species of small rodents, Mastacomys fuscus and Rattus fuscipes, and one small dasyurid marsupial Antechinus swainsonii live sympatrically in the subalpine habitat of SE Australia. This paper describes the reproductive characteristics and ontogeny of M. fuscus, and shows that the three species have different reproductive strategies that, in part, are a reflection of their different phylogenies. Cold and snow in winter, and a short summer season, limit the length of time available for reproduction and development. The rodent species exhibit similar reproductive characteristics to those in alpine regions of Europe, North America and South Africa.

The foreshore of Sydney Harbour includes extensive areas of protected native bushland that are an iconic and world-renowned feature of the Sydney landscape. Despite this vegetative cover, however, native small mammals are uncommon and the bushland is dominated by introduced Black Rats Rattus rattus. In particular, the Bush Rat Rattus fuscipes is absent yet remains abundant in comparable habitats to the north and south of Sydney; the last record of the Bush Rat near Sydney Harbour is from 1901. In this paper we explore the idea that the arrival and spread of bubonic plague in the port City of Sydney between 1900 and 1910 was a primary cause of the extirpation of Bush Rats around the harbour foreshore. The plague killed 181 people in Sydney during three major outbreaks, and also killed hundreds of thousands of rats and 52 native Australian mammals in the Moore Park Zoo. The ensuing hysteria and fear of plague resulted in a determined campaign to rid Sydney of rats, including the introduction of a rat bounty...

Cold environments are challenging for small endotherms because they must increase heat production to compensate for increased heat loss to the environment. Mammals that endure cold without entering torpor may have thicker fur and a lower body temperature (Tb) than those in warm environments to save energy. Activity levels also may be reduced in the cold. We aimed to determine whether activity level, exposure to chronic cold, or an interaction between the 2 could reduce the Tb of an endotherm. Wild bush rats (Rattus fuscipes) were brought into captivity and acclimated to cold (12uC) or warm (22uC) ambient temperatures and were either sedentary or exercised. Daily exercise increased maximum Tb in cold-acclimated bush rats but also decreased minimum Tb. Mean (6SE) daily Tb was significantly lower in cold-acclimated bush rats (sedentary: 36.5uC 6 0.1uC; exercised: 36.4uC 6 0.2uC) compared to warm-acclimated bush rats (sedentary: 37.3uC 6 0.2uC; exercised: 37.0uC 6 0.1uC). Body temperature decreased significantly over the time of cold acclimation. Thicker fur and lower Tbs in cold-acclimated bush rats conferred an energy saving equivalent to 11% of daily food intake in exercised rats and 22% of daily food intake in sedentary rats. The lower Tbs recorded in some small mammals in winter are not necessarily due to lower levels of activity but can result from a regulated reduction in Tb in response to cooler ambient temperatures. DOI: 10.1644/10-MAMM-A-003.1.

The movement of organisms between subdivided populations is considered a key influence on the persistence of species in modified landscapes. In particular, the ability to recolonize ‘empty’ fragments of habitat is directly relevant to conservation management, and to understanding the link between pattern and process in metapopulations. We studied the movement and recolonization ability of the bush rat, Rattus fuscipes, in a highly fragmented agricultural landscape in south-western Victoria, Australia. Populations were monitored in seven small ( 49 ha) forest fragments before removal of all residents from four of the small fragments. Subsequent monitoring (for up to 16 months) allowed the detection of colonizing individuals, and comparisons between ‘experimental’ and ‘control’ fragments. Rattus fuscipes readily moved between fragments and successfully recolonized (i.e. both males and females arrived) two of four fragments in which extinctions were simulated. A single male moved into a third experimental fragment. In one fragment, new animals were detected 1 month after the removal of residents, indicating that recolonization can occur rapidly. Dispersers were not a random sample of the population: although both males and females, and adults and sub-adults were recorded dispersing, adult males in reproductive condition predominated. Functional connectivity appears to be high for R. fuscipes in the study landscape. Results from this manipulative experiment provide direct empirical evidence that a capacity for movement allows recolonization of fragments of suitable habitat and is a key process responsible for species persistence in fragmented landscapes, as predicted by theory.

Fragmentation theory predicts that population persistence should be positively correlated with the size of habitat fragments. The patterns of occurrence of many species are consistent with this prediction, but the demographic processes that determine how species respond to fragmentation are poorly understood. In addition, habitat quality may interact with fragment size as an influence on demographic performance. We investigated these predictions for the native bush rat Rattus fuscipes by testing the following hypotheses: 1) population performance (i.e. viability as determined by various demographic parameters) is positively correlated with fragment size; and 2) population performance is positively correlated with habitat quality. Populations of R. fuscipes were censused in two large (>49 ha) and eight small ( R. fuscipes populations are profoundly impacted by habitat fragmentation, with population performance declining with fragment size. Studies based on patterns of species occurrence should be interpreted with caution as they may mask critical processes occurring at the population level. For a thorough understanding of the effects of habitat fragmentation, population-level studies are required.

Laboratory studies showed that bush rats will hoard food pellets when deprived of food and water-soaked pledgets when deprived of water. Some evidence for retrieval of sweet-tasting objects was also obtained. The general retrieval system demonstrated in Norway rats is therefore also present in this non-commensal Rattus species. An analysis of the component responses of the hoarding sequence during these experiments supported this conclusion. In both species hoarding seems to be regulated by incentive and valuation processes related to oral stimuli and responses. Zusammenfassung Die Allgemeingultigkeit der bei hamsternden Wanderratten gefundenen Objektbevorzugung wurde bei der Australischen Buschratte, einer nichtkulturfolgenden Rattenart, untersucht. Fallengefangene Buschratten beider Geschlechter lebten in Einzelkafigen, und jedes Tier durfte Objekte aus einem abgeschlossenen Gang in den Heimkafig wahrend taglicher Versuche von 20 bis 30 min Dauer eintragen. In Experiment 1 wurden Futterpillen normal ernahrten und kurzgehaltenen Ratten geboten. Auf der Mitte des Futterentzugs bekam jedes Tier 1 h vor dem Hamsterversuch etwas zu fressen. Futterentzug steigerte das Hamstern, wahrend Vorfuttern es minderte, obwohl das Korpergewicht unter dem normal ernahrter Tiere lag. In Experiment 2 erhielten die Tiere wassergetrankte oder in einer Natrium-Sacharin-Losung getrankte Zellstoffstucke nebeneinander. Normal getrankte Ratten wurden mit durstigen verglichen. Bei den beiden letzten Versuchen mit beiden Gruppen wurde die bevorzugte Losung zusammen mit Futterpillen geboten. Die nichtdurstigen Tiere bevorzugten andeutungsweise Sacharin, vielleicht wegen der benutzten Konzentration von 1%. Durstige Tiere zogen Wassergetranktes vor und trugen es zu Beginn der letzten beiden Laufe bevorzugt ein. In beiden Versuchen beeinfluste Entzug die Appetenz, sich dem Hamsterobjekt zu nahern und es aufzunehmen. Unterschiede im Fressen und Belecken entsprachen solchen des Hamsterns. Die Versuche belegen, das Objekteigenschaften, die bei Laborratten Hamstern auslosen, auch bei Buschratten wirksam sind. Auch sind die Verhaltensfolgen ahnlich. Es wird geschlossen, das das Erkennen auslosender Reize und deren Verknupfung mit korperlichen Mangelzustanden bei beiden Arten in enger Beziehung zu oralen Faktoren, die ihrerseits Hamstern bestimmen, evolviert wurden.

Genetic analysis of individual origins works best with populations that are genetically distinct but which exchange a high rate of immigrants, conditions that don't normally coexist since immigration acts to prevent the accumulation of genetic differences. We provide empirical results from a newly constructed habitat linkage to illustrate the unique suitability of such analysis to monitoring the re-establishment of connections between previously isolated populations. Donaghy's Corridor links a previously isolated 498 ha fragment of rainforest to an adjacent 80 000 ha of intact forest. Starting in the final year of the planting programme that established the corridor, we trapped two species of native small mammals, the Bush Rat (Rattus fuscipes) and the Cape York Rat (Rattus leucopus), within and nearby the linkage. We used genetic data from ear clippings to determine which side of the corridor individual animals originated from, and by comparing this information to trap locations, we identified 16 long-distance movements through the corridor. As genetic analysis of origins allowed movements to be detected from a single capture event and as it reflected movement since birth, this approach yielded considerably more data than capture records alone. The combination of movement and capture records allowed species-specific assessment of corridor function, revealing that the use and occupation of the corridor was higher for Bush Rat than for Cape York Rat and was neither symmetrical nor uniform. Long-distance movements through the corridor were most common immediately after habitat restoration, dropping off as the reconstructed habitat was colonized.

Summary 1. Interspecific competition is a recognized but under-studied mechanism by which invasive species affect native fauna. 2. We experimentally reduced populations of the introduced black rat Rattus rattus in relatively undisturbed littoral rainforest in south-eastern Australia to test its competitive impact on populations of the native bush rat Rattus fuscipes. 3. Removal of R. rattus resulted in significant and sustained increases in populations of the native rodent due to immigration, juvenile recruitment and increases in residency of females. Native juveniles were particularly vulnerable to R. rattus, being largely absent from untreated populations despite indications of breeding in females, but responding rapidly to their removal. 4. The absence of changes in body condition and reproduction of adult R. fuscipes with long-term removal of R. rattus suggests that direct interference by R. rattus rather than competition for resources best explains the low densities and poor juvenile recruitment of R. fuscipes. 5. The behavioural dominance of R. rattus was not due to an inherent competitive ability because they did not re-establish post-removal as expected if competition was asymmetrical. Instead, competitive dominance seemingly shifted to R. fuscipes with changes in residency status of populations. Improved survivorship among native females reveals that they were particularly important in establishing resident populations following removal of R. rattus. 6.Synthesis and applications. These findings identify R. rattus as a significant competitive threat to native R. fuscipes. Removal of invasive rodents and active conservation of common native species is recommended to forest managers based on the potential for R. fuscipes to prevent re-invasion subsequent to pest control efforts and maintain invasion resistance.

Summary Four reproductively isolated populations of the Australian bush-rat, Rattus fuscipes greyii, are polymorphic for electrophoretic variants of the mitochondrial enzyme, NADP-dependent iso-citrate dehydrogenase (M-Idh). The electrophoretic patterns of M-Idh and a small amount of breeding data are in agreement with the hypothesis that the variation is controlled by two alleles at an autosomal locus, Idh-2. In three relatively large populations, the proportion of heterozygotes at the Idh-2 locus ranges from 0.07 to 0.23, while on a small off-shore island it is 0.60. In this latter population there is an excess of heterozygotes which is on the borderline of statistical significance, suggesting that heterotic selection may be maintaining the polymorphism. Populations on eight other small islands are monomorphic for the allele which is the most frequent in the large populations. In most species M-Idh is less variable than most other enzymic proteins and the results presented here constitute one of the few published examples of an extensive M-Idh polymorphism.