Rattus Fuscipes Research Articles

Utility of owl pellets for monitoring threatened mammal communities: an Australian case study

Context Predictive modelling of the impacts of climate change has highlighted a need for on-ground monitoring of mammal communities within the Wet Tropics bioregion of Queensland to inform wildlife conservation management. Standard mammal-survey techniques are labour intensive and often incapable of detecting rare, trap-shy or otherwise elusive species, effectively rendering them invisible to researchers even when substantial resources are applied. Aims To assess the utility of feeding remains (regurgitated pellets) from lesser sooty owls, Tyto tenebricosa multipunctata, for monitoring populations of small to medium-sized mammals within the Wet Tropics. Methods Three female lesser sooty owls were radio-tracked to determine home-range areas. Radio-tracking and targeted systematic searches were used to locate diurnal roosts containing owl pellets from which prey species were identified. Owl-pellet data were directly compared with live-trap data within three putative owl home ranges. Additionally, analyses of a dataset spanning more than 15 years demonstrated the utility of owl-pellet data for monitoring mammal communities. Key results Owl-pellet surveys yielded 14 mammal species (840 individuals) from 152 man-hours, compared with six mammal species (361 individuals) from 194 man-hours of live trapping. Both survey methods identified Rattus fuscipes, Melomys spp. and Antechinus spp. as the most abundant species but live-trap data were found to under-represent relative abundance of Melomys spp. and over-represent relative abundance of R. fuscipes in comparison to owl-pellet data. Conclusions Analysis of lesser sooty owl pellets is a particularly useful method for compilation of species inventories of small to medium-sized mammals, being more effective than standard live-trapping surveys within the rainforests of the Wet Tropics. Implications Owl-pellet analysis is well suited for monitoring mammal communities, as long as periodic data are collected from the same roost(s) and the pellets have been deposited by the same individual bird(s). Additional research relating to variability in behavioural traits between individual lesser sooty owls that have potential to confound results via sampling bias must be undertaken before owl-pellet data can be used for comparison of mammal community structure among sites, or for monitoring a site over a period spanning a change in the individual owls that are depositing pellets at that site.

Trappability of introduced and native rodents in different trap types in coastal forests of south-eastern Australia

Trapping is an invaluable tool for estimating community composition and population size and structure of mammals. Bias in the relative contribution of species to a community and the age and sex structure of populations can occur where the traps used do not equally trap all species, sexes or cohorts. The aim of this study was to compare the efficiency of enclosed Elliott traps and open wire cage traps in trapping the invasive black rat, Rattus rattus, and the native rodent, Rattus fuscipes. Both trap types were suitable for trapping R. fuscipes and there was no apparent bias in capture of sex and age classes. In contrast, black rats were considerably more trappable in cage traps. Juveniles were more readily trapped in Elliott traps than adults, but were still considerably undersampled where only Elliott traps were used. These findings have important implications for sampling invasive rodents in Australian forests where Elliott traps are commonly used to census small mammals. Only using Elliott traps will underestimate density, distribution and impacts of R. rattus in native habitats. Cage traps or a combination of traps are recommended for reliably trapping black rats and obtaining representative data on presence, abundance and distribution.

Can rodents enhance germination rates in rainforest seeds?

SummaryThe 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.

Temporal activity patterns of the swamp rat (Rattus lutreolus) and other rodents in north-eastern New South Wales, Australia

The activity patterns and partitioning of time by four small mammal species, with a focus on the swamp rat (Rattus lutreolus) in north-eastern New South Wales, was investigated using camera trap data from two studies. Analysis was carried out on 1079 camera trap events over 1530 camera trap–nights or 36 720 h of camera trap deployment in the field. The activity patterns of Rattus lutreolus were distinctly diurnal with crepuscular peaks of activity but this differed between sites and when in the presence of competitors. The Hastings River mouse (Pseudomys oralis) and the bush rat (Rattus fuscipes) displayed typical bimodal patterns of nocturnal activity. Antechinus were mostly nocturnal but were occasionally active during the day. These data indicate that where species of Muridae co-occur, diurnal time partitioning by R. lutreolus may reduce competition for food resources. It also confirms the speculation that R. lutreolus displays diurnal behaviour, albeit dependent on the presence of other murids.

Determining the factors affecting seed germination in Livistona australis (Arecaceae) for the recovery of fragmented populations

Understanding seed germination and seedling recruitment is important for managing long-lived plant species, particularly palms that are transplanted from the wild and where regeneration is suppressed by seed predators and exotic herbivores. Seed viability, the timing of germination, and the factors influencing germination were investigated for the cabbage tree palm, Livistona australis (R.Br.) Mart. Greenhouse studies were combined with in situ experiments conducted on the Australian mainland and on a nearby mammal-free island. Under greenhouse conditions, >90% of seed germinated within 4 months. In the field, burial rather than surface sowing of seed increased germination success. Seed without mesocarp and in sunlight had increased germination when compared with fruits in shade on the island, whereas neither presence/absence of mesocarp or light levels had any effect on the mainland. Germination success was substantially lower on the mainland, primarily because of high seed predation from the native bush rat, Rattus fuscipes. When caged to exclude vertebrates, 44% of seed were damaged over time by pathogens and invertebrates, with losses greater in sunlight than in shade. Results from the present study indicate that freshly buried seed with the mesocarp removed would have the greatest potential success in promoting the restoration of L. australis at degraded sites.

Thermal adaptation in endotherms: climate and phylogeny interact to determine population‐level responses in a wild rat

Summary1. 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.

Influence of residency and social odors in interactions between competing native and alien rodents

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.

Population and behavioural responses of native prey to alien predation

The introduction of invasive alien predators often has catastrophic effects on populations of naïve native prey, but in situations where prey survive the initial impact a predator may act as a strong selective agent for prey that can discriminate and avoid it. Using two common species of Australian small mammals that have persisted in the presence of an alien predator, the European red fox Vulpes vulpes, for over a century, we hypothesised that populations of both would perform better where the activity of the predator was low than where it was high and that prey individuals would avoid signs of the predator's presence. We found no difference in prey abundance in sites with high and low fox activity, but survival of one species-the bush rat Rattus fuscipes-was almost twofold higher where fox activity was low. Juvenile, but not adult rats, avoided fox odour on traps, as did individuals of the second prey species, the brown antechinus, Antechinus stuartii. Both species also showed reduced activity at foraging trays bearing fox odour in giving-up density (GUD) experiments, although GUDs and avoidance of fox odour declined over time. Young rats avoided fox odour more strongly where fox activity was high than where it was low, but neither adult R. fuscipes nor A. stuartii responded differently to different levels of fox activity. Conservation managers often attempt to eliminate alien predators or to protect predator-naïve prey in protected reserves. Our results suggest that, if predator pressure can be reduced, otherwise susceptible prey may survive the initial impact of an alien predator, and experience selection to discriminate cues to its presence and avoid it over the longer term. Although predator reduction is often feasible, identifying the level of reduction that will conserve prey and allow selection for avoidance remains an important challenge.

Diversity of Bartonella species detected in arthropod vectors from animals in Australia

A variety of Bartonella species were detected in two species of ticks and three species of fleas collected from marsupial hosts; brush-tailed bettong or woylie (Bettongia penicillata) and western barred bandicoots (Perameles bougainville) and from a rodent host; Rattus fuscipes in Western Australia. Bartonella species were detected using nested-PCR of the gltA gene and the 16S-23S ribosomal internal transcribed spacer region (ITS), and species were characterized using DNA sequencing of the 16S rRNA, gltA, rpoB, ftsZ genes and the ITS region. Bartonella rattaustraliani and B. coopersplainsensis were detected in Ixodes spp. ticks and fleas (Stephanocircus pectinipes) respectively collected from rodents. Two novel Bartonella species were detected from marsupials; Candidatus Bartonella woyliei n. sp. was detected in both fleas (Pygiopsylla hilli) and ticks (Ixodes australiensis) collected from woylies and Candidatus Bartonella bandicootii n. sp. was detected in fleas (Pygiopsylla tunneyi) collected from western barred bandicoots. Concatenated phylogenetic analysis of all 5 loci clarified the marsupial cluster of Bartonella species in Australia and confirmed the species status of these two Bartonella species in ticks and fleas from woylies and western barred bandicoots, which are classified as threatened species and are vulnerable to extinction.

Genetic characterization of flea-derived Bartonella species from native animals in Australia suggests host–parasite co-evolution

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.

Identification of novel trypanosome genotypes in native Australian marsupials

In the present study, the occurrence and molecular phylogeny of trypanosome parasites were studied in both wild and captive marsupials from Western Australia and Queensland. Blood samples were screened by PCR at the 18S rDNA locus, and the glycosomal glyceraldehyde phosphate dehydrogenase gene.Overall, 5.3% of the blood samples were positive at the 18S rDNA locus. All positives belonged to wild-captured Western Australian individuals, where trypanosome-specific DNA was detected in 9.8% of the screened samples from wild marsupials, in common brushtail possums, and woylies. The detection rate of trypanosome DNA in these two host species was 12.5% and 20%, respectively.Phylogenetic analyses based on two loci, indicated that the possum-derived trypanosome isolates were genetically distinct, and most closely related to the Australian marsupial trypanosomes H25 from a kangaroo, and BRA2 from a bush rat. This is the first study to genetically characterise trypanosome isolates from possums.The analysis of the woylie-derived isolates demonstrated that this marsupial host can harbour multiple genotypes within the same geographical location and furthermore multiple genotypes within the same host, indicative of mixed infections. All the woylie-derived genotypes grouped with trypanosomes found in Australian marsupials, suggesting that they are more likely to belong to an endemic or Australasian trypanosome species.This is the first study to genetically characterise trypanosome isolates from possums (Trichosurus vulpecula). Although the clinical significance of these infections is currently unknown, the identification of these novel sequences may support future investigations on transmission, threats to endangered wildlife, and evolutionary history of the genus Trypanosoma.

Evolutionary history of the Karoo bush rat, Myotomys unisulcatus (Rodentia: Muridae): disconcordance between morphology and genetics

Morphological characters have historically been used as the basis for mammalian taxonomic designations and, in a geographic context, subspecies descriptions. Geographic genetic structuring of a species, however, often reflects a contrasting classification for sampled populations. To investigate morphological and genetic congruence, geometric morphometrics and phylogeographic mitochondrial DNA sequence analyses of a South African plains-dwelling species, Myotomys unisulcatus, the Karoo bush rat, was performed across its range. A Bayesian population structure analysis identified two closely-related distinct genetic assemblages: the first contains populations from both the eastern, southern, and western parts of the species range (coastal lowland group), and the second comprises individuals from the Little Karoo (central interior group). Areas of sharp elevation (the Great Escarpment), coupled to vegetational differences, appeared to be the main factor limiting gene flow between these two groups. Geometric morphometric analyses on the ventral and dorsal views of the crania of M. unisulcatus failed to support the genetic groupings. Instead environmental factors in the respective biomes appeared to play a more important role in shaping the crania of both genders. The contrasting patterns obtained between morphology and genetics in M. unisulcatus is probably indicative of phenotypic plasticity throughout the range of the species, and it is hypothesized that regional environmental factors play a prominent role in explaining geographic morphological variation within the species. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102, 510–526.

Sydney's bubonic plague outbreak 1900-1910: a disaster for foreshore wildlife?

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...

Reproduction and ontogeny of Mastacomys fuscus (Rodentia: Muridae) in the Australian Alps and comparisons with other small mammals living in alpine communities

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.

Starting points for small mammal population recovery after wildfire: recolonisation or residual populations?

Wildfire is a major driver of spatio‐temporal variation in terrestrial ecosystems. Large wildfires are predicted to occur more frequently due to climate change. The mechanisms by which post‐fire recovery proceeds are influenced by the abundance of survivors, and their distribution in relation to habitat variability and refugia. Thus, characterising early post‐fire demographic processes is critical to understanding the demographic and community‐level responses of ecosystems to fire. The Black Saturday fires of February 2009 burnt an area of approximately 3500 km2 in Victoria, Australia. We quantified the effects of this high severity forest fire on the habitat, abundance, sex ratio and body mass of two small mammal species, the agile antechinus Antechinus agilis and bush rat Rattus fuscipes. We developed a hypothetical framework to distinguish in situ survival and rapid recolonisation as the processes underlying short‐term post‐fire distributions. These hypotheses were based on expected patterns of abundance over increasing distances from unburnt sources, and the estimated recolonisation capabilities of each species and sex. The agile antechinus and bush rat were present in burnt sites at 30% and 12% of the density observed in unburnt sites. In situ survival, and not recolonisation, was the most plausible explanation for our findings. Abundance and body mass data indicated a greater effect of fire on the bush rat than the agile antechinus. The bush rat showed a shift in topographic association, whereby drainage lines acted as post‐fire refugia. Our findings suggest these species do not depend on recolonisation for recovery, and that the bush rat will follow a nucleated recovery, expanding from topographic refugia. Thus, connectivity‐reducing management activities, such as salvage logging and firebreak and road construction, may not affect the early stages of population recovery in remaining stands of burnt forest. Rather, ongoing recovery is likely to be limited by demographic rates and resource availability.

Evolutionary relationships and divergence times among the native rats of Australia

BackgroundThe genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level.ResultsAnalyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya). Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long), Rattus database generally give well supported species clades.ConclusionsOur whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea. While problematic for inference of deeper divergences, we report that the analysis of shorter mitochondrial sequences is very useful for species identification in rats.

Advantage to lower body temperatures for a small mammal (Rattus fuscipes) experiencing chronic cold

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.

Habitat fragmentation disrupts the demography of a widespread native mammal

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 (<2.5 ha) forest fragments in an agricultural region of southeastern Australia. Fragments with high and low quality habitat were included in each size category. Fragment size influenced multiple aspects of population demography; populations in large fragments had higher densities, older age structures, received more potential immigrants, and were more likely to recruit adults than those in small fragments. Reproductive patterns were more predictable in large fragments. Habitat quality per se had less marked effects; adult females were heavier and subadults more prevalent in fragments with high quality habitat. However, high quality habitat enhanced population performance in small fragments more so than in large ones. Despite being widespread in the study area, 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.

Recolonization of forest fragments by a native rodent following experimental ‘extinctions’

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.

Low Levels of Physical Activity Increase Metabolic Responsiveness to Cold in a Rat (Rattus fuscipes)

BackgroundPhysical activity modulates expression of metabolic genes and may therefore be a prerequisite for metabolic responses to environmental stimuli. However, the extent to which exercise interacts with environmental conditions to modulate metabolism is unresolved. Hence, we tested the hypothesis that even low levels of physical activity are beneficial by improving metabolic responsiveness to temperatures below the thermal neutral zone, thereby increasing the capacity for substrate oxidation and energy expenditure.Methodology/Principal FindingsWe used wild rats (Rattus fuscipes) to avoid potential effects of breeding on physiological phenotypes. Exercise acclimation (for 30 min/day on 5 days/week for 30 days at 60% of maximal performance) at 22°C increased mRNA concentrations of PGC1α, PPARδ, and NRF-1 in skeletal muscle and brown adipose tissue compared to sedentary animals. Lowering ambient temperature to 12°C caused further increases in relative expression of NRF-1 in skeletal muscle, and of PPARδ of brown adipose tissue. Surprisingly, relative expression of UCP1 increased only when both exercise and cold stimuli were present. Importantly, in sedentary animals cold acclimation (12°C) alone did not change any of the above variables. Similarly, cold alone did not increase maximum capacity for substrate oxidation in mitochondria (cytochrome c oxidase and citrate synthase activities) of either muscle or brown adipose tissue. Animals that exercised regularly had higher exercise induced metabolic rates in colder environments than sedentary rats, and temperature induced metabolic scope was greater in exercised rats.Conclusions/SignificancePhysical activity is a necessary prerequisite for the expression of transcriptional regulators that influence a broad range of physiological functions from energy metabolism to cardiovascular function and nutrient uptake. A sedentary lifestyle leads to decreased daily energy expenditure because of a lack of direct use of energy and a muted metabolic response to ambient temperature, which can be reversed even by low levels of physical activity.