Evolution of a contagious cancer: epigenetic variation in devil facial tumour disease

The emergence of Devil Facial Tumour Disease (DFTD), a highly contagious cancer, is driving Tasmanian devils (Sarcophilus harrisii) to extinction. The cancer is a genetically and chromosomally stable clonal cell line which is transmitted by biting during social interactions. In the present study, we explore the Devil Facial Tumour (DFT) epigenome and the genes involved in DNA methylation homeostasis. We show that tumour cells have similar levels of methylation to peripheral nerves, the tissue from which DFTD originated. We did not observe any strain or region-specific epimutations. However, we revealed a significant increase in hypomethylation in DFT samples over time (p < 0.0001). We propose that loss of methylation is not because of a maintenance deficiency, as an upregulation of DNA methyltransferase 1 gene was observed in tumours compared with nerves (p < 0.005). Instead, we believe that loss of methylation is owing to active demethylation, supported by the temporal increase in MBD2 and MBD4 (p < 0.001). The implications of these changes on disease phenotypes need to be explored. Our work shows that DFTD should not be treated as a static entity, but rather as an evolving parasite with epigenetic plasticity. Understanding the role of epimutations in the evolution of this parasitic cancer will provide unique insights into the role of epigenetic plasticity in cancer evolution and progression in traditional cancers that arise and die with their hosts.

New insights into the role of MHC diversity in devil facial tumour disease

Devil facial tumour disease (DFTD) is a fatal contagious cancer that has decimated Tasmanian devil populations. The tumour has spread without invoking immune responses, possibly due to low levels of Major Histocompatibility Complex (MHC) diversity in Tasmanian devils. Animals from a region in north-western Tasmania have lower infection rates than those in the east of the state. This area is a genetic transition zone between sub-populations, with individuals from north-western Tasmania displaying greater diversity than eastern devils at MHC genes, primarily through MHC class I gene copy number variation. Here we test the hypothesis that animals that remain healthy and tumour free show predictable differences at MHC loci compared to animals that develop the disease.

Increased mortality of naive varanid lizards after the invasion of non-native can toads (bufo marinus)

Exotic animal and plant species introduced into the Australian continent often imparted catastrophic effects on the indigenous fauna and flora. Proponents of biological control introduced the South American Cane Toad (Bufo marinus) into the sugar cane fields of Queensland in 1935. The Cane Toad is one of the most toxic bufonids and when seized by naive Australian predators, the toxin usually kills the attacker. One group of Australian squamate reptiles that are very susceptible to Cane Toad toxins is varanid lizards. Prior to Cane Toad invasion of our study area, the Adelaide River floodplain of the Northern Territory of Australia, annual mortality of adult male radio-tagged yellow-spotted Goannas (Varanus panoptes) was very low. After the arrival of toads in October 2005, all radio-tracked goannas were found dead in August 2006, most likely attempting to feed on the toads. Our results suggest that invasive Cane Toads place naive adult male Yellow-spotted Goannas at risk of possibly >90% mortality. This increase in mortality could reduce the genetic diversity and hamper long-term survival of these large carnivorous lizards.

Differing impact of a major biogeographic barrier on genetic structure in two large kangaroos from the monsoon tropics of Northern Australia

Tropical savannas cover 20-30% of the world's land surface and exhibit high levels of regional endemism, but the evolutionary histories of their biota remain poorly studied. The most extensive and unmodified tropical savannas occur in Northern Australia, and recent studies suggest this region supports high levels of previously undetected genetic diversity. To examine the importance of barriers to gene flow and the environmental history of Northern Australia in influencing patterns of diversity, we investigated the phylogeography of two closely related, large, vagile macropodid marsupials, the antilopine wallaroo (Macropus antilopinus; n = 78), and the common wallaroo (Macropus robustus; n = 21). Both species are widespread across the tropical savannas of Australia except across the Carpentarian Barrier (CB) where there is a break in the distribution of M. antilopinus. We determined sequence variation in the hypervariable Domain I of the mitochondrial DNA control region and genotyped individuals at 12 polymorphic microsatellite loci to assess the historical and contemporary influence of the CB on these species. Surprisingly, we detected only limited differentiation between the disjunct Northern Territory and QueenslandM. antilopinus populations. In contrast, the continuously distributedM. robustus was highly divergent across the CB. Although unexpected, these contrasting responses appear related to minor differences in species biology. Our results suggest that vicariance may not explain well the phylogeographic patterns in Australia's dynamic monsoonal environments. This is because Quaternary environmental changes in this region have been complex, and diverse individual species' biologies have resulted in less predictable and idiosyncratic responses.

Photoreceptor topography and spectral sensitivity in the common brushtail possum (Trichosurus vulpecula)

Marsupials are believed to be the only non-primate mammals with both trichromatic and dichromatic color vision. The diversity of color vision systems present in marsupials remains mostly unexplored. Marsupials occupy a diverse range of habitats, which may have led to considerable variation in the presence, density, distribution, and spectral sensitivity of retinal photoreceptors. In this study we analyzed the distribution of photoreceptors in the common brushtail possum (Trichosurus vulpecula). Immunohistochemistry in wholemounts revealed three cone subpopulations recognized within two spectrally distinct cone classes. Long-wavelength sensitive (LWS) single cones were the largest cone subgroup (67-86%), and formed a weak horizontal visual streak (peak density 2,106 ± 435/mm2) across the central retina. LWS double cones were strongly concentrated ventrally (569 ± 66/mm2), and created a "negative" visual streak (134 ± 45/mm2) in the central retina. The strong regionalization between LWS cone topographies suggests differing visual functions. Short-wavelength sensitive (SWS) cones were present in much lower densities (3-10%), mostly located ventrally (179 ± 101/mm2). A minority population of cones (0-2.4%) remained unlabeled by both SWS- and LWS-specific antibodies, and may represent another cone population. Microspectrophotometry of LWS cone and rod visual pigments shows peak spectral sensitivities at 544 nm and 500 nm, respectively. Cone to ganglion cell convergences remain low and constant across the retina, thereby maintaining good visual acuity, but poor contrast sensitivity during photopic vision. Given that brushtail possums are so strongly nocturnal, we hypothesize that their acuity is set by the scotopic visual system, and have minimized the number of cones necessary to serve the ganglion cells for photopic vision.

Characterization of antibody V segment diversity in the Tasmanian devil (Sarcophilus harrisii)

The Tasmanian devil (Sarcophilus harrisii) immune system has recently been under scrutiny because of the emergence of a contagious cancer, which has decimated devil numbers. Here we provide a comprehensive description of the Tasmanian devil immunoglobulin variable regions. We show that heavy chain variable (VH) and light chain variable (VL) repertoires are similar to those described in other marsupial taxa: VL diversity is high, but VH diversity is restricted and belongs only to clan III. As in other mammals, one VH and one Vλ germline family and multiple incomplete Vκ germline sequences were identified in the genome. High Vκ variation was observed in transcripts and we predict that it may have arisen by gene conversion and/or somatic mutations, as it does not appear to have originated from germline variation. Phylogenetic analyses revealed that devil VL gene segments are highly complex and ancient, with some lineages predating the separation of marsupials and eutherians. These results indicate that although the evolutionary history of immune genes lead to the expansions and contractions of immune gene families between different mammalian lineages, some of the ancestral immune gene variants are still maintained in extant species. A high degree of similarity was found between devil and other marsupial VH segments, demonstrating that they originated from a common clade of closely related sequences. The VL families had a higher variation than VH both between and within species. We suggest that, similar to other studied marsupial species, the complex VL segment repertoire compensates for the limited VH diversity in Tasmanian devils.

Fire severity and fire-induced landscape heterogeneity affect arboreal mammals in fire-prone forests

In fire-prone regions, wildfire influences spatial and temporal patterns of landscape heterogeneity. The likely impacts of climate change on the frequency and intensity of wildfire highlights the importance of understanding how fire-induced heterogeneity may affect different components of the biota. Here, we examine the influence of wildfire, as an agent of landscape heterogeneity, on the distribution of arboreal mammals in fire-prone forests in south-eastern Australia. First, we used a stratified design to examine the role of topography, and the relative influence of fire severity and fire history, on the occurrence of arboreal mammals 2-3 years after wildfire. Second, we investigated the influence of landscape context on the occurrence of arboreal mammals at severely burnt sites. Forested gullies supported a higher abundance of arboreal mammals than slopes. Fire severity was the strongest influence, with abundance lower at severely burnt than unburnt sites. The occurrence of mammals at severely burned sites was influenced by landscape context: abundance increased with increasing amount of unburnt and understorey-only burnt forest within a 1 km radius. These results support the hypothesis that unburnt forest and moist gullies can serve as refuges for fauna in the post-fire environment and assist recolonization of severely burned forest. They highlight the importance of spatial heterogeneity created by wildfire and the need to incorporate spatial aspects of fire regimes (e.g., creation and protection of refuges) for fire management in fire-prone landscapes.

Use of expert knowledge to elicit population trends for the koala (Phascolarctos cinereus)

Aim: The koala is a widely distributed Australian marsupial with regional populations that are in rapid decline, are stable or have increased in size. This study examined whether it is possible to use expert elicitation to estimate abundance and trends of populations of this species. Diverse opinions exist about estimates of abundance and, consequently, the status of populations. Location: Eastern and south-eastern Australia Methods: Using a structured, four-step question format, a panel of 15 experts estimated population sizes of koalas and changes in those sizes for bioregions within four states. They provided their lowest plausible estimate, highest plausible estimate, best estimate and their degree of confidence that the true values were contained within these upper and lower estimates. We derived estimates of the mean population size of koalas and associated uncertainties for each bioregion and state. Results: On the basis of estimates of mean population sizes for each bioregion and state, we estimated that the total number of koalas for Australia is 329,000 (range 144,000-605,000) with an estimated average decline of 24% over the past three generations and the next three generations. Estimated percentage of loss in Queensland, New South Wales, Victoria and South Australia was 53%, 26%, 14% and 3%, respectively. Main conclusions: It was not necessary to achieve high levels of certainty or consensus among experts before making informed estimates. A quantitative, scientific method for deriving estimates of koala populations and trends was possible, in the absence of empirical data on abundances.

Effects of multiple disturbance processes on arboreal vertebrates in Eastern Australia: implications for management

Habitat loss and invasive predators increasingly threaten global biodiversity. Here we use a landscape-scale experimental approach to explore the individual and synergistic effects of logging and an invasive predator, the red fox Vulpes vulpes on two common native arboreal vertebrates (a predator and prey species) in south-eastern Australia. We used site occupancy methods to evaluate different models evaluating the effects of site specific forest logging disturbance, lethal fox baiting and forest structural elements for explaining variation in site occupancy of a large monitor lizard Varanus varius, and a marsupial prey, the common ringtail possum Pseudocheirus peregrinus across a complex forest landscape. Site occupancy of ringtail possum was influenced by habitat resources and the structural complexity of forest, which indirectly mediated predation risk. Presence of fox baiting had no direct effect on the ringtail site occupancy. In contrast, access to prey resources and fox baiting appeared to best explain site occupancy variation in monitor lizards across the landscape. While these species are affected primarily by separate disturbances, synergistic interactions between the processes may intensify their effects. Our results demonstrate that species susceptibility to disturbance processes are highly idiosyncratic. This approach makes efficient use of integrated modelling to aid conservation management at both local and landscape levels.

Stress triangle: do introduced predators exert indirect costs on native predators and prey?

Non-consumptive effects of predators on each other and on prey populations often exceed the effects of direct predation. These effects can arise from fear responses elevating glucocorticoid (GC) hormone levels (predator stress hypothesis) or from increased vigilance that reduces foraging efficiency and body condition (predator sensitive foraging hypothesis); both responses can lead to immunosuppression and increased parasite loads. Non-consumptive effects of invasive predators have been little studied, even though their direct impacts on local species are usually greater than those of their native counterparts. To address this issue, we explored the non-consumptive effects of the invasive red fox Vulpes vulpes on two native species in eastern Australia: a reptilian predator, the lace monitor Varanus varius and a marsupial, the ringtail possum Pseudocheirus peregrinus. In particular, we tested predictions derived from the above two hypotheses by comparing the basal glucocorticoid levels, foraging behaviour, body condition and haemoparasite loads of both native species in areas with and without fox suppression. Lace monitors showed no GC response or differences in haemoparasite loads but were more likely to trade safety for higher food rewards, and had higher body condition, in areas of fox suppression than in areas where foxes remained abundant. In contrast, ringtails showed no physiological or behavioural differences between fox-suppressed and control areas. Predator sensitive foraging is a non-consumptive cost for lace monitors in the presence of the fox and most likely represents a response to competition. The ringtail's lack of response to the fox potentially represents complete naiveté or strong and rapid selection to the invasive predator. We suggest evolutionary responses are often overlooked in interactions between native and introduced species, but must be incorporated if we are to understand the suite of forces that shape community assembly and function in the wake of biological invasions.

Feasibility of the Reintroduction of Wolves in Maine: a GIS Study

The eastern timber wolf (Canis lupus lycaon) once inhabited Maine, as well as the rest of the eastern United States and southern Canada. As a result of human land use and widespread extermination campaigns, wolf numbers dramatically decreased, and by the early twentieth century, no wolves remained in Maine. As large carnivorous and territorial mammals, wolves require contiguous undeveloped areas with abundant prey. This project is a feasibility study that identifies the areas in Maine that are suitable for the reintroduction of wolves. We used GIS modeling to identify contiguous forested areas over 1,000 km2, calculate road and population density, and map the presence or absence of prey throughout the state. These variables were combined in a habitat suitability model to determine the location and amount of suitable wolf habitat in Maine. The northwestern part of the state appears most suitable for wolf reintroduction as it is relatively undeveloped with low road and population densities. There is also a smaller isolated area in Washington County that might be suitable, but further investigation is required.

Projeto raia de fogo: aspectos populacionais da raia de fogo (Dasyatis marianae Gomes, Rosa & Gadig, 2000) e pesca de elasmobrânquios no complexo recifal do Parracho de Maracajaú

The species Dasyatis marianae inhabits coastal areas associated with coral reefs, considered endemic to the northeast of Brazil, occurring from the State of Maranhão to the south of Bahia. Specimens of this species are commonly sighted by divers and fishermen in the area of Maracajaú reefs, a complex reef that is part of the Environmental Protection Area of Coral Reefs (EPACR), which was developed in this study about the ecology and biology of the D. marianae, in order to characterize aspects of population structure in the area of the reef complex of Parracho de Maracajaú. We analyzed 120 specimens caught by artisanal fishing site of the size, weight, sex, stage of maturity and stomach contents. Most subjects were adult males (1.7:1) and was more abundant for rays with lengths between 25 and 29cm of LD, where females reach larger sizes, a feature common to other rays. The largest specimens were captured in the area of seagrass, which is preferred for the species. The distribution of species in the area showed an ontogenetic and sexual segregation, where the youthful occur near the beach, which is a likely area for nursery and growth of the adult females prevail in the seagrass, which apparently has a high prey availability, and Adult males are more distant, a higher proportion occurring in outlying areas, suggesting a habit more exploratory than the females. The evaluation of the reproductive system indicated 3 reproductive cycles per year, one young per pregnancy, and showed that the mature males were smaller than females. The cubs of D. marianae size at birth 12 to 15cm LD. As for diet, the species was characterized as carnivorous crustacean specialist. The performance of visual censuses in different localities allowed to evaluate the density of D. marianae in different environments of the complex. The species occurs in greater numbers in seagrass, environment very important for the conservation of the species. 100 individuals of D. marianae marked in reef complex area enrolled in a recapture rate of 3%. Some behavioral aspects were evaluated, as diurnal pattern of activity, interaction with cleaning and fish Pomacanthus paru followers as Lutjanus analis and Carangoides bartholomaei. Overall, much of the information obtained should be used for management of the species

Biologia alimentar e morfohistologia do tubo digestório do mussum, synbranchus marmoratus, bloch (osteichthyes: synbranchidae) no açude Marechal Dutra Gargalheiras , localizado no semi-árido brasileiro

Food habits and morpho-histology of the digestive tract of marbled swamp eel, Synbranchus marmoratus (Block, 1917) were investigated. The fish samples were captured during August, 2007 to July, 2008 in the Marechal Dutra reservoir, Acari, Rio Grande do Norte. The rain fall data was obtained from EMPARN. The fish captured, were measured, weighed, dissected, eviscerated and individual stomach weights were registered. The stomach contents analyses were carried out based on volumetric method, points, frequency of occurrence and applying the Index of Relative Importance. The degrees of repletion of the stomachs were determined besides the Index of Repletion relating to feeding activity variations and frequency of ingestion during the rainy and dry seasons. The rainfall varied from 0 mm a 335 mm with a mean value of 71.62 mm. Highest rainfall of 335.5 mm was registered in March, 2008 and August to December was the dry period. During the dry period the study species presented high degrees of repletion of the stomachs, with a peak value in the month of September (mean = 4.54; ± SD = 0.56). The minimum mean value of = 3.99 ± SD = 0.25 was registered in the month of May during the rainy period. The stomach contents of S. marmoratus registered show that this fish prefers animals, 78.22% of crustaceans 2.85% of mollusks, 3.25% of fish, 1.4% of insects and 13.5% of semi-digested organic matter, thus characterizing the study species as a carnivore with a preference for crustaceans. The morpho-histological aspects of the digestive tract of S. marmoratus indicate that the mouth is terminal adapted to open widely, thin lips with taste buds, small villiform teeth forming a single series on maxillas, four pairs of branchial arches with short and widely spaced branchial rays. The oesophagus is short and cylindrical with a small diameter. The oesophagus wall is thick with mucas surface and internal parallel folds. The stomach is retilinical in form, presenting cardiac, caecal and pyloric portions. The caecal portion is long and is intermediary in position between the cardiac and pyloric portions. The cardiac portion of the stomach is short and cylindrical formed of simple epithelial cylindrical mucus cells. The caecal portion is long with narrow walls, a big cavity and smaller folds which give rise to gastric glands. The phyloric portion has no glands and primary or secondary mucas folds. The morphohistological aspects of the digestive tract of S. marmoratus indicate its adaptation to a carnivorous feeding habit

Bioecologia da ictiofauna marinha descartada pelo arrasto camaroeiro em praias da Bacia Potiguar, Brasil

The composition of ichthyofauna discarded by trawling shrimping, their reproductive status and feeding ecology were studied on the beaches of Basin Rio Grande do Norte, Brazil. Fish were collected monthly in the year of 2012. During biometrics, portions of the digestive tract and of gonads were removed, fixed in formalin 10% and Bouin, respectively, for be submitted to histological processing by the techniques of hematoxylin-eosin. Stomach content analyzes were performed using the methods of Frequency of Occurrence and Volumetric and was calculated the repletion index. Throughout the study period were recorded a total of 49 species. The fish assemblages differed between sections monitoring, with the highest abundance, biomass and indices of richness and diversity in sections B, D and C. Already the excerpt A, showed higher values for dominance and equitability. In the cluster analysis according to the faunal similarity was observed the formation of three groups: group I formed by excerpts B and D, group II by excerpt C and group III formed by excerpt A. The assessment of reproductive stage revealed that the fish assemblages discarded by trawling are composed mainly of juveniles. Regarding the feeding ecology, the species Larimus breviceps, Menticirrhus littoralis and Pomadasys corvinaeformis characterized as carnivorous with tendency to carcinofagia. Already Conodon nobilis characterized as carnivorous with tendency to piscivory, but all proved generalist-opportunistic with increase of feeding activity during drought. The dendrogram of grouping of the species developed based on the food items used shows the formation of four groups: Group I consists of species that feed mainly of "gastropod" and "sediment"; group II of "teleost fish"; the group III of "crustacea" and group IV of "echinodermata" and "bivalve". The anatomical and histological characteristics of the digestive tract were consistent with the dietary habits of the analyzed species. In this context, the Costa Branca of Rio Grande do Norte can be considered a feeding site and recruitment for juveniles, which, opportunistically, utilize resources associated with the background

Size-related shifts in dietary composition of Centropomus parallelus (Perciformes: Centropomidae) in an estuarine ecosystem of the southeastern coast of Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)