MHC screening for marsupial conservation: extremely low levels of class II diversity indicate population vulnerability for an endangered Australian marsupial

Red-tailed phascogales: A review of their biology and importance as model marsupial species

There are many limitations when using traditional laboratory species. Limits on variation, may result in limited outcomes, at both the species and individual level, due to different individuals/species having diverse physiological processes, or differing molecular and genetic mechanisms. By using a variety of model species, we will be able to develop creative solutions to biological problems and identify differences of which we were not previously aware. The laboratory mouse has been a suitable model species for various mammalian studies, however most are bred specifically for laboratory research with limited variability due to selective breeding. Marsupial models offer unique research opportunities compared to eutherian models. We believe that there should be an expansion in marsupial model species, and the introduction of the red-tailed phascogale (Phascogale calura), a dasyurid marsupial, should be one of them. Phascogales are easily managed in captivity, and there are now multiple studies involving their development, reproduction, nutrition, behavior and immune system, which can serve as a baseline for future studies. The addition of the phascogale as a model species will improve future mammalian studies by introducing variability and offer alternate solutions to biological problems, particularly in the areas of genetics, nutrition, immunology, the neuro-endocrine system, and ageing, due to their semelparous reproductive strategy and hence, subsequent predictive physiology. In this review, we provide information based on existing research on red-tailed phascogales to support their inclusion as a model species.

MHC Class II variability in bare-nosed wombats (Vombatus ursinus)

Studies of gene diversity are used to investigate population dynamics, including immunological fitness. Aside from the selection of an appropriate gene target, an important factor that underpins these studies is the ability to recover viable DNA samples from native animals that are protected, threatened or difficult to sample or locate such as the bare-nosed wombat (Vombatus ursinus). In this study, we used genomic DNA extracted from muscle tissue samples and also identified the optimal method to extract DNA from fresh wombat scat samples to enable further analyses to be performed using non-invasive techniques. The DNA was probed via the polymerase chain reaction using previously targeted marsupial Major Histocompatibility Complex (MHC) gene primers. These genes are highly variable and associated with binding and presentation of pathogens in the immune system. Twenty-three unique MHC Class II DAB V. ursinus gene sequences were translated to 21 unique predicted peptide sequences from 34 individual tissue or scat samples. Vombatus ursinus MHC Class II DAB gene and peptide sequences were most similar to other marsupial DNA and peptide sequences. Further analysis also indicated the likelihood of MHC Class II DAB family membership through motif identification. Additional sampling is required to assess the full level of diversity of MHC Class II DAB genes among V. ursinus populations; however, this study is the first to identify MHC genes in a wombat and will advance immunological and disease studies of the species.

Sarcoptic mange in wombats-A review and future research directions

Sarcoptic mange is caused by the mite Sarcoptes scabiei and has recently been recognized as an emerging infectious disease of wildlife worldwide. The mite is one of the main causes of population decline in southern hairy-nosed (Lasiorhinus latifrons) and bare-nosed wombats (Vombatus ursinus). This review focuses on Sarcoptes scabiei infestations in wombats and provides insights into why the disease may be so prevalent in wombats. Current treatment practices and trials conducted in the field to reduce the incidence of sarcoptic mange in wombats are described and critically reviewed. Current and potential future avenues of research are discussed.

Major Histocompatibility Complex Class II in the red-tailed phascogale (Phascogale calura)

Diversity in major histocompatibility complex (MHC) genes can be correlated with the level of immunological fitness of an individual or group of individuals. This study tested published primer sets designed to amplify fragments of the MHC Class II DAB and DBB genes to amplify the equivalent gene fragments in red-tailed phascogales (Phascogale calura). Seventeen genomic DNA samples extracted from phascogale muscle tissue were used to amplify the initial DAB and DBB fragments; however, only DAB PCR proved successful. The fragments were 172 bp in length between the primers and had a high level of identity to other known marsupial MHC Class II DAB gene sequences (89–98%), including those of the koala (Phascolarctos cinereus), Tasmanian devil (Sarcophilus harrisii), common brushtail possum (Trichosurus vulpecula) and several wallaby species. Multiple sequence alignment revealed limited variability of MHC Class II genes between the individuals, but eight individual sequences in total. Genomic DNA was subsequently extracted from three fresh red-tailed phascogale scat samples and DAB fragments successfully amplified. The technique will allow for red-tailed phascogales to be sampled non-invasively in the wild and to determine the level of MHC diversity among individuals in the population.

Genomic Porosity between Invasive Chondrostoma nasus and Endangered Endemic Parachondrostoma toxostoma (Cyprinidae): The Evolution of MHC IIB Genes

Two cyprinid species, Parachondrostoma toxostoma, an endemic threatened species, and Chondrostoma nasus, an invasive species, live in sympatry in southern France and form two sympatric zones where the presence of intergeneric hybrids is reported. To estimate the potential threat to endemic species linked to the introduction of invasive species, we focused on the DAB genes (functional MHC IIB genes) because of their adaptive significance and role in parasite resistance. More specifically, we investigated (1) the variability of MHC IIB genes, (2) the selection pattern shaping MHC polymorphism, and (3) the extent to which trans-species evolution and intergeneric hybridization affect MHC polymorphism. In sympatric areas, the native species has more diversified MHC IIB genes when compared to the invasive species, probably resulting from the different origins and dispersal of both species. A similar level of MHC polymorphism was found at population level in both species, suggesting similar mechanisms generating MHC diversity. In contrast, a higher number of DAB-like alleles per specimen were found in invasive species. Invasive species tended to express the alleles of two DAB lineages, whilst native species tended to express the alleles of only the DAB3 lineage. Hybrids have a pattern of MHC expression intermediate between both species. Whilst positive selection acting on peptide binding sites (PBS) was demonstrated in both species, a slightly higher number of positively selected sites were identified in C. nasus, which could result from parasite-mediated selection. Bayesian clustering analysis revealed a similar pattern of structuring for the genetic variation when using microsatellites or the MHC approach. We confirmed the importance of trans-species evolution for MHC polymorphism. In addition, we demonstrated bidirectional gene flow for MHC IIB genes in sympatric areas. The positive significant correlation between MHC and microsatellites suggests that demographic factors may contribute to MHC variation on a short time scale.

Marsupial genome sequences: providing insight into evolution and disease

Marsupials (metatherians), with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil), with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. The emergence of a transmissible cancer, which is obliterating the Tasmanian devil population, has increased the importance of obtaining and analysing marsupial genome sequence for understanding such diseases as well as for conservation efforts. In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences.

Diversity of MHC class II DAB1 in the koala (Phascolarctos cinereus)

The host immune response is an important factor determining the outcome of the host–pathogen–environment interaction. At the gateway between the innate and adaptive immune systems are MHC molecules, which facilitate antigen presentation to T lymphocytes, and initiate the adaptive immune response. Despite their integral role in adaptive immunity, the genes encoding class II MHC molecules have not been examined directly in koalas. Furthermore, indirect historical evidence suggests that this species might lack functional diversity in class II MHC genes, with potential implications for disease susceptibility. We have examined diversity in the β chain genes of the koala class II MHC DA gene family and identified 23 alleles, including several atypical alleles. The levels of diversity observed are consistent with other marsupial and eutherian species, and do not support the paucity of variation suggested by the early literature. These findings are relevant to the conservation management of koalas and provide both a benchmark for maintaining population diversity and a platform for further conservation genetic research in this species.

Major Histocompatibility Complex (MHC) markers in conservation biology

Human impacts through habitat destruction, introduction of invasive species and climate change are increasing the number of species threatened with extinction. Decreases in population size simultaneously lead to reductions in genetic diversity, ultimately reducing the ability of populations to adapt to a changing environment. In this way, loss of genetic polymorphism is linked with extinction risk. Recent advances in sequencing technologies mean that obtaining measures of genetic diversity at functionally important genes is within reach for conservation programs. A key region of the genome that should be targeted for population genetic studies is the Major Histocompatibility Complex (MHC). MHC genes, found in all jawed vertebrates, are the most polymorphic genes in vertebrate genomes. They play key roles in immune function via immune-recognition and -surveillance and host-parasite interaction. Therefore, measuring levels of polymorphism at these genes can provide indirect measures of the immunological fitness of populations. The MHC has also been linked with mate-choice and pregnancy outcomes and has application for improving mating success in captive breeding programs. The recent discovery that genetic diversity at MHC genes may protect against the spread of contagious cancers provides an added impetus for managing and protecting MHC diversity in wild populations. Here we review the field and focus on the successful applications of MHC-typing for conservation management. We emphasize the importance of using MHC markers when planning and executing wildlife rescue and conservation programs but stress that this should not be done to the detriment of genome-wide diversity.