Research Project highlights
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The Oz Mammals Genomics Initiative
I'm currently working on projects associated with the Oz Mammals Genomics Initiative. These include whole genomes, evolutionary studies, and conservation genomics projects contributing to management and reintroductions of threatened species. In particular I'm contributing to:
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Connecting genetic diversity monitoring with policy
The GEOBON Genetic Composition Working Group is working to develop and improve approaches to measuring, monitoring and interpreting genetic diversity. We work to support the integration of genetic monitoring into management actions and policy guidelines. Projects I've been working on as part of the Working Group include:
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Defining "units" for wildlife management
Understanding how genetic diversity varies within wildlife populations can provide information to guide their management. To effectively conserve wildlife we need to be able to determine appropriate management "units" (which could be species, subspecies, or distinct populations). This is because we aim to conserve all independent evolutionary lineages. The trouble is, we often know very little about the geographic distributions and connectivity between populations of rare or threatened taxa: the grassland earless dragons (genus Tympanocryptis) are one such example. In a population genetic study led by Honours student Emma Carlson, we identified management units for grassland earless dragons in the Australian Capital Territory and New South Wales. We identified three distinct genetic populations that should each be managed separately (I wrote a blog post about this research here). More recently, we have combined population genomics with morphological analyses, revising the taxonomy of these charismatic lizards and describing new species (a blog post on this research here). |
An adult grassland earless dragon
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A southern brown bandicoot from Tasmania. Photo credit Simon Troman.
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Understanding bandicoot taxonomy for conservation
Several bandicoot species have become extinct since Europeans colonised Australia, and other bandicoot species have suffered severe declines. Conservation managers aim to protect all evolutionary lineages, but in this case we are not sure how some of the remaining species and populations are related to one another. This taxonomic uncertainty impedes effective conservation. We are using a phylogeographic approach to review species and subspecies boundaries and conservation management units for the genus Isoodon. First, we focused on southern brown bandicoots from south-eastern Australia. We showed that Tasmanian southern brown bandicoots have been separated from mainland populations for thousands of years and should be managed separately from their south-eastern mainland counterparts. More recently, we've shown genetic variation does not reflect currently recognised subspecies in mainland Australia. We're now trying to understand relationships among bandicoot populations in Western Australia. |
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Reliable methods for environmental DNA analysis
Environmental DNA (eDNA) is DNA that is obtained indirectly from the environment (e.g. from soil, water or faeces), rather than directly from an organism. eDNA has great potential to measure and monitor biodiversity and to reveal much about wildlife distributions and interactions. Diagnostic DNA tests to identify species or individuals from eDNA samples are becoming increasingly common, but the sensitivity and specificity of these tests are not routinely validated in field conditions. To successfully use eDNA to address ecological questions, we need to understand the strengths and limitations of eDNA methods, and sources of bias and error. This can also be relevant to degraded or trace DNA from other sources, for example DNA from historical museum specimens. We have developed a framework that explains how to develop and validate DNA tests for specimen identification from eDNA, and evaluated different methods for DNA extraction from scats. We have also conducted laboratory trials (using scats from captive animals) and bioinformatic analyses to understand the risks of false positive and false negative results associated with a fox DNA test (see below). We demonstrated that, using this DNA test in Australia, there is a very low risk of erroneous fox identification. |
Swabs can be used to collect DNA from scat samples in the field
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A feral cat at Mungo National Park
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DNA detection of invasive species from predator poo
Foxes and cats are not native to Australia and have had a devastating impact on the native Australian fauna. Wildlife managers need to understand the distributions of invasive species so they can monitor and control them. In some areas introduced predators occur at low densities and are difficult to detect using traditional methods. We can use DNA to detect introduced predators from their scats. It is often much easier to find scats from cryptic animals than it is to find the animals themselves, but different species can have similar-looking scats, so DNA detection provides a reliable method to determine the species of origin. We have used DNA analysis of scats to detect the red fox (Vulpes vulpes) in Tasmania. From 2007 to 2014, over 12,000 predator scats were collected from across Tasmania for DNA testing. In surveys up to 2011, we detected fox DNA from scats from different locations in Tasmania. We detected no further evidence of foxes during the 2014 survey. We have also developed a new predator DNA test that can simultaneously detect and distinguish among all large terrestrial mammal predators in Australia, including cats, dogs, foxes, devils, and the four species of quoll. |
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Using genetics to understand invasive species
Characterising genetic diversity in populations of invasive species can provide useful information about the origins and dynamics of those populations. In a study of introduced brushtail possums (Trichosurus vulpecula) in New Zealand, we found evidence of a hybrid zone between possums of Tasmanian ancestry and possums of mainland Australian ancestry. These two groups of possums would never meet in their native ranges, and this may influence the evolutionary and ecological dynamics of these populations, and how they respond to management actions. Sugar gliders (Petaurus breviceps) are native to much of Australia, but historical records suggest they were introduced to Tasmania by Europeans. Recently, predation by sugar gliders has been blamed for declines of several bird species in Tasmania, but the uncertain status of the sugar glider population makes this difficult to manage. PhD student Catriona Campbell conducted the first genetic study of Tasmanian sugar gliders. Her results show that they are genetically very similar to Victorian and South Australian animals, which supports the idea that they were relatively recently introduced to Tasmania. |
A brushtail possum (Trichosurus vulpecula)
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Extracting DNA from predator poo
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DNA detection of prey species from predator scats
As well as using DNA to detect predators, it is also incredibly useful to learn what those predators eat. This can help us to understand which native species might be most threatened by introduced predators and how ecosystems might be affected by changes in predator-prey dynamics (e.g. if a native predator declines or becomes extinct). We can develop species-specific DNA tests to screen predator scats or stomach contents for the presence of a particular species of interest. For example, we developed a DNA test to detect an endangered Australian fish, the Macquarie perch (Macquaria australasica), which is at risk of predation by introduced trout. We can also use DNA metabarcoding and high throughput DNA sequencing methods to detect DNA from multiple prey species AND the predator at the same time. For example we can isolate DNA from all mammals or vertebrates that are represented in a scat in a single sequencing analysis. By comparing these unknown DNA sequences against a reference database of known DNA sequences, we can then determine who left the scat... and who is in it... more to come... |
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Genotyping reliability and microsatellite mutations
Microsatellite DNA is a type of genetic marker that has been widely used in population and conservation genetics. To correctly interpret patterns of genetic variation at microsatellite markers, we need to understand the mutation processes that generate this variation. We also need to understand possible sources of genotyping errors. During my PhD, I used a method known as small-pool PCR to study rates and types of mutations at tammar wallaby (Notamacropus eugenii) microsatellite markers. I observed mutations involving multiple repeat units, which suggested that the stepwise mutation model (a model commonly applied to analysis of microsatellite genotyping data) may not be appropriate for these markers. I also assessed genotyping success and identified the types of genotyping errors encountered, to investigate the reliability of genotyping from trace amounts of DNA. I demonstrated that genotyping reliability is compromised below a threshold amount of DNA and proposed an approach to minimise and quantify genotyping errors in future studies. |
A tammar wallaby with her joey
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Anna with tammar wallabies (photo credit Lyn Hinds)
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Sex chromosome genetic markers in conservation and population genetics
In mammals, the Y chromosome is male-specific and is passed directly from father to son, whereas inheritance of the X chromosome varies. Each female inherits two copies of the X chromosome, one from each parent, but each male inherits only one copy of the X chromosome, from his mother. By studying patterns of gene flow on the sex chromosomes, we can learn about differences in patterns of dispersal and reproductive behaviour between males and females. During my PhD, I developed genetic markers called microsatellites from the tammar wallaby X chromosome and Y chromosome. I then compared genetic variation on different chromosomes in two tammar wallaby populations. I found evidence for a male-bias to dispersal on Kangaroo Island. I also observed extremely low Y chromosome diversity on Garden Island, which might be explained by a skew in male reproductive success: this can occur when only a small number of males are able to father most of the offspring. |
All photographs copyright of Anna MacDonald unless otherwise stated. Please contact me if you wish to use any of these images.
