Research Project highlights
Swabs can be used to collect DNA from scat samples in the field
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Reliable methods for DNA analysis of environmental and historic samples
Environmental DNA (eDNA) is DNA that is obtained indirectly from the environment (for example from soil, water or faeces), rather than directly from an organism. eDNA analysis offers tremendous 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 apply genetic tools to address ecological questions, we need to understand sources of bias and error. These issues are also important when analysing other types of degraded or trace DNA, for example from museum specimens. Much of our research relies upon environmental or trace DNA samples, and I am a strong advocate for evaluating and understanding the limitations of these methods. In recent work we outlined a framework for the development and validation of DNA tests for specimen identification from eDNA, using Australian bandicoots as a case study. We have 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 DNA test used to detect introduced foxes in Australia (see below). We were able to demonstrate that, using this DNA test in Australia, there is a very low risk of erroneous fox identification. |
An adult grassland earless dragon
Defining "units" for wildlife management
Understanding patterns of genetic diversity within wildlife populations can tell us about the structure of those populations, and provide information to guide management and conservation. To effectively conserve wildlife we need to be able to determine appropriate management "units". This is because we aim to conserve all independent evolutionary lineages. The trouble is, we often know very little about the geographic distributions and reproductive behaviours of many rare and threatened taxa: the threatened grassland earless dragon (Tympanocryptis pinguicolla) is one such example. In work led by Honours student Emma Carlson, we used microsatellite genotyping to identify management units for this species 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). We are now using SNP markers, to try to better understand the population genetics of these charismatic lizards.
Understanding patterns of genetic diversity within wildlife populations can tell us about the structure of those populations, and provide information to guide management and conservation. To effectively conserve wildlife we need to be able to determine appropriate management "units". This is because we aim to conserve all independent evolutionary lineages. The trouble is, we often know very little about the geographic distributions and reproductive behaviours of many rare and threatened taxa: the threatened grassland earless dragon (Tympanocryptis pinguicolla) is one such example. In work led by Honours student Emma Carlson, we used microsatellite genotyping to identify management units for this species 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). We are now using SNP markers, to try to better understand the population genetics of these charismatic lizards.
A southern brown bandicoot from Tasmania. Photo credit Simon Troman.
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Bandicoot phylogenetics and conservation
I am part of a group of researchers who are trying to understand relationships among the different groups of Isoodon bandicoots. One aim is to identify the most appropriate conservation management units for this genus. The southern brown bandicoot (I. obesulus) occurs across large parts of southern Australia, from the east to west coasts of the mainland, and in Tasmania. However, the species has suffered dramatic declines and some populations have relatively recently become extinct. Conservation managers aim to conserve all evolutionary lineages, but in this case there has been considerable debate about where the boundaries between lineages (recognised as subspecies) should be drawn. To date we have focused on southern brown bandicoots from south-eastern Australia. We have shown that Tasmanian southern brown bandicoots form a distinct lineage that has been separated from the mainland for thousands of years (providing support for the subspecies I. o. affinis) , and that the subspecies I. o. obesulus is in fact only found in NSW, Victoria and south-east SA, which equates to a reduction in its known range. |
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Population genetics of invasive species
It is important to understand genetic diversity in populations of invasive species, so that they can be effectively managed. In a population genetic study of introduced brushtail possums (Trichosurus vulpecula) in New Zealand, we uncovered 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. Understanding the evolutionary and ecological dynamics of such human-mediated hybrid zones will be important for future management. 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 hollow-nesting 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 of a recent introduction... a paper on this coming soon! We have also been investigating population genetics of the Australian fox population. Despite the large number of foxes in Australia, they seem to have relatively little genetic structure. This most likely reflects the very small number of individuals that were introduced from Europe to found the Australian population. Watch this space for more details when our analysis is complete... |
A brushtail possum (Trichosurus vulpecula)
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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 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 mammal predators 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 61 scats from different locations in Tasmania. We have also developed a new predator DNA test that can simultaneously distinguish among all large terrestrial mammal predators in Australia, including the four species of quoll. |
A predator scat, for DNA extraction
DNA barcoding and metabarcoding to detect prey species from 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). If we are only interested in detecting predation of a single species, we can develop a species-specific test to screen predator scats or stomach contents for the presence of that species. 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 in the Canberra region. We also developed a DNA test to detect endangered bandicoot species, which are at risk of predation by foxes and cats across much of Australia. However, in many cases we are interested in detecting DNA from multiple prey species AND the predator at the same time. New high throughput DNA sequencing methods allow us to apply more generic DNA tests. 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. This is a relatively new method, known as DNA metabarcoding. Watch this space for exciting results...!
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). If we are only interested in detecting predation of a single species, we can develop a species-specific test to screen predator scats or stomach contents for the presence of that species. 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 in the Canberra region. We also developed a DNA test to detect endangered bandicoot species, which are at risk of predation by foxes and cats across much of Australia. However, in many cases we are interested in detecting DNA from multiple prey species AND the predator at the same time. New high throughput DNA sequencing methods allow us to apply more generic DNA tests. 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. This is a relatively new method, known as DNA metabarcoding. Watch this space for exciting results...!
Anna with tammar wallaby joeys. Photo credit Lyn Hinds
Sex chromosome genetic markers in conservation and population genetics
In mammals, the Y chromosome is male-specific and is transmitted directly from father to son. The X chromosome is diploid in females (this means that a female inherits two copies of the chromosome, one from each parent) but haploid in males (a male inherits only one copy of the 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 microsatellite markers from the X chromosome and Y chromosome of the tammar wallaby (Notamacropus eugenii), which was the first Australian marsupial to have its genome sequenced. In subsequent research I compared genetic variation at autosomal, X- and Y- chromosome markers in two tammar wallaby populations. We found evidence for a male-bias to dispersal on Kangaroo Island. We 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 a small number of males are able to father most of the offspring, meaning that most males do not get to reproduce.
Tammar wallaby with her joey
Genotyping reliability and detection of 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 error during the genotyping process. During my PhD I used a method known as small-pool PCR to study rates and types of mutations at tammar wallaby 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. This work highlighted sources of PCR error that may have lead to incorrect interpretation of results from unknown samples. 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.
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 error during the genotyping process. During my PhD I used a method known as small-pool PCR to study rates and types of mutations at tammar wallaby 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. This work highlighted sources of PCR error that may have lead to incorrect interpretation of results from unknown samples. 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.
All photographs copyright of Anna MacDonald unless otherwise stated. Please contact me if you wish to use any of these images.
