Anna J. MacDonald

Anna J. MacDonald
Australian Antarctic Division

BSc (Hons), PhD

About

77
Publications
10,996
Reads
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420
Citations
Introduction
I focus on genetics, conservation and ecology. My work covers molecular ecology, conservation genetics, eDNA, DNA metabarcoding, population genetics, and phylogenetics. I'm particularly interested in how genetic information is used in wildlife management and policy, and I also work to develop guidelines and tools for evaluation, monitoring, and reporting of genetic diversity.
Additional affiliations
January 2021 - present
Australian Antarctic Division
Position
  • Molecular Ecologist
January 2017 - December 2020
Australian National University
Position
  • Project Manager
Description
  • Developing genomic resources for Australia’s mammals, tackling wildlife genomics at a continental scale. https://ozmammalsgenomics.com/
October 2016 - January 2017
Australian Government
Position
  • Researcher
Education
December 2002 - February 2008
University of Canberra
Field of study
  • Applied Science
September 1996 - July 1999
The University of Sheffield
Field of study
  • Zoology and Genetics

Publications

Publications (77)
Article
Taxon-specific DNA tests are applied to many ecological and management questions, increasingly using environmental DNA (eDNA). eDNA facilitates non-invasive ecological studies, but introduces additional risks of bias and error. For effective application, PCR primers must be developed for each taxon and validated in each system. We outline a nine st...
Article
Full-text available
Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been d...
Article
Full-text available
Genetic diversity is one of the three main levels of biodiversity recognised in the Convention on Biological Diversity (CBD). Fundamental for species adaptation to environmental change, genetic diversity is nonetheless under‐reported within global and national indicators. When it is reported, the focus is often narrow and confined to domesticated o...
Article
Full-text available
Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are...
Article
Full-text available
The Coalition for Conservation Genetics (CCG) brings together four eminent organizations with the shared goal of improving the integration of genetic information into conservation policy and practice. We provide a historical context of conservation genetics as a field and reflect on current barriers to conserving genetic diversity, highlighting the...
Article
Full-text available
The introduction of species into new environments provides the opportunity for the evolution of new forms through admixture and novel selection pressures. The common brushtail possum, Trichosurus vulpecula vulpecula from the Australian mainland and T.v.fuliginosus from Tasmania, were introduced multiple times to New Zealand from Australia to become...
Article
Full-text available
A correction to this paper has been published: https://doi.org/10.1007/s10592-021-01376-9
Article
Full-text available
International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve, and sustainably and equitably use, biodiversity. The CBD is a vital instrument for global conservation because it guides 195 countries and the European Union in setting priorities and allocating resources, and requires regular reporting on prog...
Article
Australia has the highest historically recorded rate of mammalian extinction in the world, with 34 terrestrial species declared extinct since European colonization in 1788. Among Australian mammals, rodents have been the most severely affected by these recent extinctions ; however, given a sparse historical record, the scale and timing of their dec...
Preprint
Full-text available
Genetic diversity is critically important for all species-domesticated and wild- to adapt to environmental change, and for ecosystem resilience to extreme events. International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve and sustainably and equitably use all levels of biodiversity-genes, species and ec...
Article
Full-text available
1. Identification of the geographic extent of population boundaries, the distribution of genetic lineages, and the amount of genetic exchange among breeding groups is needed for effective conservation of vulnerable marine migratory species. This is particularly true of the flatback turtle (Natator depressus), which only breeds in Australia but has...
Article
Southern brown (Isoodon obesulus) and golden (Isoodon auratus) bandicoots are iconic Australian marsupials that have experienced dramatic declines since European settlement. Conservation management programs seek to protect the remaining populations; however, these programs are impeded by major taxonomic uncertainties. We investigated the history of...
Article
Full-text available
Taxonomic research is of fundamental importance in conservation management of threatened species, providing an understanding of species diversity on which management plans are based. The grassland earless dragon lizards (Agamidae: Tympanocryptis) of southeastern Australia have long been of conservation concern but there have been ongoing taxonomic...
Conference Paper
The Australo-Papuan region has a unique mammal fauna, which faces unique threats and poses important evolutionary and ecological questions. Genomics has great potential to advance our understanding of the region’s mammals and their conservation. The Oz Mammals Genomics Initiative brings together museum collections, researchers, data specialists and...
Article
The DNA detection of wildlife from environmental samples has the potential to contribute significantly to wildlife management and ecological research. In terrestrial ecosystems, much work has focused on the identification of mammal predators from faecal (scat) samples. However, the relatively high time and financial costs of collecting and analysin...
Data
Figure 2 from Campbell et al (2018) Diversity and Distributions When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data
Data
Figure 3 from Campbell et al (2018) Diversity and Distributions When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data
Data
Figure 1 from Campbell et al (2018) Diversity and Distributions When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data
Data
Figure 4 from Campbell et al (2018) Diversity and Distributions When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data
Data
Supplementary file for Campbell et al (2018) Diversity and Distributions When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data
Article
Full-text available
Range expansions facilitated by humans or in response to local biotic or abiotic stressors provide the opportunity for species to occupy novel environments. Classifying the status of newly expanded populations can be difficult, particularly when the timing and nature of the range expansion are unclear. Should native species in new habitats be consi...
Article
Full-text available
The ability to detect the incursion of an invasive species or destroy the last individuals during an eradication program are some of the most difficult aspects of invasive species management. The presence of foxes in Tasmania is a contentious issue with recent structured monitoring efforts, involving collection of carnivore scats and testing for fo...
Data
Supplementary information for Ramsey et al (2017) Ecology and Evolution 2017:1-12. Detecting rare carnivores using scats: Implications for monitoring a fox incursion into Tasmania
Data
Supplementary information for Ramsey et al (2017) Ecology and Evolution 2017:1-12. Detecting rare carnivores using scats: Implications for monitoring a fox incursion into Tasmania
Data
Supplementary information for Ramsey et al (2017) Ecology and Evolution 2017:1-12. Detecting rare carnivores using scats: Implications for monitoring a fox incursion into Tasmania
Data
Supplementary information for Ramsey et al (2017) Ecology and Evolution 2017:1-12. Detecting rare carnivores using scats: Implications for monitoring a fox incursion into Tasmania
Data
Supplementary information for Ramsey et al (2017) Ecology and Evolution 2017:1-12. Detecting rare carnivores using scats: Implications for monitoring a fox incursion into Tasmania
Data
Supplementary information for Ramsey et al (2017) Ecology and Evolution 2017:1-12. Detecting rare carnivores using scats: Implications for monitoring a fox incursion into Tasmania
Article
Full-text available
Background: Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for manage...
Data
Reviewer 2 report on revisions for Modave et al (2017) GigaScience 6(8):gix052. A single mini-barcode test to screen for Australian mammalian predators from environmental samples
Data
Supplementary information for Modave et al (2017) GigaScience 6(8):gix052. A single mini-barcode test to screen for Australian mammalian predators from environmental samples
Data
Original submitted version of Modave et al (2017) GigaScience 6(8):gix052. A single mini-barcode test to screen for Australian mammalian predators from environmental samples
Data
Reviewer 1 report for Modave et al (2017) GigaScience 6(8):gix052. A single mini-barcode test to screen for Australian mammalian predators from environmental samples
Data
Reviewer 2 report for Modave et al (2017) GigaScience 6(8):gix052. A single mini-barcode test to screen for Australian mammalian predators from environmental samples
Data
Revision file 1 for Modave et al (2017) GigaScience 6(8):gix052. A single mini-barcode test to screen for Australian mammalian predators from environmental samples
Data
Data file for MacDonald et al (2014) Heredity. Sex-linked and autosomal microsatellites provide new insights into island populations of the tammar wallaby
Data
Supplementary information for Ramsey et al (2015) Journal of Applied Ecology. An examination of the accuracy of a sequential PCR and sequencing test used to detect the incursion of an invasive species: The case of the red fox in Tasmania
Data
Supplementary information from MacDonald and Sarre (2017) Molecular Ecology Resources. A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA
Data
Supplementary information from MacDonald and Sarre (2017) Molecular Ecology Resources. A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA
Data
Supplementary information from MacDonald and Sarre (2017) Molecular Ecology Resources. A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA
Data
Full-text available
Supplementary information from MacDonald and Sarre (2015) Journal of Applied Ecology. Species assignment from trace DNA sequences: An in silico assessment of the test used to survey for foxes in Tasmania.
Data
Supplementary information from MacDonald and Sarre (2017) Molecular Ecology Resources. A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA
Data
Supplementary information from MacDonald and Sarre (2015) Journal of Applied Ecology. Species assignment from trace DNA sequences: An in silico assessment of the test used to survey for foxes in Tasmania.
Data
Supplementary information from MacDonald and Sarre (2015) Journal of Applied Ecology. Species assignment from trace DNA sequences: An in silico assessment of the test used to survey for foxes in Tasmania.
Data
Supplementary information from MacDonald and Sarre (2015) Journal of Applied Ecology. Species assignment from trace DNA sequences: An in silico assessment of the test used to survey for foxes in Tasmania.
Data
Supplementary information from MacDonald and Sarre (2015) Journal of Applied Ecology. Species assignment from trace DNA sequences: An in silico assessment of the test used to survey for foxes in Tasmania.
Data
Full-text available
Supplementary information from MacDonald and Sarre (2015) Journal of Applied Ecology. Species assignment from trace DNA sequences: An in silico assessment of the test used to survey for foxes in Tasmania.
Data
Supplementary information for MacDonald et al (2015) Australian Journal of Zoology. The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge)
Data
Supplementary information for MacDonald et al (2015) Australian Journal of Zoology. The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge)
Article
Full-text available
Species are the most commonly recognised unit for conservation management, yet significant variation can exist below the level of taxonomic recognition and there is a lack of consensus around how a species might be defined. This definition has particular relevance when species designations are used to apportion conservation effort and when definiti...
Data
Supplementary material 1 Supplementary Fig. 1: Estimates of average pairwise relatedness within Canberra and Monaro sampling sites for T. pinguicolla. Sites with 2 individuals or less are not included. A value of 0.5 indicates a parent-sibling or full sibling relationship, 0.25 indicates half-siblings and below 0.125 indicates unrelated individuals...
Data
Supplementary material 2 Supplementary Fig. 4: Supplemental Figure XXX Deviance information criterion (DIC) plot for each replicate of K (replicates = 20) for K = 2 to 10 (grey points). Durand et al. (2009) recommend examining the DIC values of the lowest 10 to 20 % of replicate values for each K in order to identify the ideal number of clusters as...
Technical Report
Full-text available
The sub-specific status of different populations of Isoodon obesulus has been questioned in several genetic studies utilising mitochondrial DNA (mtDNA) and nuclear gene sequence data, leading to a proposal to revise the current distribution of the eastern Australian sub-species I. o. obesulus to include additional localities in South Australia (SA)...
Article
1.Diagnostic DNA tests have become important for species detection from environmental samples and are increasingly applied to the analysis of ecological systems and in wildlife management. The availability of reference DNA sequences from many taxa enables the development of diagnostic PCR primers. 2.Where there is a high risk of false positive PCR...
Poster
Full-text available
DNA detection of species from environmental samples is an effective means of studying rare and cryptic wildlife, and diagnostic DNA tests are increasingly applied to management questions. Taxon-specific DNA tests rely upon PCR primers that selectively amplify DNA from target species. Where DNA from several species might be amplified, or where false...
Poster
Full-text available
The sugar glider (Petaurus breviceps) is widely distributed through Australia and Papua New Guinea and is found on a number of Indonesian islands. Historical records suggest that the species was introduced to Tasmania in 1835, as pets, from Port Phillip in Victoria. The population is now widespread but their provenance has not been investigated. Re...
Article
1.Polymerase Chain Reaction (PCR) diagnostic tests are increasingly applied to the identification of wildlife. Yet rigorous verification is rare and the estimation of test accuracy (the probability that true positive and true negative samples are correctly identified – test sensitivity and specificity, respectively), particularly in combination wit...
Article
The Pygopodidae comprise an enigmatic group of legless lizards endemic to the Australo-Papuan region. Here we present the first complete mitochondrial genome for a member of this family, Aprasia parapulchella, from Australia. The mitochondrial genome of A. parapulchella is 16 528 base pairs long and contains 13 protein-coding genes, 22 tRNA genes,...
Presentation
Full-text available
DNA from animal scats (faeces) constitutes a unique resource for ecological studies. Each scat contains DNA from the scat producer, as well as DNA from plants and animals that were eaten in the time leading up to defecation. Genetic analysis of scats collected from known sampling locations can provide information about predator-prey interactions an...
Conference Paper
Full-text available
Tasmania supports a number of native Australian mammals whose mainland counterparts have severely declined or disappeared since European settlement. This provides a unique opportunity to study ecosystem changes occurring through the ongoing collapse of the Tasmanian devil (Sarcophilus harrisii) population along with the recent introduction of the f...
Poster
Full-text available
Understanding how mammal populations interact with each other and their immediate environment is of critical importance to predicting responses to environmental change while knowledge on diet and distribution of emerging invasive species is vital to management efforts. However, estimating species distributions, let alone interactions among them, ha...
Article
Rapid increases in global trade and human movement have created novel mixtures of organisms bringing with them the potential to rapidly accelerate the evolution of new forms. The common brushtail possum (Trichosurus vulpecula), introduced into New Zealand from Australia in the 19th Century, is one such species having been sourced from multiple popu...
Article
Full-text available
Predation by invasive salmonids threatens the conservation of the endangered Australian freshwater fish Macquarie perch (Macquaria australasica). Predation is difficult to detect visually because larval fish are rapidly digested. Here, we present PCR primers that will enable the detection of M. australasica from trace samples, removing the need to...
Article
Full-text available
The emerging availability of microsatellite markers from mammalian sex chromosomes provides opportunities to investigate both male- and female-mediated gene flow in wild populations, identifying patterns not apparent from the analysis of autosomal markers alone. Tammar wallabies (Macropus eugenii), once spread over the southern mainland, have been...
Poster
Full-text available
Tasmania is one of the last safe havens for several of Australia’s marsupial species with the Island remaining relatively untouched in regards to extinction compared to the Australian mainland. Numerous extinctions have been caused by human disturbances to land management while several species have disappeared through direct interaction with introd...
Article
Invasive vertebrate species are a world-wide threat to biodiversity and agricultural production. The presence of foxes, one of the most damaging invasive vertebrates introduced to Australia, has now been confirmed in the island state of Tasmania, placing at risk many species of native vertebrates and substantial agricultural industry. Effective era...
Article
Full-text available
Infectious wildlife diseases have enormous global impacts, leading to human pandemics, global biodiversity declines and socio-economic hardship. Understanding how infection persists and is transmitted in wildlife is critical for managing diseases, but our understanding is limited. Our study aim was to better understand how infectious disease persis...
Article
Full-text available
Microsatellite genotyping from trace DNA is now common in fields as diverse as medicine, forensics and wildlife genetics. Conversely, small-pool PCR (SP-PCR) has been used to investigate microsatellite mutation mechanisms in human DNA, but has had only limited application to non-human species. Trace DNA and SP-PCR studies share many challenges, inc...
Chapter
Microsatellites are important genetic markers that have been applied to answer questions at the population level in a range of macropod species. Most studies to date have been restricted to analyses of variation at autosomal microsatellite loci, sometimes in conjunction with mitochondrial sequence data. The recent development of microsatellite mark...
Thesis
Full-text available
Microsatellites are simple repetitive DNA sequences that are used as genetic markers throughout the biological sciences. The high levels of variation observed at microsatellite loci contribute to their utility in studies at the population and individual levels. This variation is a consequence of mutations that change the length of microsatellite re...
Article
Microsatellites were identified from fully sequenced bacterial artificial chromosome clones from the X chromosome and chromosome 2 of the tammar wallaby, Macropus eugenii. A total of 20 microsatellites were genotyped. Seven X chromosome loci and eight loci from chromosome 2 were polymorphic, with between two and 11 alleles per locus. These markers...