Anna J. MacDonaldAustralian Antarctic Division
Anna J. MacDonald
BSc (Hons), PhD
About
107
Publications
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Introduction
My work spans molecular ecology and conservation genetics. I use genetic information to inform wildlife management and policy, and for biodiversity monitoring. I work to develop guidelines and tools to evaluate, monitor, and report on genetic diversity. I use methods like environmental DNA (eDNA) and scat DNA analysis, DNA metabarcoding, and population genetics / genomics. My focus is Antarctica and the Southern Ocean, but I'll always have a soft spot for marsupials.
Additional affiliations
October 2016 - January 2017
January 2017 - December 2020
Position
- Oz Mammals Genomics Initiative
Description
- Developing genomic resources for Australia’s mammals, tackling wildlife genomics at a continental scale. https://ozmammalsgenomics.com/
August 2016 - December 2016
Education
December 2002 - February 2008
September 1996 - July 1999
Publications
Publications (107)
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...
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...
Antarctic krill (Euphausia superba) is a keystone species in the Southern Ocean ecosystem, and monitoring its distribution and abundance is crucial for the sustainable management of expanding fisheries targeting the species. Environmental DNA (eDNA)‐based monitoring could complement conventional krill surveys, but its applicability is limited by a...
Signatories to the Antarctic Treaty System’s Environmental Protocol are committed to preventing incursions of non-native species into Antarctica, but systematic surveillance is rare.Environmental DNA (eDNA) methods provide new opportunities for enhancing detection of non-native species and biosecurity monitoring. To be effective for Antarctic biose...
Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across insti...
Incidental mortality in fisheries is a major driver of population declines for albatrosses and petrels globally. However, accurate identification of species can be difficult due to the poor condition of bycaught birds and/or visual similarities between closely related species. We assessed three genetic markers for their ability to distinguish the 3...
Genetic diversity is essential for maintaining healthy populations and ecosystems. Several approaches have recently been developed to evaluate population genetic trends without necessarily collecting new genetic data. Such “genetic diversity indicators” enable rapid, large-scale evaluation across dozens to thousands of species. Empirical genetic st...
Genetic diversity is fundamental to biological diversity, vital for species’ health and adaptation to environmental change. Under the recently adopted Kunming-Montreal Global Biodiversity Framework (GBF), 196 Parties committed to report the status of genetic diversity for both wild and domesticated species. For this, three genetic diversity indicat...
Under the recently adopted Kunming‐Montreal Global Biodiversity Framework, 196 Parties committed to reporting the status of genetic diversity for all species. To facilitate reporting, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: maintaining genetically distinct po...
Context
DNA recovered from predator faeces (scats) can be used to determine the presence of fauna and shed light on their life histories and inter-species interactions. DNA metabarcoding, which involves concurrent amplification and sequencing of DNA from multiple taxa, represents an important advance by enabling the simultaneous detection of multip...
The eastern quoll (Dasyurus viverrinus) is an endangered marsupial native to Australia. Since the extirpation of its mainland populations in the 20th century, wild eastern quolls have been restricted to two islands at the southern end of their historical range. Eastern quolls are the subject of captive breeding programs and attempts have been made...
Measuring genetic diversity of wild species using DNA-based data remains resource intensive and time consuming for nearly all species. However, genetic assessments are needed for global conservation commitments, including the Convention on Biological Diversity, and for governments and managers to evaluate conservation progress, as well as prioritiz...
The eastern quoll (Dasyurus viverrinus) is an endangered marsupial mesopredator native to Australia. Since the extirpation of the last mainland Australian populations in the late 20th century, wild populations of this species have been restricted to two islands at the far southern end of its historical range. Eastern quolls are the subject of capti...
Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation progr...
The rate and extent of global biodiversity change is surpassing our ability to measure, monitor and forecast trends. We propose an interconnected worldwide system of observation networks — a global biodiversity observing system (GBiOS) — to coordinate monitoring worldwide and inform action to reach international biodiversity targets.
Recent scientific evidence shows that genetic diversity must be maintained, managed, and monitored to protect biodiversity and nature's contributions to people. Three genetic diversity indicators, two of which do not require DNA-based assessment, have been proposed for reporting to the Convention on Biological Diversity and other conservation and p...
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Abstract Environmental DNA (eDNA)-based methods are increasingly used by government agencies to detect pests and threatened species, and for broader...
Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework...
Genetic diversity among and within populations of all species is necessary for people and the planet to survive in a changing world. Over the past three years, the conservation of genetic diversity has received increased ambition and specificity in commitments under the draft Convention on Biological Diversity's (CBD) post 2020 Global Biodiversity...
Recent scientific evidence shows that genetic diversity must be maintained, managed, and monitored to maintain biodiversity and nature's contributions to people. Three genetic diversity indicators, two of which do not require DNA-based studies, were previously proposed for reporting to the Convention on Biological Diversity and other conservation a...
The use of correct taxonomy to describe and name the earth's biodiversity is fundamental to conservation and management. However, there are issues that need to be overcome to ensure that the described taxa and their scientific names are both appropriate and widely adopted. Obstacles to this include the use of different species definitions, taxonomi...
Abstract Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species‐wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an E...
Sahul unites the world’s largest and highest tropical island and the oldest and most arid continent on the backdrop of dynamic environmental conditions. Massive geological uplift in New Guinea is predicted to have acted as a species pump from the late Miocene onward, but the impact of this process on biogeography and diversification remains unteste...
The use of environmental DNA (eDNA) and RNA (eRNA) methods is a rapidly advancing field that provides fast, cost-effective, non-invasive methods to identify the presence
of target species. These methods can be used, for example, to screen for pest species as part of biosecurity measures and risk management, to screen for threatened species as part...
The use of molecular assays to assess the presence of species using environmental DNA (eDNA) and RNA (eRNA) as analytes has diversified as the field of environmental surveillance advances. These methods can be used, for example, to screen for pest species as part of biosecurity measures and risk management, to screen for threatened species as part...
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...
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...
A correction to this paper has been published: https://doi.org/10.1007/s10592-021-01376-9
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...
Significance
Native rodents represent 41% of Australian mammal extinctions since European colonization. To determine the scale and timing of their decline, we used museum specimens to generate genome-scale data from eight extinct Australian rodents and their 42 living relatives. Relatively high genetic diversity in extinct species immediately prior...
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...
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...
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...
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...
This protocol describes how to swab mammal scats in the field, for DNA sampling. Swabs are air-dryed for storage in the field and transport to the laboratory.
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...
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...
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...
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
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
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
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
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
Aim
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 c...
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...
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
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
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
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
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
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
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...
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
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
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
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
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
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
We developed a mini-barcode based on the 12S rRNA gene to identify predator from scats in Tasmania. To test the sensitivity of our primers to detect low template DNA samples, we set up serial dilutions of six DNA extracts originating from museum samples, representing each of the six mammal predators that might be detected in Tasmania (Tasmanian dev...
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...
Data file for MacDonald et al (2014) Heredity. Sex-linked and autosomal microsatellites provide new insights into island populations of the tammar wallaby
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
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
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
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
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.
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
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.
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.
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.
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.
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.
Supplementary information for MacDonald et al (2015) Australian Journal of Zoology. The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge)
Supplementary information for MacDonald et al (2015) Australian Journal of Zoology. The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge)
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...
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...
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...
