Publications

Journal articles
  1. Laikre L, Hoban S, Bruford MW, Segelbacher G, Allendorf FW, Gajardo G, Rodríguez AG, Hedrick PW, Heuertz M, Hohenlohe PA, Jaffé R, Johannesson K, Liggins L, MacDonald AJ, OrozcoterWengel P, Reusch TBH, Rodríguez-Correa H, Russo IRM, Ryman N, Vernesi C (2020) Post-2020 goals overlook genetic diversity. Science 367 (6482): 1083-1085.
  2. FitzSimmons NN, Pittard SD, McIntyre N, Jensen MP, Guinea M, Hamann M, Kennett R, Leis B, Limpus CJ, Limpus DJ, McCann MJ, MacDonald AJ, McFarlane G, Parmenter CJ, Pendoley K, Prince RT, Scheltinga L, Theissinger K, Tucker AD, Waayers D, Whiting A, Whiting S (2020). Phylogeography, genetic stocks, and conservation implications for an Australian endemic marine turtle. Aquatic Conservation: Marine and Freshwater Ecosystems 30 (3): 440-460.
  3. Cooper S, Ottewell K, MacDonald AJ, Adams M, Byrne M, Carthew S, Eldridge M, Li Y, Pope L, Saint K and Westerman M (2019). Phylogeography of southern brown and golden bandicoots: implications for the taxonomy and distribution of endangered subspecies and species. Australian Journal of Zoology 66 (6) 379-393.
  4. Melville J, Chaplin K, Hutchinson M, Sumner J, Gruber B, MacDonald AJ and Sarre SD (2019). Taxonomy and conservation of Grassland Earless Dragons: new species and an assessment of first possible extinction of a reptile on mainland Australia. Royal Society Open Science 6: 190233 (open access). I wrote a blog post at WildlifeSNPits to accompany this.
  5. Quasim S, MacDonald AJ and Sarre SD (2018) Towards more efficient large-scale DNA-based detection of terrestrial mammal predators from scats. Mammal Research 63, 387-393 (link to ResearchGate).
  6. Campbell CD, Sarre SD, Stojanovic D, Gruber B, Medlock K, Harris S, MacDonald AJ and Holleley CE (2018) When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data. Diversity and Distributions 24: 831–840 (open access). I wrote a blog post at WildlifeSNPits to accompany this.
  7. ​​Ramsey DSL, Barclay C, Campbell CD, Dewar E, MacDonald AJ, Modave E, Quasim S and Sarre SD (2018) Detecting rare carnivores using scats: Implications for monitoring a fox incursion into Tasmania. Ecology and Evolution 8, 732-743 (open access).
  8. ​Modave E, MacDonald AJ and Sarre SD (2017) A single mini-barcode test to screen for Australian mammalian predators from environmental samples Gigascience 6, gix052 (open access).
  9. MacDonald AJ and Sarre SD (2017) A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA. Molecular Ecology Resources 17, 708-720 (link to ResearchGate). ​​I wrote a blog post at WildlifeSNPits to accompany this.
  10. ​Carlson E, MacDonald AJ, Adamack A, McGrath T, Doucette LI, Osborne WS, Gruber B, Sarre SD (2016) How many conservation units are there for the endangered grassland earless dragons? Conservation Genetics 17, 761–774 (​link to ResearchGate). ​I wrote a blog post at WildlifeSNPits to accompany this.
  11. MacDonald AJ and Sarre SD (2015) Species assignment from trace DNA sequences: an in silico assessment of the test used to survey for foxes in Tasmania. Journal of Applied Ecology 52, 1649–1655 (open access). I wrote a blog post for The Applied Ecologist's blog to accompany this.
  12. MacDonald AJ, Knopp T, Pepper M, Keogh JS, Sarre SD (2015) The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge). Australian Journal of Zoology 63, 111-114 (link to ResearchGate).​
  13. Ramsey DSL, MacDonald AJ, Quasim S, Barclay C, Sarre SD (2015) 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. Journal of Applied Ecology 52, 562-570 (open access). ​I wrote a blog post at WildlifeSNPits to accompany this.
  14. Sarre SD, MacDonald AJ, Berry OF, Barclay C, Saunders GR and Ramsey DSL (2014) Defining specificity in DNA detection of wildlife: Response to Gonçalves et al. "The risks of using "species-specific" PCR assays in wildlife research: The case of red fox (Vulpes vulpes) identification in Tasmania". Forensic Science International: Genetics 13, 206-207 (link to ResearchGate).
  15. Sarre SD, Aitken N, Adamack AT, MacDonald AJ, Gruber B and Cowan P (2014) Creating new evolutionary pathways through bioinvasion: the population genetics of brushtail possums in New Zealand. Molecular Ecology 23, 3419-3433 (link to ResearchGate).
  16. MacDonald AJ, Young M, Lintermans M and Sarre SD (2014) Primers for detection of Macquarie perch from environmental and trace DNA samples. Conservation Genetics Resources 6, 551-553 (link to ResearchGate).
  17. MacDonald AJ, FitzSimmons NN, Chambers B, Renfree MB and Sarre SD (2014) Sex-linked and autosomal microsatellites provide new insights into island populations of the tammar wallaby. Heredity 112, 333-342 (link to ResearchGate).
  18. Sarre SD, MacDonald AJ, Barclay C, Saunders GR and Ramsey DSL (2013) Foxes are now widespread in Tasmania: DNA detection defines the distribution of this rare but invasive carnivore. Journal of Applied Ecology 50, 459–468 (open access).
  19. Cowled BD, Ward MP, Laffan SW, Galea F, Garner MG, MacDonald AJ, Marsh I, Muellner P, Negus K, Quasim S, Woolnough A and Sarre SD (2012) Integrating survey and molecular approaches to better understand wildlife disease ecology. PLoS ONE 7(10): e46310. doi:10.1371/journal.pone.0046310 (open access).​
  20. MacDonald AJ, Sarre SD, FitzSimmons NN, Aitken, N (2011) Determining microsatellite genotyping reliability and mutation detection ability: an approach using small-pool PCR from sperm DNA. Molecular Genetics and Genomics 285 (1) 1-18 (​link to ResearchGate).
  21. MacDonald AJ, Sarre SD, FitzSimmons NN, Graves JAM (2007) Chromosome-specific microsatellites from the tammar wallaby X chromosome and chromosome 2. Molecular Ecology Notes 7, 1063-1066 (​link to ResearchGate).
  22. MacDonald AJ, Sankovic N, Sarre SD, FitzSimmons NN, Wakefield MJ, Graves JAM and Zenger KR (2006) Y chromosome microsatellite markers identified from the tammar wallaby (Macropus eugenii) and their amplification in three other macropod species. Molecular Ecology Notes 6, 1202-1204 (link to ResearchGate).
Book chapter
  1. MacDonald AJ, Sarre SD, FitzSimmons NN (2010) Sex chromosome microsatellites: new tools for macropod population ecology. Pp. 53-64 In: Coulson G, Eldridge, M.D.B.; Macropods: The Biology of Kangaroos, Wallabies and Rat-kangaroos. CSIRO Publishing.
Scientific reports
  1. MacDonald AJ, Doucette LI, Gruber B and Sarre SD (2016) Genotype-By-Sequencing analysis of grassland earless dragons. A report to the Australian Capital Territory Government.
  2. Cooper S, Ottewell K and MacDonald AJ (2015) The taxonomic status of populations of southern brown bandicoots, Isoodon obesulus, from eastern and southern Australia based on mitochondrial and nuclear gene analyses. A report for Natural Resources Adelaide and Mount Lofty Ranges South Australia and the federal Department of Environment (link to full text).
  3. MacDonald AJ and Sarre SD (2015). Analysis of predator DNA from scats collected in a Tasmanian cave. A report to the Department of Primary Industries, Parks, Water and Environment, Tasmania.
  4. MacDonald AJ and Sarre SD (2015). Analysis of predator DNA from a putative fox scat collected on Kangaroo Island. A report to the Department of Environment, Water and Natural Resources, South Australia.
  5. Robley A, Newell G, White M, MacDonald A, Sarre S, Triggs B, Currie J and Smith S (2012) Strategic Red Fox control on bushfire affected public land in Victoria – Black Saturday Victoria 2009 – Natural values fire recovery program. Department of Environment and Primary Industries, East Melbourne, Victoria (​link to full text).
  6. ​MacDonald AJ and Sarre SD (2011). DNA detection of foxes in Tasmania in support of eradication effort: marker development for fox genotyping and prey identification. A report to the Invasive Animals Cooperative Research Centre, Canberra.
  7. MacDonald AJ and Sarre SD (2011). DNA detection of foxes in Tasmania in support of eradication effort: scat DNA analysis. A report to the Invasive Animals Cooperative Research Centre, Canberra.
  8. MacDonald AJ and Sarre SD (2011). Genetic species identification and microsatellite genotyping of a putative fox skull and fox-positive scats collected in Tasmania. A report to the Department of Primary Industries, Parks, Water and Environment, Tasmania.
  9. MacDonald AJ and Sarre SD (2011). DNA species identification and microsatellite profiling of fox scats collected pre- and post-control in Rubicon State Forest, Victoria. A report to the Arthur Rylah Institute for Environmental Research, Victoria.
  10. MacDonald AJ, Aitken, N and Sarre SD (2010). Development of an introductory short course in Wildlife Genetics: A short course for vertebrate pest managers and ecologists. A report to the Invasive Animals Cooperative Research Centre, Canberra.
Thesis
  1. MacDonald AJ, (2008) Sex chromosome microsatellite markers from an Australian marsupial: development, application and evolution. PhD Thesis, University of Canberra, Australia (link to full text).
Data
  1. Sarre SD, Aitken N, Adamack AT, MacDonald AJ, Gruber B, Cowan P (2014) Data from: Creating new evolutionary pathways through bio-invasion: the population genetics of brushtail possums in New Zealand. Dryad Digital Repository http://dx.doi.org/10.5061/dryad.8364h
  2. MacDonald AJ, FitzSimmons NN, Chambers B, Renfree MB and Sarre SD (2013) Data from: Sex-linked and autosomal microsatellites provide new insights into island populations of the tammar wallaby. Dryad Digital Repository http://dx.doi.org/10.5061/dryad.s76t7