Publications

Journal articles
  1. Genetic diversity is considered important but interpreted narrowly in country reports to the Convention on Biological Diversity: Current actions and indicators are insufficient. Hoban S, Campbell CD, da Silva JM, Ekblom R, Funk WC, Garner BA, Godoy JA, Kershaw F, MacDonald AJ, Mergeay J, Minter M, O'Brien D, Paz Vinas I, Pearson SK, Pérez-Espona S, Potter KM, Russo IRM, Segelbacher G, Vernesi C, Hunter ME. Biological Conservation (2021) 261: 109233
  2. Museum genomics reveals the rapid decline and extinction of Australian rodents since European settlement. Roycroft E, MacDonald AJ, Moritz C, Moussalli A,  Portela Miguez R, Rowe KC. PNAS (2021): 118 (27) e2021390118.
  3. Global commitments to conserving and monitoring genetic diversity are now necessary and feasible. Hoban S, Bruford MW, Funk WC, Galbusera P, Griffith MP, Grueber CE, Heuertz M, Hunter ME, Hvilsom C, Kalamujic Stroil B, Kershaw F, Khoury CK, Laikre L, Lopes-Fernandes M, MacDonald AJ, Mergeay J, Meek M, Mittan C, Mukassabi TA, O'Brien D, Ogden R, Palma-Silva C, Ramakrishnan U, Segelbacher G, Shaw RE, Sjögren-Gulve P, Veličković N, Vernesi C. BioScience (2021) biab054.
  4. Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD. Laikre L, Hohenlohe PA, Allendorf F, Bertola LD, Breed MF, Bruford MW, Funk WC, Gajardo G, Gonzalez-Rodriguez A, Grueber CE, Hedrick PW, Heuertz M, Hunter ME, Johannesson K, Liggins L, MacDonald AJ, Mergeay J, Moharrek F, O’Brien D, Ogden R, Orozco-terWengel P, Palma-Silva C, Pierson J, Paz-Vinas I, Russo IRM, Ryman N, Segelbacher G, Sjogren-Gulve P, Waits LP, Vernesi C, Hoban S. Conservation Genetics (2021) DOI 10.1007/s10592-021-01359-w.
  5. Post-2020 goals overlook genetic diversity. 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 and Vernesi C. Science (2020) 367 (6482): 1083-1085.
  6. Phylogeography, genetic stocks, and conservation implications for an Australian endemic marine turtle. 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 and Whiting S. Aquatic Conservation: Marine and Freshwater Ecosystems (2020) 30 (3): 440-460.
  7. The Oz Mammals Genomics (OMG) initiative: developing genomic resources for mammal conservation at a continental scale. Eldridge MDB, Deakin JE, MacDonald AJ, Byrne M, Fitzgerald A, Johnson RN, Moritz C, Palmer S and Young A. Australian Zoologist (2020) 40 (3): 505-509.
  8. Phylogeography of southern brown and golden bandicoots: implications for the taxonomy and distribution of endangered subspecies and species. Cooper S, Ottewell K, MacDonald AJ, Adams M, Byrne M, Carthew S, Eldridge M, Li Y, Pope L, Saint K and Westerman M. Australian Journal of Zoology (2019) 66 (6) 379-393.
  9. Taxonomy and conservation of Grassland Earless Dragons: new species and an assessment of first possible extinction of a reptile on mainland Australia. Melville J, Chaplin K, Hutchinson M, Sumner J, Gruber B, MacDonald AJ and Sarre SD. Royal Society Open Science (2019) 6: 190233 (open access). I wrote a blog post at WildlifeSNPits to accompany this.
  10. Towards more efficient large-scale DNA-based detection of terrestrial mammal predators from scats. Quasim S, MacDonald AJ and Sarre SD. Mammal Research (2018) 63, 387-393 (link to ResearchGate).
  11. When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data. Campbell CD, Sarre SD, Stojanovic D, Gruber B, Medlock K, Harris S, MacDonald AJ and Holleley CE. Diversity and Distributions (2018) 24: 831–840 (open access). I wrote a blog post at WildlifeSNPits to accompany this.
  12. Detecting rare carnivores using scats: Implications for monitoring a fox incursion into Tasmania. ​​Ramsey DSL, Barclay C, Campbell CD, Dewar E, MacDonald AJ, Modave E, Quasim S and Sarre SD. Ecology and Evolution (2018) 8, 732-743 (open access).
  13. A single mini-barcode test to screen for Australian mammalian predators from environmental samples. ​Modave E, MacDonald AJ and Sarre SD. Gigascience (2017) 6, gix052 (open access).
  14. A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA. MacDonald AJ and Sarre SD. Molecular Ecology Resources (2017) 17, 708-720 (link to ResearchGate). ​​I wrote a blog post at WildlifeSNPits to accompany this.
  15. How many conservation units are there for the endangered grassland earless dragons? ​Carlson E, MacDonald AJ, Adamack A, McGrath T, Doucette LI, Osborne WS, Gruber B, Sarre SD. Conservation Genetics (2016) 17, 761–774 (​link to ResearchGate). ​I wrote a blog post at WildlifeSNPits to accompany this.
  16. Species assignment from trace DNA sequences: an in silico assessment of the test used to survey for foxes in Tasmania. MacDonald AJ and Sarre SD. Journal of Applied Ecology (2015) 52, 1649–1655 (open access). I wrote a blog post for The Applied Ecologist's blog to accompany this.
  17. The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge). MacDonald AJ, Knopp T, Pepper M, Keogh JS, Sarre SD. Australian Journal of Zoology (2015) 63, 111-114 (link to ResearchGate).​
  18. 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. Ramsey DSL, MacDonald AJ, Quasim S, Barclay C, Sarre SD. Journal of Applied Ecology (2015) 52, 562-570 (open access). ​I wrote a blog post at WildlifeSNPits to accompany this.
  19. 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". Sarre SD, MacDonald AJ, Berry OF, Barclay C, Saunders GR and Ramsey DSL. Forensic Science International: Genetics (2014) 13, 206-207 (link to ResearchGate).
  20. Creating new evolutionary pathways through bioinvasion: the population genetics of brushtail possums in New Zealand. Sarre SD, Aitken N, Adamack AT, MacDonald AJ, Gruber B and Cowan P. Molecular Ecology (2014) 23, 3419-3433 (link to ResearchGate).
  21. Primers for detection of Macquarie perch from environmental and trace DNA samples. MacDonald AJ, Young M, Lintermans M and Sarre SD. Conservation Genetics Resources (2014) 6, 551-553 (link to ResearchGate).
  22. Sex-linked and autosomal microsatellites provide new insights into island populations of the tammar wallaby. MacDonald AJ, FitzSimmons NN, Chambers B, Renfree MB and Sarre SD. Heredity (2014) 112, 333-342 (link to ResearchGate).
  23. Foxes are now widespread in Tasmania: DNA detection defines the distribution of this rare but invasive carnivore. Sarre SD, MacDonald AJ, Barclay C, Saunders GR and Ramsey DSL. Journal of Applied Ecology (2013) 50, 459–468 (open access).
  24. Integrating survey and molecular approaches to better understand wildlife disease ecology. 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. PLoS ONE (2012) 7(10): e46310. doi:10.1371/journal.pone.0046310 (open access).​
  25. Determining microsatellite genotyping reliability and mutation detection ability: an approach using small-pool PCR from sperm DNA. MacDonald AJ, Sarre SD, FitzSimmons NN, Aitken, N. Molecular Genetics and Genomics (2011) 285 (1) 1-18 (​link to ResearchGate).
  26. Chromosome-specific microsatellites from the tammar wallaby X chromosome and chromosome 2. MacDonald AJ, Sarre SD, FitzSimmons NN, Graves JAM. Molecular Ecology Notes (2007) 7, 1063-1066 (​link to ResearchGate).
  27. Y chromosome microsatellite markers identified from the tammar wallaby (Macropus eugenii) and their amplification in three other macropod species. MacDonald AJ, Sankovic N, Sarre SD, FitzSimmons NN, Wakefield MJ, Graves JAM and Zenger KR. Molecular Ecology Notes (2006) 6, 1202-1204 (link to ResearchGate).
Book chapter
  1. Sex chromosome microsatellites: new tools for macropod population ecology. MacDonald AJ, Sarre SD, FitzSimmons NN. Pp. 53-64 In: Coulson G, Eldridge, M.D.B.; Macropods: The Biology of Kangaroos, Wallabies and Rat-kangaroos (2010) CSIRO Publishing.
Preprints (not yet peer-reviewed)
  1. An analysis of genetic diversity actions, indicators and targets in 114 National Reports to the Convention on Biological Diversity. Hoban S, Campbell CD, da Silva J, Ekblom R, Funk WC, Garner B, Godoy JA, Kershaw F, MacDonald AJ, Mergeay J, Minter M, O'Brien D, Paz-Vinas I, Pearson AK, Perez-Espona S, Potter K, Russo IR, Segelbacher G, Vernesi C, Hunter M. bioRxiv (2020) 2020.08.28.254672; doi: https://doi.org/10.1101/2020.08.28.254672
Scientific reports
  1. Genotype-By-Sequencing analysis of grassland earless dragons. MacDonald AJ, Doucette LI, Gruber B and Sarre SD. A report to the Australian Capital Territory Government (2016).
  2. The taxonomic status of populations of southern brown bandicoots, Isoodon obesulus, from eastern and southern Australia based on mitochondrial and nuclear gene analyses. Cooper S, Ottewell K and MacDonald AJ. A report for Natural Resources Adelaide and Mount Lofty Ranges South Australia and the federal Department of Environment (2015) (link to full text).
  3. Analysis of predator DNA from scats collected in a Tasmanian cave. MacDonald AJ and Sarre SD. A report to the Department of Primary Industries, Parks, Water and Environment, Tasmania (2015).
  4. Analysis of predator DNA from a putative fox scat collected on Kangaroo Island. MacDonald AJ and Sarre SD. A report to the Department of Environment, Water and Natural Resources, South Australia (2015).
  5. Strategic Red Fox control on bushfire affected public land in Victoria – Black Saturday Victoria 2009 – Natural values fire recovery program. Robley A, Newell G, White M, MacDonald A, Sarre S, Triggs B, Currie J and Smith S. Department of Environment and Primary Industries, East Melbourne, Victoria (2012) (​link to full text).
  6. DNA detection of foxes in Tasmania in support of eradication effort: marker development for fox genotyping and prey identification. MacDonald AJ and Sarre SD. A report to the Invasive Animals Cooperative Research Centre, Canberra (2011).
  7. DNA detection of foxes in Tasmania in support of eradication effort: scat DNA analysis. MacDonald AJ and Sarre SD. A report to the Invasive Animals Cooperative Research Centre, Canberra (2011).
  8. Genetic species identification and microsatellite genotyping of a putative fox skull and fox-positive scats collected in Tasmania. MacDonald AJ and Sarre SD. A report to the Department of Primary Industries, Parks, Water and Environment, Tasmania  (2011).
  9. DNA species identification and microsatellite profiling of fox scats collected pre- and post-control in Rubicon State Forest, Victoria. MacDonald AJ and Sarre SD. A report to the Arthur Rylah Institute for Environmental Research, Victoria (2011).
  10. Development of an introductory short course in Wildlife Genetics: A short course for vertebrate pest managers and ecologists. MacDonald AJ, Aitken, N and Sarre SD. A report to the Invasive Animals Cooperative Research Centre, Canberra (2010).
Thesis
  1. Sex chromosome microsatellite markers from an Australian marsupial: development, application and evolution. MacDonald AJ. PhD Thesis, University of Canberra, Australia (2008) (link to full text).