Publications

ORCID: 0000-0003-2972-200X
ResearcherID: B-4462-2011
Scopus Author ID: 15073252300
Journal articles
  1. The importance of appropriate taxonomy in Australian mammalogy. Jackson SM, Baker AM, Eldridge MDB, Fisher DO, Frankham GJ, Lavery TH, MacDonald AJ, Menkhorst PW, Phillips MJ, Potter S, Rowe KC, Travouillon KJ, and Umbrello LS. 
    Australian Mammalogy (2022) https://doi.org/10.1071/AM22016
  2. Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads. von Takach B, Ranjard L, Burridge CP, Cameron SF, Cremona T, Eldridge MDB, Fisher DO, Frankenberg S, Hill BM, Hohnen R, Jolly CJ, Kelly E, MacDonald AJ, Moussalli A, Ottewell K, Phillips BL, Radford IJ, Spencer PBS, Trewella GJ, Umbrello LS and Banks SC. 
    Molecular Ecology (2022): https://doi.org/10.1111/mec.16680
  3. New Guinea uplift opens ecological opportunity across a continent. Roycroft E, Fabre PH, MacDonald AJ, Moritz C, Moussalli A, and Rowe KC. Current Biology (2022): doi:10.1016/j.cub.2022.08.021
  4. Bringing together approaches to reporting on within species genetic diversity. O'Brien D, Laikre L, Hoban S, Bruford MW, Ekblom R, Fischer MC, Hall J, Hollingsworth PM, Hvilsom C, Kershaw F, Mittan CS, Mukassabi TA, Ogden R, Segelbacher G, Shaw RE, Vernesi C, and MacDonald AJ. Journal of Applied Ecology (2022): doi:10.1111/1365-2664.14225
  5. Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition. Hoban S, Archer FI, Bertola LD, Bragg JG, Breed MF, Bruford MW, Coleman MA, Ekblom R, Funk WC, Grueber CE, Hand BK, Jaffé R, Jensen E, Johnson JS, Kershaw F, Liggins L, MacDonald AJ, Mergeay J, Miller JM, Muller-Karger F, O'Brien D, Paz-Vinas I, Potter KM, Razgour O, Vernesi C and Hunter ME. Biological Reviews (2022): https://doi.org/10.1111/brv.12852
  6. The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice. Kershaw F, Bruford MW, Funk WC, Grueber CE, Hoban S, Hunter M, Laikre L, MacDonald AJ, Meek M, Mittan C, O'Brien D, Ogden R, Shaw R, Vernesi C, Segelbacher G. Conservation Science and Practice (2022): e12635.  https://doi.org/10.1111/csp2.12635
  7. Has the introduction of two subspecies generated dispersal barriers among invasive possums in New Zealand? Campbell CD, Cowan P, Gruber B, MacDonald AJ, Holleley C, Sarre SD. Biological Invasions (2021) https://doi.org/10.1007/s10530-021-02609-1
  8. 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
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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. I wrote a blog post at WildlifeSNPits to accompany this.
  17. 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.
  18. 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. I wrote a blog post at WildlifeSNPits to accompany this.
  19. 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.
  20. 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.
  21. 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. ​​Companion blog post at WildlifeSNPits.
  22. 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. ​Companion blog post at WildlifeSNPits.
  23. 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. Companion blog post for The Applied Ecologist's blog.
  24. 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.​
  25. 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. ​Companion blog post at WildlifeSNPits.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.​
  32. 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.
  33. 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.
  34. 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.
Book chapters
  1. Observing wildlife and its signs. Smith BP, Waudby HP, Dickman CR, Soennichsen K, Mills C, Howe A, Woolley LA, Griffiths SR, Cox TE, Clayton J, Penton C, Morrant DS, Letnic M, Cullen D, Stobo-Wilson A, Taggart DA, Gleeson D, Cripps JK, Gill MJ, MacDonald AJ. Chapter 4 in Smith BP, Waudby HP, Alberthsen C, Hampton JO; Wildlife Research in Australia: Practical and Applied Methods (2022) CSIRO Publishing.
  2. Sex chromosome microsatellites: new tools for macropod population ecology. MacDonald AJ, Sarre SD, FitzSimmons NN. Pp. 53-64 In: Coulson G, Eldridge, MDB; Macropods: The Biology of Kangaroos, Wallabies and Rat-kangaroos (2010) CSIRO Publishing.
Preprints (not yet peer-reviewed)
  1. Genetic diversity Goals and Targets have improved, but remain insufficient. Hoban S, Bruford MW, da Silva JM, Funk WC, Gill MJ, Grueber CE, Heuertz M, Hunter ME, Kershaw F, Lacy RC, Lees C, MacDonald AJ, Mastretta-Yanes A, McGowan PJK, Meek MH, Mergeay J, Millette KL, Mittan-Moreau CS, Navarro LM, O'Brien D, Ogden R, Paz-Vinas I, Frankham R, Segelbacher G, Vernesi C, Laikre L. Authorea (2022). DOI: 10.22541/au.166785459.91522683/v2
  2. Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: an ongoing assessment of genetic indicators in nine countries. Hoban S, da Silva J, Mastretta-Yanes A, Grueber C, Heuertz M, Hunter M, Mergeay J, Paz-Vinas I, Fukaya K, Ishihama F, Jordan R, Latorre MC, MacDonald AJ, Rincon-Parra V, Sjögren-Gulve P, Tani N, Thurfjell H, Laikre L. Authorea (2022). DOI: 10.22541/au.166627692.27077414/v1
  3. Supplemental Materials for: “Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: an ongoing assessment of genetic indicators in nine countries”. Hoban S, da Silva J, Mastretta-Yanes A, Grueber C, Heuertz M, Hunter M, Mergeay J, Paz-Vinas I, Fukaya K, Ishihama F, Jordan R, Latorre MC, MacDonald AJ, Rincon-Parra V, Sjögren-Gulve P, Tani N, Thurfjell H, Laikre L. Authorea (2022) DOI: 10.22541/au.166672613.34943821/v1
  4. 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
    ​- ​​​now published as: Genetic diversity is considered important but interpreted narrowly in country reports to the Convention on Biological Diversity: Current actions and indicators are insufficient in Biological Conservation
​Scientific Reports
  1. Environmental DNA protocol development guide for biomonitoring. De Brauwer M, Chariton A, Clarke LJ, Cooper MK, DiBattista J, Furlan E, Giblot-Ducray D, Gleeson D, Harford A,Herbert S, MacDonald AJ, Miller A, Montgomery K, Mooney T, Noble LM, Rourke M, Sherman CDH, Stat M,Suter L, West KM, White N, Villacorta-Rath C, Zaiko A and Trujillo-Gonzalez A (2022). National eDNA Reference Centre, Canberra.
  2. Environmental DNA test validation guidelines. De Brauwer M, Chariton A, Clarke LJ, Cooper MK, DiBattista J, Furlan E, Giblot-Ducray D, Gleeson D, Harford A,Herbert S, MacDonald AJ, Miller A, Montgomery K, Mooney T, Noble LM, Rourke M, Sherman CDH, Stat M,Suter L, West KM, White N, Villacorta-Rath C, Zaiko A and Trujillo-Gonzalez A (2022). National eDNA Reference Centre, Canberra.
  3. A framework for applying environmental DNA to biosecurity in the Australian Antarctic Program. Clarke LJ, Ammitzboll H, Bergstrom DM, King CK, Shaw JD, Suter L, Stark JS and MacDonald AJ (2022). Australian Antarctic Division, Australian Government Department of Agriculture, Water and the Environment, Canberra.
  4. Genotype-By-Sequencing analysis of grassland earless dragons. MacDonald AJ, Doucette LI, Gruber B and Sarre SD (2016). A report to the Australian Capital Territory Government.
  5. 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 (2015). A report for Natural Resources Adelaide and Mount Lofty Ranges South Australia and the federal Department of Environment.
  6. Analysis of predator DNA from scats collected in a Tasmanian cave. MacDonald AJ and Sarre SD (2015). A report to the Department of Primary Industries, Parks, Water and Environment, Tasmania.
  7. Analysis of predator DNA from a putative fox scat collected on Kangaroo Island. MacDonald AJ and Sarre SD (2015). A report to the Department of Environment, Water and Natural Resources, South Australia.
  8. 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 (2012). Department of Environment and Primary Industries, East Melbourne, Victoria.
  9. 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).
  10. 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).
  11. 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).
  12. 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).
  13. 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).