Dr Vicki Thomson
Vicki's Twitter handle: @Vicki_Thomson
Vicki's Facebook profile
Vicki's Linkedin profile
Honours projects on offer in 2015 within our research group are:
1. Investigation of mitochondrial diversity in the Australian Emu.
2. Investigation into Echidna populations in the Kimberley region.
3. Optimisation of methods for surveying endangered Australian marsupials.
2016- ARC Postdoctoral Research Associate
School of Biological Sciences, University of Adelaide, Adelaide, South Australia.
DP140103650 - Tracking the development of agricultural lifestyles in island Southeast Asia through modern and prehistoric rodent communities.
2013- 2016 ARC Postdoctoral Research Associate
Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia.
DP13010455 - Reconstructing the impact of climate change on Australian native species.
2012-2103 Research Assistant
Dr. Scott Keogh, Australian National University, Canberra, ACT.
2012 Research Assistant
Dr. Chris Burridge, University of Tasmania, Hobart, Tasmania.
Wedge-tailed Eagle phylogeography project – optimization of microsatellite amplification for low template DNA samples.
2012 Research Assistant
Dr. Steve Donnellan, South Australian Museum, Adelaide, South Australia.
Rattus rattus species complex – phylogenomics to refine species boundaries.
2012 Research Assistant
Dr. Fred Gurgel, State Herbarium, Department of Environment, Water and Natural Resources, South Australia.
Phycology project – optimization of PCR conditions for inhibited and contaminated algae and sponge samples.
Dr. Thomson was awarded her PhD in 2013 on ‘Using ancient DNA as an essential tool to explore past Australian biodiversity’ utilizing modern and ancient DNA (at the Australian Centre for Ancient DNA, University of Adelaide) to answer phylogenetic, phylogeographic, population and conservation genetic questions. She has investigated issues in archaeology and ancient human migration using commensal chicken phylogeography (Thomson, Lebrasseur, Austin, et al. 2014 PNAS), phylogeography of commensal rodents (Thomson, Aplin, Cooper et al. 2014 PLoS One), conservation of a declining rodent species (Thomson, Ford, Rowe et al. in prep.), evolutionary history of Emu species, population genetics of a declining bat species (Thomson, Armstrong, Medlin, & Cooper in prep.), and phylogenetics of rare rodents. This research has allowed her to conduct fieldwork in outback Australia, learn morphological identification and morphometric skills, gain ancient DNA laboratory skills, develop relationships with collaborators, museum staff, and other researchers internationally, and learn many cutting-edge analysis methods. Dr. Thomson has also recently developed skills in the extraction of high molecular weight genomic DNA for RAD sequencing and exome capture, and in R and bash scripting.
2008-2012 Doctor of Philosophy (PhD), Australian
Centre for Ancient DNA, School of Earth and Environmental Sciences, University
of Adelaide, Adelaide, South Australia.
Supervised by Professor Alan Cooper, Professor Steve Donnellan, and Dr.
2006-2007 BSc (Honours) Degree, School of Biological
Sciences, University of Queensland, Brisbane, Australia. Supervised by Associate Professor Anne
Goldizen and Dr. Jennifer Seddon.
2002-2005 Bachelor of Science, majoring in Biochemistry, School of Biological
Sciences; Bachelor of Arts, majoring in Archaeology, School of Social Science,
University of Queensland, Brisbane, Australia. (GPA: 6.28).
1992-1996 Gisborne Girls High
School, Gisborne, New Zealand.
Awards & Achievements
2016 'History Hunters' presentation to students from Elizabeth North Primary School about classification and its application to conservation (25 May 2016).
2015 Adelaide Channel 7 news interview on Kangaroo Island emus (aired on 10th October 2015).
2015 'History Hunters' presentation to Year 7 students from John Hartley School about classification and its application to conservation (28 May 2015) - promotional video
2015 Off The Fence Productions interview on mice plagues (recorded on 13 March 2015, to be advised when broadcast)
2015 Presentation to Birds SA (27 February 2015): 'The birds of Australasia'
2014 E-science magazine article (University of Adelaide e-newsletter, Issue 10: 28 July 2014): Ancient chickens key to reconstructing early Polynesian migrations.
2014 Presentation to Royal Society of South Australia (12 June 2014): Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific.
2014 Interview on Radio Adelaide (23 March 2014): Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific.
2014 Interview on Radio New Zealand (18 March 2014): Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific.
2014 The Conversation article (online newsletter, 18 March 2014): Chickens tell tale of human migration across Pacific.
2010 The Genographic Project: Tracing Your Family Roots with the University of Adelaide.
2014-6 Treasurer of the School of Biological Sciences Post-Doc Association.
2014-6 Social Media officer of the Biological Society of South Australia.
2014-6 Founding member of the 'Stat Solution' network.
2015 Approximate Bayesian Computation (ABC) workshop, Adelaide, Australia. Featuring Xander Xue from Mike Hickerson's lab at City College of New York.
2015 SNPseq workshop, Adelaide, Australia.
2016 ARC Linkage grant 'Testing evolutionary processes driving venom diversity in tiger snakes' (AU$480,647)
2015 The University of Adelaide's Environment Institute small grant award (AU$10,670)
2014 Asia Pacific Science Foundation Grant (AU$43,672 over 3 years)
2014 Environment Institute Travel Grant (AU$2,500)
2013 Sir Mark Mitchell Research Foundation Grant (AU$6,200)
2009 Field Naturalists Society of South Australia – Lirabenda Endowment Fund Research Grant (AU$4,000)
2009 Nature Conservation Society of South Australia - NCSSA Conservation Biology Grant (AU$400)
2008-2009 Environmental Futures Network – Early Career Researcher Program Grant (AU$2,320)
2008-2011 Australian Postgraduate Award (AU$20,453 per annum/three years six months)
2016 Guest lecturer for ENV BIOL 3550: Evolution of the Australian Biota III, University of Adelaide, Australia - Phylogenetics on the command line.
2016 Tutor for ENV BIOL 3550: Evolution of the Australian Biota III, University of Adelaide, Australia - Using Geneious.
2016 Supervisor of Research Project for ENV BIOL 3550: Evolution of the Australian Biota III, University of Adelaide, Australia - Examining growth genes in tiger snakes.
2015 Guest lecturer in Epigenetics for ENV BIOL 3123: Issues in Evolutionary Biology, University of Adelaide, Australia - Epigenetics (and its implications in phenotypic plasticity).
2014 Supervisor of Research Project in Epigenetics for ENV BIOL 3123: Issues in Evolutionary Biology, University of Adelaide, Australia - Using BayeSSC and ABC to reconstruct human demography.
2015 SNPseq workshop, Adelaide, Australia - Developing GBS for a range of Australian terrestrial vertebrates: the problems and pitfalls
2015 Poster presentation at Genetic Society of AustralAsia (GSA) conference in Adelaide, Australia - Using genetics to understand the impacts of climate change on Australian endemics
2014 International Council on Archaeozoology (ICAZ) conference in San Rafael, Argentina - Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific.
2014 Indo-Pacific Prehistory Association (IPPA) conference in Siem Reap, Cambodia - (Why) Did the chicken cross the Pacific?
2013 CAVEPS, Adelaide, Australia - Birds of a feather: island dwarfs flock together with mainland Emus.
2012 Australian Mammal Society, Port Augusta, Australia - A ghost of a chance? Evolutionary history of the Ghost Bat (Macroderma gigas) and its chances of surviving future climate change.
2010 Australian Mammal Society, Sydney, Australia - Climate change may invigorate endangered Hastings River Mouse (Pseudomys oralis): Ancient DNA informs conservation decisions.
2009 Palaeontological surveying and excavations of Ghost Bat cave deposits, Flinders Ranges, South Australia.
2009 Palaeontological surveying and excavations of Ghost Bat cave deposits, Northern Agricultural Regions, Western Australia.
2006 Biological surveying of Eastern Grey Kangaroos, Lake Cootharabra, Queensland.
Australian Journal of Botany
Diversity and Distributions
Genes and Genetics
Philippine Agricultural Scientist
Philosophical Transactions of the Royal Society
of mitochondrial diversity in the Australian Emu
(Family: Dromaiidae) is one of Australia’s most iconic species. Until recently the abundant
nature of the mainland species was thought to reflect a high level of genetic diversity.
However, recent work by our lab has highlighted a distinct lack of
mitochondrial control region diversity in both island and mainland forms of the
Emu, with this loss of genetic diversity thought to stem from extreme
demographic events prior to the last glacial maximum. This honours project will
allow the student to gain valuable lab experience by generating whole
mitochondrial genomes (WMG) of exemplar specimens, plus essential analysis
techniques as the student will examine WMG diversity levels with a view to
evaluate the potential for expansion of the project into a PhD project in later
years. Potential applicants should have a background in molecular
biology/ecology, population genetics, or evolutionary biology, and have strong
self-motivation, time management, and writing skills. Please
direct your expression of interest including your CV to Dr. Vicki Thomson and
Dr. Jeremy Austin.
into echidna populations in the Kimberley region.
echidna (Family: Tachyglossidae) is
one of Australia’s most iconic species. Until recently only one species, the
short nosed echidna (Tachyglossus
aculeatus), was known in Australia although three longer nosed species are
found in Papua New Guinea. The renowned mammalogist Kris Helgen from the
Smithsonian, has recently described a long nosed echidna (Zaglossus bruijnii) skeleton from the Kimberley region of northern Australia that was
collected in 1901. This honours project will examine echidna scats from
northern Australia to explore the likelihood that a cryptic population of long
nosed echidna has survived in the Kimberley region. The project will be lab
based, with the student developing molecular species identification methods for
the scats, and if a long nosed echidna population is found the student will
investigate the population genetics of this species in Australia. Please direct your expression of interest including your CV to Dr.
Vicki Thomson and Dr. Jeremy Austin.
Optimisation of non-invasively
collected sampling methods for surveying endangered Australian marsupials.
The northern-hairy nosed
wombat (Family: Vombatidae) is one of
Australia’s most iconic species. One of the last surviving populations of
northern-hairy nosed wombats is protected at Epping Forest National Park, where
monitoring of the population occurs regularly. One aspect of this monitoring
involves undertaking a census to estimate the number of wombats present in the
population. This monitoring is done by collecting hair from sticky tape
stretched across burrow entrances, with these hair samples being retrieved for
DNA extraction in the field. Although the current field-based DNA extraction
method is adequate for immediate PCR amplification and sequencing of population
genetic markers, it does not preserve the DNA well for future downstream
applications. Therefore, another relatively cheap and time-efficient extraction
method is required. The project will be lab based, with the student trialling
and optimising alternate extraction methods for the 2013 census samples and analysing
the degree of improvement over current methods, and using multiple year’s
census data to investigate inbreeding and kinship relationships within the
Epping Forest National Park population. Please direct your expression of
interest including your CV to Dr. Vicki Thomson and Dr. Jeremy Austin.
2016 Bover P, Mitchell MJ, Llamas B, Thomson VA, Pons J, Alcover JA, Cooper A. First ancient DNA from an endemic insular Mediterranean micromammal: the extinct dormouse Hypnomys morpheus. PLoS One (submitted Sept 2016).
2016 Herrera MJB, Thomson VA, Wadley JJ, Macqueen P, Piper PJ, Sulundari S, Dharmayanti AB, Kraitsek S, Eusebio MS, Rubio RO, Cooper A, Gongora J, Austin JJ. Philippine origin and dispersal of Polynesian chickens indicated by mitochondrial DNA. Nature communications (submitted Sept 2016).
2016 Thomson VA, Armstrong KN, Medlin G, Cooper A. A ghost of a chance? Evolutionary history of the Australian Ghost Bat (Macroderma gigas) and its chances of surviving future climate change. Molecular Ecology (in review August 2016).
2016 Herrera MJB, Thomson VA, Piper PJ, Wadley JJ, Cooper A, Austin JJ. East African origins for Malagasy chickens as indicated by mitochondrial DNA. PLoS One (in review June 2016).
2016 Thomson VA, Wiewel A, Chinen A, Maryanto I, Sinaga MH, How R, Aplin K, Suzuki H. A perspective for resolving the systematics of Rattus, the vertebrates with the most influence on human welfare. Zootaxa (in review August 2016).
2016 Sasamori S, Wiewel A, Thomson VA, Kobayashi M, Nakata K, Suzuki H. A potential causative mutation of the agouti signaling protein gene (Asip) for melanism in the Rattus rattus species complex from the Okinawa Island, Japan. Journal of Zoology (submitted Sept 2016).
2016 Coghlan BA, Seddon JM, Best EC, Thomson VA, Goldizen AW. Evidence of male-biased dispersal in eastern grey kangaroo (Macropus giganteus). Australian Journal of Zoology (submitted 18 July 2016).
2016 Wadley JJ, Fordham D, Thomson VA, Ritchie E, Austin JJ. Phylogeography of the antilopine wallaroo (Macropus antilopinus) across tropical northern Australia. Ecology and Evolution (accepted 19 July 2016).
2016 Timm RM, Weijola VS-A, Aplin KA, Donnellan SC, Flannery TF, Thomson VA, Pine RH. A new species of Rattus (Rodentia: Muridae) from Manus Island, Papua New Guinea. Journal of Mammalogy http://dx.doi.org/10.1093/jmammal/gyw034.
2015 Coghlan BA, Goldizen AW, Thomson VA, Seddon JM. Phylogeography of eastern grey kangaroos, Macropus giganteus, suggests a mesic refugium in eastern Australia. PLoS One 10(5): e0128160; doi:10.1371/journal.pone.0128160.
2014 Llamas B, Brotherton P, Mitchell KJ, Templeton JE, Thomson VA, Metcalf JL, Armstrong KN, Kasper M, Richards SM, Camens AB, Lee MS, Cooper A. Late Pleistocene Australian marsupial DNA clarifies the affinities of extinct megafaunal kangaroos and wallabies. Molecular Biology and Evolution 32(3):574-84; doi:10.1093/molbev/msu338.
2014 Thomson VA, Lebrasseur O, Austin JJ, Hunt TL, Burney DA, Denham T, Rawlence NJ, Wood JR, Gongora J, Girdland Flink L, Linderholm A, Dobney K, Larson G, Cooper A. Reply to Beavan, Bryant, and Storey and Matisoo-Smith: Ancestral Polynesian 'D' haplotypes reflect authentic Pacific chicken lineages. PNAS 111(35):E3585-E3586; doi: 10.1073/pnas.1411566111.
2014 Thomson VA Thomson VA, Lebrasseur O, Austin JJ, Hunt TL, Burney DA, Denham T, Rawlence NJ, Wood JR, Gongora J, Girdland Flink L, Linderholm A, Dobney K, Larson G, Cooper A. Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific. PNAS 111(13):4826-31; doi: 10.1073/pnas.1320412111.
2014 Thomson VA, Aplin KP, Cooper A, Hisheh S, Suzuki H, Maryanto I, Yap G, Donnellan SC. Molecular genetic evidence for the place of origin of the Pacific Rat, Rattus exulans. PLoS One 9(3):e91356; doi: 10.1371/journal.pone.0091356.
2014 Sheng G-L, Soubrier J, Liu J-Y, Werdelin L, Llamas B, Thomson VA, Tuke J, Wu L-J, Hou X-D, Chen Q-J, Lai X-L, Cooper A. Pleistocene Chinese cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta. Molecular Ecology 23:522-533; doi: 10.1111/mec.12576.
We even have a cool picture on the cover, see below:
2009 Carter AJ, Macdonald SL, Thomson VA, Goldizen AW. Structured association patterns and their energetic benefits in female eastern grey kangaroos, Macropus giganteus. Animal Behaviour 77(4):839-846; doi: 10.1016/j.anbehav.2008.12.007.
Entry last updated: Saturday, 17 Sep 2016