Curriculum vitae

I was awarded my 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.  I 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 (Thomson, Aplin, Donnellan et al. in prep).  This research has allowed me 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. I have 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.

Academic positions

ARC Postdoctoral Research Associate (2016-)

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.

ARC Postdoctoral Research Associate (2013-2016)

Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia.

DP13010455 – Reconstructing the impact of climate change on Australian native species.

Research Assistant (2012-2103)

Dr. Scott Keogh, Australian National University, Canberra, ACT.

Reptile phylogenomics

Research Assistant (2012)

Dr. Chris Burridge, University of Tasmania, Hobart, Tasmania.

Wedge-tailed Eagle phylogeography project – optimization of microsatellite amplification for low template DNA samples.

Research Assistant (2012)

Dr. Steve Donnellan, South Australian Museum, Adelaide, South Australia.

Rattus rattus species complex – phylogenomics to refine species boundaries.

Research Assistant (2012)

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.

Qualifications

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. Ken Aplin.

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

Public Outreach

2016               ‘History Hunters’ presentation about scientific classification and its use in conservation to students from Elizabeth North Primary School (25 May 2015).

2015               Adelaide Channel 7 news interview on Kangaroo Island emus, aired on 10th October 2015.

2015               ‘History Hunters’ presentation about scientific classification and its use in conservation to Year 7 students from John Hartley School (28 May 2015).

2015               Off The Fence Productions interview on mice plagues (recorded on 13 March 2015, TBA when broadcast).

2015               Presentation to Birds SA (27 February 2015): ‘The birds of Australasia’.

2014               E-science magazine article (University of Adelaide e-newsletter 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.

Workshops organised

2015              Approximate Bayesian Computation (ABC) workshop, Adelaide, Australia. Featuring Alexander Xue from Mike Hickerson’s lab at City College of New York.

2015              SNPseq workshop, Adelaide, Australia.

RADseqFlyer_Final.pptx

Lecturing and Supervising

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 for ENV BIOL 3123: Issues in Evolutionary Biology, University of Adelaide, Australia – Using BayeSSC and ABC to reconstruct human demography.

2013-5           Co-Supervisor of PhD student (Michael Herrera).

Committee positions

2014-           Treasurer of the School of Biological Sciences Post-Doc Association.

2014-           Social Media officer of the Biological Society of South Australia.

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2014-           Founding member of the ‘Stats Solution’ network.

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Conference presentations

2015             SNPseq workshop, Adelaide, Australia – Developing GBS for a range of Australian terrestrial vertebrates: the problems and pitfalls.

2015             Poster presentation at Genetics 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 DAN informs conservation decisions.

Grants

2016                  ARC Linkage Project (AU$480,647) – Testing co-evolutionary processes driving venom diversity in tiger snakes

2015                  Environment Institute grant (AU$10,670) – Tiger snake venom: evolution in response to prey type.

2014                  Asia Pacific Science Foundation Grant (AU$43,672 over 3 years) – New Guinean Long-beaked Echindas in the Kimberley, Western Australia – using ancient DNA analysis of skins and scats to confirm their presence and corroborate an outstanding biodiversity discovery.

2013                  Sir Mark Mitchell Research Foundation Grant (AU$6,200) – The status of the New Guinean Long-beaked Echidnas in Australia’s north-west – survey by DNA analysis of scats.

2009                Field Naturalists Society of South Australia – Lirabenda Endowment Fund Research Grant (AU$4,000) – Diet analysis and phylogeographic structure of the locally extinct Ghost Bat (Macroderma gigas) of southern Australia.

2009                Nature Conservation Society of South Australia – NCSSA Conservation Biology Grant (AU$400) – Diet analysis and phylogeographic structure of the locally extinct Ghost Bat (Macroderma gigas) of southern Australia.

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)

2002-2005    Dean’s Commendation for High Achievement

2003-2008    Member of Golden Key International Honour Society

1993                Young Enterprise Scheme company member

Field Experience

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.

Reviewer for

Animal Genetics

Austral Ornithology

Australian Journal of Botany

BMC Genetics

Diversity and Distributions

Genes and Genetics

Mammalian Biology

Philippine Agricultural Scientist

Philosophical Transactions of the Royal Society

Research Interests

Investigation of mitochondrial diversity in the Australian Emu

The 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.

Investigation into echidna populations in the Kimberley region

The 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.

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