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Dr Vicki Thomson

Telephone +61 8 8313 5280
Position ARC Post-doctoral Researcher
Email vicki.thomson@adelaide.edu.au
Building Darling Building
Floor/Room 2 06
Campus North Terrace
Org Unit Genetics & Evolution

To link to this page, please use the following URL:
http://www.adelaide.edu.au/directory/vicki.thomson

Biography/ Background

Fresh Science coverage of my recent Rattus exulans paper

 


Vicki's gravatar

Vicki's personal website: vickithomson.wordpress.com

Vicki's Tiger snake website: tigersnakes.wordpress.com

Vicki's Twitter handle: @Vicki_Thomson

Vicki's google scholar page 

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.

Academic positions:

 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.

                     Reptile phylogenomics

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.

 

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 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.


Committee positions

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.


Workshops organised

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.

 

 

 

 

 

 

 

 

 

 

 

 


Grants awarded

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)


Lecturing

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.


Conference presentations

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.


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

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.

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.

Publications

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 DNANature 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 changeMolecular 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 DNAPLoS 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 welfareZootaxa (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, JapanJournal 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 GuineaJournal 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): e0128160doi: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):574-84doi: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):4826-31doi: 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 exulansPLoS One 9(3):e91356doi: 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 23:522-533doi: 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 giganteusAnimal Behaviour 77(4):839-846; doi: 10.1016/j.anbehav.2008.12.007.

 

Entry last updated: Saturday, 17 Sep 2016

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