Vicki Thomson

Research Interests

Archaeological Science Biogeography and Phylogeography Biological Adaptation Ecological Impacts of Climate Change Epigenetics Evolutionary Impacts of Climate Change Zoology

Ms Vicki Thomson

School of Biological Sciences

College of Science

I am an evolutionary biologist who uses DNA to investigate how Australasian animals have adapted / will adapt to changing environments. An animal's DNA sequence can tell us about how many of them there were in the past (did they decline almost to the point of extinction?) and about how low their genetic diversity got (did they lose individuals with important versions of genes that would otherwise have allowed them to adapt, for example, to aridity via increased desiccation resistance?).

I am interested in how animals have adapted to different environments over time. This means that I use tools from a range of disciplines depending on when and at what scale the adaptation occurred (i.e. epigenetics for detecting very recent adaptation; population genetics and phylogeography for population-level adaptation, evolutionary genetics and ancient DNA for very old adaptation).

I was recently awarded an ARC DECRA to study the role of epigenetic modifications in tiger snake adaptation. I will investigate the mechanisms underlying animal adaptation to future environmental change by examining the molecular basis for phenotypic plasticity in snakes. I will specifically examine variation in genetic/epigenetic profiles and compare against important fitness traits, such as variable head size, bite force and swallowing performance to identify relationships between molecular change and physiology. Such research is a critical first step in improving our knowledge of the mechanisms whereby animal populations may adapt to environmental change, allowing us to facilitate such processes or concentrate conservation effort where species are unable to adapt via epigenetic modification.

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.

Date Position Institution name
2018 - ongoing ARC DECRA Fellowship University of Adelaide
2016 - 2017 ARC Post-doctoral Research Associate University of Adelaide
2013 - 2016 ARC Post-doctoral Research Associate University of Adelaide
2012 - 2013 Research Assistant Australian National University

Date Type Title Institution Name Country Amount
2017 Distinction Edith Dornwell Medal for Female Early Career Researcher Excellence University of Adelaide Australia $1000
2015 Award University of Adelaide's Environment Institute small grant award University of Adelaide Australia $10,670
2015 Invitation Presentation to Birds SA - Australia -
2014 Invitation E-science magazine article University of Adelaide Australia -
2014 Invitation Presentation to Royal Society of South Australia - Australia -
2014 Award Asia Pacific Science Foundation grant Asia Pacific Science Foundation - $43,672
2014 Invitation Radio interview with Radio Adelaide University of Adelaide Australia -
2014 Invitation Radio interview with Radio New Zealand - Australia -
2013 Award Sir Mark Mitchell Research Foundation grant Sir Mark Mitchell Research Foundation Australia $6,200

Date Institution name Country Title
2008 - 2012 University of Adelaide Australia PhD
2006 - 2007 University of Queensland Australia BSc(Hons)
2001 - 2005 University of Queensland Australia BSc
2001 - 2005 University of Queensland Australia BA

Year Citation
2024 Kai, H., Takada, N., Thomson, V., & Suzuki, H. (2024). Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events. Zoological Science, 41(3), 290-301.
DOI Scopus2
2023 Hua, Q. Q. H., Thomson, V. A., Strugnell, J. M., Martino, J. C., Gillanders, B. M., & Doubleday, Z. A. (2023). Using genomics and morphometrics to monitor data-poor and commercially exploited octopod populations. Marine Biology, 170(10), 1-21.
DOI Scopus2 WoS2
2023 Ammresh., Sherratt, E., Thomson, V. A., Lee, M. S. Y., Dunstan, N., Allen, L., . . . Palci, A. (2023). Island tiger snakes (Notechis scutatus) gain a ‘head start’ in life: how both adaptation and evolution underlie skull shape differences. Evolutionary Biology, 50(1), 111-126.
DOI Scopus8 WoS6
2022 Galbraith, J. D., Ludington, A. J., Sanders, K. L., Amos, T. G., Thomson, V. A., Enosi Tuipulotu, D., . . . Adelson, D. L. (2022). Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes. Genes, 13(2), 217.
DOI Scopus3 WoS2 Europe PMC3
2022 Thomson, V. A., Wiewel, A. S., Palmer, R., Hamilton, N., Algar, D., Pink, C., . . . Donnellan, S. (2022). Genetic insights into the introduction history of black rats into the eastern Indian Ocean. Frontiers in Ecology and Evolution, 9, 786510-1-786510-15.
DOI Scopus4 WoS4
2022 Foster, N. R., van Dijk, K. -J., Biffin, E., Young, J. M., Thomson, V. A., Gillanders, B. M., . . . Waycott, M. (2022). A targeted capture approach to generating reference sequence databases for chloroplast gene regions.. Ecology and evolution, 12(4), 1-10.
DOI Scopus7 WoS7 Europe PMC5
2021 Augusto, R. D. C., Rey, O., Cosseau, C., Chaparro, C., Vidal-Dupiol, J., Allienne, J. -F., . . . Grunau, C. (2021). A simple ATAC-seq protocol for population epigenetics [Version 2]. Wellcome Open Research, 5, 121.
DOI Scopus12
2021 Galbraith, J., Ludington, A., Edwards, R., Sanders, K., Suh, A., & Adelson, D. (2021). Horizontal transfer and southern migration: the tale of Hydrophiinae’s marine journey.
DOI
2021 Foster, N. R., van Dijk, K. -J., Biffin, E., Young, J. M., Thomson, V. A., Gillanders, B. M., . . . Waycott, M. (2021). A Multi-Gene Region Targeted Capture Approach to Detect Plant DNA in Environmental Samples: A Case Study From Coastal Environments. Frontiers in Ecology and Evolution, 9, 735744-1-735744-12.
DOI Scopus14 WoS12
2021 Foster, N. R., van Dijk, K. -J., Biffin, E., Young, J. M., Thomson, V., Gillanders, B. M., . . . Waycott, M. (2021). A multi-gene region targeted capture approach to detect plant DNA in environmental samples: A case study from coastal environments.
DOI
2021 Lettoof, D. C., Thomson, V. A., Cornelis, J., Bateman, P. W., Aubret, F., Gagnon, M. M., & von Takach, B. (2021). Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow. PLoS One, 16(10), e0259124-1-e0259124-21.
DOI Scopus11 WoS10 Europe PMC3
2020 Bover, P., Mitchell, K. J., Torres-Roig, E., Llamas, B., Thomson, V. A., Alcover, J. A., . . . Pons, J. (2020). Ancient DNA from an extinct Mediterranean micromammal—Hypnomys morpheus (Rodentia: Gliridae)—Provides insight into the biogeographic history of insular dormice. Journal of Zoological Systematics and Evolutionary Research, 58(1), 427-438.
DOI Scopus7 WoS5
2020 Herrera, M. B., Kraitsek, S., Alcalde, J. A., Quiroz, D., Revelo, H., Alvarez, L. A., . . . Gongora, J. (2020). European and Asian contribution to the genetic diversity of mainland South American chickens. Royal Society Open Science, 7(2), 1-13.
DOI Scopus14 WoS12 Europe PMC10
2020 Nankivell, J. H., Goiran, C., Hourston, M., Shine, R., Rasmussen, A. R., Thomson, V. A., & Sanders, K. L. (2020). A new species of turtle-headed sea Snake (Emydocephalus: Elapidae) endemic to Western Australia. Zootaxa, 4758(1), 141-156.
DOI Scopus10 WoS8 Europe PMC2
2020 White, L. C., Thomson, V. A., West, R., Ruykys, L., Ottewell, K., Kanowski, J., . . . Austin, J. J. (2020). Genetic monitoring of the greater stick-nest rat meta-population for strategic supplementation planning. Conservation Genetics, 21(5), 16 pages.
DOI Scopus13 WoS12 Europe PMC2
2020 Louys, J., Herrera, M. B., Thomson, V. A., Wiewel, A. S., Donnellan, S. C., O'Connor, S., & Aplin, K. (2020). Expanding population edge craniometrics and genetics provide insights into dispersal of commensal rats through Nusa Tenggara, Indonesia. Records of the Australian Museum, 72(5), 287-302.
DOI Scopus7 WoS6
2020 Augusto, R. D. C., Minoda, A., & Grunau, C. (2020). A simple ATAC-seq protocol for population epigenetics [Version 1]. Wellcome Open Research, 5, 121.
DOI Europe PMC9
2019 Bover Arbos, P., Llamas, B., Mitchell, K. J., Thomson, V. A., Alcover, J. A., Lalueza-Fox, C., . . . Pons, J. (2019). Unraveling the phylogenetic relationships of the extinct bovid Myotragus balearicus Bate 1909 from the Balearic Islands. Quaternary Science Reviews, 215, 185-195.
DOI Scopus14 WoS14
2018 White, L. C., Moseby, K. E., Thomson, V. A., Donnellan, S. C., & Austin, J. J. (2018). Long-term genetic consequences of mammal reintroductions into an Australian conservation reserve. Biological Conservation, 219, 1-11.
DOI Scopus51 WoS53 Europe PMC11
2018 Allen, L., Sanders, K. L., & Thomson, V. A. (2018). Molecular evidence for the first records of facultative parthenogenesis in elapid snakes. Royal Society Open Science, 5(2), 171901-1-171901-6.
DOI Scopus17 WoS19 Europe PMC10
2018 Bover, P., Mitchell, K., Llamas, B., Rofes, J., Thomson, V., Cuenca-Bescós, G., . . . Pons, J. (2018). Molecular phylogenetics supports the origin of an endemic Balearic shrew lineage (Nesiotites) coincident with the Messinian Salinity Crisis. Molecular Phylogenetics and Evolution, 125, 188-195.
DOI Scopus9 WoS6 Europe PMC1
2018 Thomson, V., Mitchell, K., Eberhard, R., Dortch, J., Austin, J., & Cooper, A. (2018). Genetic diversity and drivers of dwarfism in extinct island emu populations. Biology Letters, 14(4), 20170617-1-20170617-4.
DOI Scopus19 WoS17 Europe PMC7
2018 Bover, P., Llamas, B., Thomson, V., Pons, J., Cooper, A., & Mitchell, K. (2018). Molecular resolution to a morphological controversy: the case of North American fossil muskoxen Bootherium and Symbos. Molecular Phylogenetics and Evolution, 129, 70-76.
DOI Scopus10 WoS9 Europe PMC1
2018 Thomson, V. A., Wiewel, A. S., Chinen, A., Maryanto, I., Sinaga, M. H., How, R., . . . Suzuki, H. (2018). A perspective for resolving the systematics of Rattus, the vertebrates with the most influence on human welfare. Zootaxa, 4459(3), 431-452.
DOI Scopus17 WoS15 Europe PMC5
2017 Herrera, M., Thomson, V., Wadley, J., Piper, P., Sulandari, S., Dharmayanthi, A., . . . Austin, J. (2017). East African origins for Madagascan chickens as indicated by mitochondrial DNA. Royal Society Open Science, 4(3), 160787-1-160787-12.
DOI Scopus21 WoS18 Europe PMC13
2017 Rodriguez Lopez, C., Konate, M., & Thomson, V. (2017). MSAP In Tiger Snakes: Island Populations Are Epigenetically More Divergent.
DOI
2017 Sasamori, S., Wiewel, A., Thomson, V., Kobayashi, M., Nakata, K., & Suzuki, H. (2017). Potential causative mutation for melanism in rats identified in the agouti signaling protein gene (Asip) of the Rattus rattus species complex on Okinawa Island, Japan. Zoological Science, 34(6), 513-522.
DOI Scopus6 WoS7 Europe PMC5
2016 Timm, R. M., Weijola, V., Aplin, K. A., Donnellan, S. C., Flannery, T. F., Thomson, V., & Pine, R. H. (2016). A new species of Rattus (Rodentia: Muridae) from Manus Island, Papua New Guinea. Journal of Mammalogy, 97(3), 861-878.
DOI Scopus17 WoS19
2016 Wadley, J., Fordham, D., Thomson, V., Ritchie, E., & Austin, J. (2016). Phylogeography of the antilopine wallaroo (Macropus antilopinus) across tropical northern Australia. Ecology and Evolution, 6(22), 8050-8061.
DOI Scopus4 WoS4 Europe PMC4
2016 Coghlan, B., Seddon, J., Best, E., Thomson, V., & Goldizen, A. (2016). Evidence of male-biased dispersal in eastern grey kangaroos (Macropus giganteus). Australian Journal of Zoology, 64(5), 360-369.
DOI Scopus4 WoS4
2015 Llamas, B., Brotherton, P., Mitchell, K., Templeton, J., Thomson, V., Metcalf, J., . . . Cooper, A. (2015). Late Pleistocene Australian Marsupial DNA Clarifies the Affinities of Extinct Megafaunal Kangaroos and Wallabies. Molecular Biology and Evolution, 32(3), 574-584.
DOI Scopus25 WoS24 Europe PMC13
2015 Coghlan, B., Goldizen, A., Thomson, V., & Seddon, J. (2015). Phylogeography of eastern grey kangaroos, Macropus giganteus, suggests a mesic refugium in eastern Australia. PLoS One, 10(5), e0128160-1-e0128160-16.
DOI Scopus8 WoS9 Europe PMC3
2014 Thomson, V., Lebrasseur, O., Austin, J., Hunt, T., Burney, D., Denham, T., . . . Cooper, A. (2014). Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific. Proceedings of the National Academy of Sciences, 111(13), 4826-4831.
DOI Scopus112 WoS104 Europe PMC55
2014 Sheng, G., Soubrier, J., Liu, J., Werdelin, L., Llamas, B., Thomson, V., . . . Cooper, A. (2014). Pleistocene Chinese cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta. Molecular Ecology, 23(3), 522-533.
DOI Scopus37 WoS31 Europe PMC12
2014 Thomson, V., Aplin, K., Cooper, A., Hisheh, S., Suzuki, H., Maryanto, I., . . . Donnellan, S. (2014). Molecular genetic evidence for the place of origin of the Pacific rat, Rattus exulanso. PLoS One, 9(3), e91356-1-e91356-11.
DOI Scopus39 WoS38 Europe PMC11
2014 Thomson, V. A., Lebrasseur, O., Austin, J. J., Hunt, T. L., Burney, D. A., Denham, T., . . . Cooper, A. (2014). Reply to Beavan, Bryant, and Storey and Matisoo-Smith: Ancestral polynesian "d" haplotypes reflect authentic pacific chicken lineages. Proceedings of the National Academy of Sciences of the United States of America, 111(35), E3585-E3586.
DOI Scopus7 WoS7 Europe PMC2
2009 Carter, A. J., Macdonald, S. L., Thomson, V. A., & Goldizen, A. W. (2009). Structured association patterns and their energetic benefits in female eastern grey kangaroos, Macropus giganteus. Animal Behaviour, 77(4), 839-846.
DOI Scopus66 WoS63

Year Citation
2022 Rull, V., & Stevenson, C. (Eds.) (2022). The Prehistory of Rapa Nui (Easter Island). Springer International Publishing.
DOI

Year Citation
2023 Watts, C. H. S., Aplin, K. P., & Thomson, V. A. (2023). Brown rat: Rattus norvegicus. In Strahan S Mammals of Australia (pp. 512-513).
2023 Aplin, K. P., Redhead, T. D., & Thomson, V. A. (2023). Canefield rat: Rattus sordidus. In Strahan S Mammals of Australia (pp. 505-506).
2023 Watts, C. H. S., Aplin, K. P., & Thomson, V. A. (2023). Pacific rat: Rattus exulans. In Strahan S Mammals of Australia (pp. 511-512).
2022 Thomson, V. A., Herrera, M., & Austin, J. J. (2022). Commensals/Domesticates on Rapa Nui: What Can Their Phylogeographic Patterns Tell Us About the Discovery and Settlement of the Island?. In Developments in Paleoenvironmental Research (pp. 41-62). Springer International Publishing.
DOI

Year Citation
2017 Rodriguez Lopez, C. M., Konate, M., Sanders, K., & Thomson, V. A. (2017). Epigenetic divergence contributes to tiger snake adaptation to island environments. Poster session presented at the meeting of ComBio 2017. Adelaide, SA.

ARC DECRA ($365,058) - The role of epigenetic modifications in tiger snake adaptation.

ARC Linkage grant ($164,427) - Testing co-evolutionary processes driving venom diversity in tiger snakes.

Environment Institute small grant award ($10,670) - Tiger snake venom: evolution in response to prey type.

Environment Institute travel grant award ($2,500) to present at the 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.

Australia Pacific Science Foundation grant ($43,672) - New Guinean Long-beaked Echidnas in the Kimberley, Western Australia: using ancient DNA analysis of skins and scats to confirm their presence and corroborate outstanding biodiversity discovery.

Sir Mark Mitchell Foundation grant ($6,200) - The status of New Guinean Long-beaked Echidnas in Australia's north west: survey by DNA analysis of scats.

In recent years I have supervised two 3rd year undergraduate research projects (ENVBIOL3550: Evolution of the Australian Biota III in 2016; ENVBIOL3123: Issues in Evolutionary Biology in 2014), presented a guest lecture on epigenetics (ENVBIOL3123 in 2015) and lectured/tutored on phylogenetic methods (ENVBIOL3550 in 2016).

Date Role Research Topic Program Degree Type Student Load Student Name
2013 - 2015 Co-Supervisor Genetic studies on prehistoric translocations of chickens in the Indo-Pacific Doctor of Philosophy Doctorate Full Time Dr Michael James Herrera

Date Role Research Topic Location Program Supervision Type Student Load Student Name
2017 - 2018 Principal Supervisor The impacts of prey type on expression profiles of venom gland genes in island and mainland populations of the Australian tiger snake, Notechis scutatus The University of Adelaide Bachelor of Science (Honours) Honours Full Time Monique Ahrens

Date Role Membership Country
2014 - ongoing Treasurer Postgraduate Association of the School of Biological Sciences Australia
2014 - ongoing Representative Biological Society of South Australia Australia
2014 - ongoing Co-Founder Statistical Solutions Australia
2013 - ongoing - Australian Mammal Society Australia

Date Engagement Type Partner Name
2016 - ongoing Consultant Museum Victoria
2016 - ongoing Consultant South Australian Museum
2016 - ongoing Consultant Venom Supplies Pty Ltd

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