Dr Raymond Tobler
School of Biological Sciences
College of Sciences
Eligible to supervise Masters and PhD - email supervisor to discuss availability.
Ray is an ARC DECRA fellow whose central interest lies in understanding how evolutionary processes have shaped the remarkable biological diversity observed in humans and other species. In his PhD work, Ray used population genetic datasets to explore how fruit flies adapt to novel thermal environments. Active projects include working with Indigenous groups across Australia, New Guinea, and Island South East Asia to build a detailed understanding of the human population history of these regions – including the original settlement and subsequent movements and interactions. An emerging focus involves leveraging large genomic datasets to investigate how historical evolutionary processes, including adaptation, have shaped modern human disease, and exploring the potential of evolutionary genetic knowledge in the development of novel medical treatments (i.e. evolutionary medicine).
| Date | Position | Institution name |
|---|---|---|
| 2021 - ongoing | Research Fellow | Evolution of Cultural Diversity Initiative |
| 2019 - ongoing | ARC DECRA Fellow | University of Adelaide |
| 2016 - 2019 | ARC DAATSIA Fellow | University of Adelaide |
| Year | Citation |
|---|---|
| 2025 | Souilmi, Y., Oliva, A., Davidson, R., Williams, M. P., Ravishankar, S., Roca-Rada, X., . . . Llamas, B. (2025). Lessons learned: Recommendations for reproducible paleogenomic data analyses.. Am J Hum Genet, 112(12), 2830-2841. |
| 2025 | Davidson, R., Roca-Rada, X., Ravishankar, S., Taufik, L., Haarkötter, C., Collen, E., . . . Llamas, B. (2025). Optimized in-solution enrichment of over a million ancient human SNPs. Genome Biology, 26(1), 190-1-190-20. Scopus5 WoS5 Europe PMC6 |
| 2025 | Purnomo, G. A., Teixeira, J. C., Sudoyo, H., Llamas, B., & Tobler, R. (2025). Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context. Molecular Ecology Resources, 25(8), e70007-1-e70007-12. |
| 2025 | Roca-Rada, X., Davidson, R., Williams, M. P., Villalba-Mouco, V., Carvalho, A. F., Ravishankar, S., . . . Teixeira, J. C. (2025). The genetic history of Portugal over the past 5,000 years.. Genome Biology, 26(1), 248-1-248-39. Scopus3 WoS4 Europe PMC1 |
| 2024 | Purnomo, G. A., Kealy, S., O'Connor, S., Schapper, A., Shaw, B., Llamas, B., . . . Tobler, R. (2024). The genetic origins and impacts of historical Papuan migrations into Wallacea. Proceedings of the National Academy of Sciences of USA, 121(52), e2412355121. Scopus6 WoS4 Europe PMC2 |
| 2024 | Souilmi, Y., Wasef, S., Williams, M. P., Conroy, G., Bar, I., Bover, P., . . . Mitchell, K. J. (2024). Ancient genomes reveal over two thousand years of dingo population structure. Proceedings of the National Academy of Sciences, 121(30), e2407584121-1-e2407584121-12. Scopus7 WoS7 Europe PMC6 |
| 2024 | Johnson, O. L., Tobler, R., Schmidt, J. M., & Huber, C. D. (2024). Population genetic simulation: Benchmarking frameworks for non-standard models of natural selection. Molecular Ecology Resources, 24(3), e13930-1-e13930-13. Scopus3 WoS3 Europe PMC4 |
| 2023 | Tobler, R., Souilmi, Y., Huber, C. D., Bean, N., Turney, C. S. M., Grey, S. T., & Cooper, A. (2023). The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.. Proc Natl Acad Sci U S A, 120(22), e2213061120. Scopus19 WoS15 Europe PMC14 |
| 2023 | Davidson, R., Williams, M. P., Roca-Rada, X., Kassadjikova, K., Tobler, R., Fehren-Schmitz, L., & Llamas, B. (2023). Allelic bias when performing in-solution enrichment of ancient human DNA. Molecular Ecology Resources, 23(8), 1823-1840. Scopus16 WoS16 Europe PMC15 |
| 2023 | Johnson, O. L., Tobler, R., Schmidt, J. M., & Huber, C. D. (2023). Fluctuating selection and the determinants of genetic variation. Trends in Genetics, 39(6), 491-504. Scopus37 WoS33 Europe PMC44 |
| 2023 | Taufik, L., Teixeira, J. C., Llamas, B., Sudoyo, H., Tobler, R., & Purnomo, G. A. (2023). Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects. Genes, 13(12), 1-11. Scopus6 WoS4 Europe PMC3 |
| 2022 | Lan, D., Purnomo, G., Tobler, R., Souilmi, Y., & Llamas, B. (2022). Genozip Dual-Coordinate VCF format enables efficient genomic analyses and alleviates liftover limitations. |
| 2022 | Souilmi, Y., Tobler, R., Johar, A., Williams, M., Grey, S. T., Schmidt, J., . . . Huber, C. D. (2022). Admixture has obscured signals of historical hard sweeps in humans. Nature Ecology & Evolution, 6(12), 2003-2015. Scopus20 WoS19 Europe PMC31 |
| 2021 | Cooper, A., Turney, C. S. M., Palmer, J., Hogg, A., McGlone, M., Wilmshurst, J., . . . Zech, R. (2021). A global environmental crisis 42,000 years ago. Science in China Series C: Life Sciences, 371(6531), 811-818. Scopus94 WoS82 Europe PMC23 |
| 2021 | Lan, D., Tobler, R., Souilmi, Y., & Llamas, B. (2021). Genozip - a universal extensible genomic data compressor. Bioinformatics, 37(16), 2225-2230. Scopus36 WoS31 Europe PMC26 |
| 2021 | Aguiar Macedo Teixeira, J. C., Jacobs, G. S., Stringer, C., Tuke, S., Hudjashov, G., Purnomo, G. A., . . . Helgen, K. M. (2021). Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture. Nature Ecology & Evolution, 5(5), 616-624. Scopus45 WoS33 Europe PMC20 |
| 2021 | Oliva, A., Tobler, R., Cooper, A., Llamas, B., & Souilmi, Y. (2021). Systematic benchmark of ancient DNA read mapping. Briefings in bioinformatics, 22(5), 1-12. Scopus33 WoS30 Europe PMC33 |
| 2021 | Souilmi, Y., Lauterbur, M. E., Tobler, R., Huber, C. D., Johar, A. S., Moradi, S. V., . . . Enard, D. (2021). An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia. Current Biology, 31(16), 3504-3514. Scopus65 WoS61 Europe PMC58 |
| 2021 | Purnomo, G. A., Mitchell, K. J., O'Connor, S., Kealy, S., Taufik, L., Schiller, S., . . . Tobler, R. (2021). Mitogenomes reveal two major influxes of Papuan ancestry across Wallacea following the last glacial maximum and Austronesian contact. Genes, 12(7), 1-21. Scopus26 WoS24 Europe PMC16 |
| 2021 | Oliva, A., Tobler, R., Llamas, B., & Souilmi, Y. (2021). BWA-mem is not the best aligner for ancient DNA short reads. Europe PMC2 |
| 2021 | Herrando-Pérez, S., Tobler, R., & Huber, C. D. (2021). smartsnp, an r package for fast multivariate analyses of big genomic data. Methods in Ecology and Evolution, 12(11), 2084-2093. Scopus24 WoS23 |
| 2021 | Souilmi, Y., Lauterbur, M. E., Tobler, R., Huber, C. D., Johar, A. S., Moradi, S. V., . . . Enard, D. (2021). An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.. Curr Biol, 31(16), 3704. Scopus4 WoS2 Europe PMC11 |
| 2021 | Alpaslan-Roodenberg, S., Anthony, D., Babiker, H., Bánffy, E., Booth, T., Capone, P., . . . Zahir, M. (2021). Ethics of DNA research on human remains: five globally applicable guidelines. Nature, 599(7883), 41-46. Scopus95 WoS77 Europe PMC55 |
| 2021 | Cooper, A., Turney, C. S. M., Palmer, J., Hogg, A., McGlone, M., Wilmshurst, J., . . . Zech, R. (2021). Response to Comment on "A global environmental crisis 42,000 years ago". Science New York N Y, 374(6570), eabi9756. Scopus2 WoS2 Europe PMC2 |
| 2021 | Cooper, A., Turney, C. S. M., Palmer, J., Hogg, A., McGlone, M., Wilmshurst, J., . . . Zech, R. (2021). Response to comment on “A global environmental crisis 42,000 years ago”. Science, 374(6570), 3 pages. Scopus2 |
| 2021 | Oliva, A., Tobler, R., Llamas, B., & Souilmi, Y. (2021). Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment. Ecology and Evolution, 11(24), 18743-18748. Scopus17 WoS15 Europe PMC19 |
| 2020 | Tobler, R., Johar, A., Huber, C., & Souilmi, Y. (2020). PolyLinkR: A linkage-sensitive gene set enrichment R package. |
| 2020 | Lan, D., Tobler, R., Souilmi, Y., & Llamas, B. (2020). genozip: a fast and efficient compression tool for VCF files. Bioinformatics, 36(13), 4091-4092. Scopus12 WoS10 Europe PMC12 |
| 2020 | Teixeira, J., Jacobs, G., Stringer, C., Tuke, J., Hudjashov, G., Purnomo, G., . . . Helgen, K. (2020). Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia. |
| 2020 | Souilmi, Y., Tobler, R., Johar, A., Williams, M., Grey, S., Schmidt, J., . . . Cooper, A. (2020). Ancient human genomes reveal a hidden history of strong selection in Eurasia. Europe PMC1 |
| 2020 | Souilmi, Y., Lauterbur, E., Tobler, R., Huber, C., Johar, A., & Enard, D. (2020). An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia. Europe PMC3 |
| 2019 | Richards, S. M., Mitchell, K. J., Tobler, R., & Cooper, A. (2019). Recombinase Polymerase Amplification (RPA) versus PCR for ancient DNA library amplification. |
| 2019 | Richards, S., Mitchell, K., Tobler, R., & Cooper, A. (2019). Recombinase Polymerase Amplification (RPA) versus PCR for ancient DNA library amplification. Europe PMC1 |
| 2019 | Barghi, N., Tobler, R., Nolte, V., Jakšić, A. M., Mallard, F., Otte, K. A., . . . Schlötterer, C. (2019). Genetic redundancy fuels polygenic adaptation in Drosophila. PLoS Biology, 17(2), 31 pages. Scopus185 WoS178 Europe PMC229 |
| 2018 | Kofler, R., Senti, K. -A., Nolte, V., Tobler, R., & Schlötterer, C. (2018). Molecular dissection of a natural transposable element invasion.. Genome research, 28(6), 824-835. Scopus54 WoS51 Europe PMC69 |
| 2018 | Mallard, F., Nolte, V., Tobler, R., Kapun, M., & Schlötterer, C. (2018). A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila. Genome Biology, 19(1), 119-1-119-15. Scopus73 WoS74 Europe PMC77 |
| 2018 | Rohrlach, A. B., Bean, N., Glonek, G., Holland, B., Tobler, R., Tuke, J., & Cooper, A. (2018). Unsupervized Quantification of Demographic Structure for Single-copy Alignments. |
| 2018 | Barghi, N., Tobler, R., Nolte, V., Jaksic, A. M., Mallard, F., Otte, K. A., . . . Schlöetterer, C. (2018). Polygenic adaptation fuels genetic redundancy in<i>Drosophila</i>. |
| 2017 | Mallard, F., Nolte, V., Tobler, R., Kapun, M., & Schlötterer, C. (2017). A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila. Europe PMC1 |
| 2017 | Tobler, R., Rohrlach, A., Soubrier, J., Bover Arbos, P., Llamas, B., Tuke, J., . . . Cooper, A. (2017). Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia. Nature, 544(7649), 180-184. Scopus169 WoS156 Europe PMC69 |
| 2017 | Barghi, N., Tobler, R., Nolte, V., & Schlötterer, C. (2017). Drosophila simulans: a species with improved resolution in evolve and resequence studies. G3: Genes, Genomes, Genetics, 7(7), 2337-2343. Scopus22 WoS21 Europe PMC20 |
| 2017 | Tobler, R., Nolte, V., & Schlötterer, C. (2017). High rate of translocation-based gene birth on the Drosophila Y chromosome. Proceedings of the National Academy of Sciences of the United States of America, 114(44), 11721-11726. Scopus34 WoS34 Europe PMC34 |
| 2016 | Schlötterer, C., Kofler, R., Versace, E., Tobler, R., & Franssen, S. U. (2016). Erratum: Combining experimental evolution with next-generation sequencing: A powerful tool to study adaptation from standing genetic variation (Heredity (2015) 114 (431-440)). Heredity, 116(2), 248. Scopus6 WoS7 Europe PMC11 |
| 2016 | Bergland, A. O., Tobler, R., González, J., Schmidt, P., & Petrov, D. (2016). Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster. Molecular Ecology, 25(5), 1157-1174. Scopus102 WoS103 Europe PMC128 |
| 2016 | Nouhaud, P., Tobler, R., Nolte, V., & Schlötterer, C. (2016). Ancestral population reconstitution from isofemale lines as a tool for experimental evolution. Ecology and Evolution, 6(20), 7169-7175. Scopus20 WoS20 Europe PMC24 |
| 2015 | Franssen, S. U., Nolte, V., Tobler, R., & Schlötterer, C. (2015). Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations.. Molecular biology and evolution, 32(2), 495-509. Scopus65 WoS67 Europe PMC76 |
| 2015 | Tobler, R., Hermisson, J., & Schlötterer, C. (2015). Parallel trait adaptation across opposing thermal environments in experimental Drosophila melanogaster populations.. Evolution; international journal of organic evolution, 69(7), 1745-1759. Scopus32 WoS32 Europe PMC28 |
| 2015 | Schlötterer, C., Kofler, R., Versace, E., Tobler, R., & Franssen, S. (2015). Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. Heredity, 114(5), 431-440. Scopus198 WoS199 Europe PMC199 |
| 2014 | Schlötterer, C., Tobler, R., Kofler, R., & Nolte, V. (2014). Sequencing pools of individuals - mining genome-wide polymorphism data without big funding.. Nature reviews. Genetics, 15(11), 749-763. Scopus558 WoS544 Europe PMC527 |
| 2014 | Tobler, R., Franssen, S. U., Kofler, R., Orozco-Terwengel, P., Nolte, V., Hermisson, J., & Schlötterer, C. (2014). Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments.. Molecular biology and evolution, 31(2), 364-375. Scopus111 WoS110 Europe PMC116 |
| 2014 | Versace, E., Nolte, V., Pandey, R. V., Tobler, R., & Schlötterer, C. (2014). Experimental evolution reveals habitat-specific fitness dynamics among Wolbachia clades in Drosophila melanogaster.. Molecular ecology, 23(4), 802-814. Scopus34 WoS33 Europe PMC32 |
| 2014 | Bergland, A., Tobler, R., Gonzalez, J., Schmidt, P., & Petrov, D. (2014). Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster. Europe PMC3 |
| 2013 | Bastide, H., Betancourt, A., Nolte, V., Tobler, R., Stöbe, P., Futschik, A., & Schlötterer, C. (2013). A Genome-Wide, Fine-Scale Map of Natural Pigmentation Variation in Drosophila melanogaster. Plos Genetics, 9(6), 8 pages. Scopus122 WoS115 Europe PMC127 |
| 2010 | Tobler, R., Pledger, S., & Linklater, W. (2010). No evidence for ovarian synchrony or asynchrony in hamadryas baboons. Animal Behaviour, 80(5), 829-837. Scopus9 WoS8 |
| Year | Citation |
|---|---|
| 2025 | Bowern, C., Llamas, B., Miceli, L., Tobler, R., & Veth, P. (2025). AUSTRALIAN ARCHAEOLINGUISTICS. In Oxford Handbook of Archaeology and Language (pp. 518-539). Oxford University Press. DOI Scopus1 |
| Year | Citation |
|---|---|
| 2021 | Souilmi, Y., Lauterbur, E., Tobler, R., Huber, C., Johar, A. S., & Enard, D. (2021). An ancient coronavirus-like epidemic 25,000 years in ancestral populations from East Asia. Poster session presented at the meeting of AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY. WILEY. |
| Year | Citation |
|---|---|
| 2024 | Purnomo, G., Kealy, S., O’Connor, S., Schapper, A., Shaw, B., Llamas, B., . . . Tobler, R. (2024). The genetic origins and impacts of historical Papuan migrations into Wallacea. DOI |
| 2024 | Purnomo, G., Teixeira, J., Sudoyo, H., Llamas, B., & Tobler, R. (2024). Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context. DOI |
| 2024 | Roca-Rada, X., Davidson, R., Williams, M., Ravishankar, S., Collen, E., Haarkötter, C., . . . Teixeira, J. (2024). The genetic history of Portugal over the past 5,000 years. DOI |
| 2024 | Williams, A., Tobler, R., Griffiths, B., Ulm, S., Nitschke, M., Bird, M., . . . Bradshaw, C. (2024). Large size of the Australian Indigenous population prior to its massive decline following European invasion. DOI |
| Date | Role | Research Topic | Program | Degree Type | Student Load | Student Name |
|---|---|---|---|---|---|---|
| 2024 | Co-Supervisor | Genetic Continuity and Population Dynamics in Eastern Indonesia | Doctor of Philosophy | Doctorate | Full Time | Mr Leonard . |
| 2024 | Co-Supervisor | Genetic Continuity and Population Dynamics in Eastern Indonesia | - | Doctorate | Full Time | Mr Leonard . |
| Date | Role | Research Topic | Program | Degree Type | Student Load | Student Name |
|---|---|---|---|---|---|---|
| 2021 - 2022 | Co-Supervisor | Advances in Genomic Data Compression | Doctor of Philosophy | Doctorate | Full Time | Mr Divon Mordechai Lan |
| 2021 - 2024 | Co-Supervisor | Fluctuating Selection and its Effects on Neutral Genetic Variation | Doctor of Philosophy | Doctorate | Full Time | Miss Olivia Lenore Johnson |
| 2018 - 2022 | Co-Supervisor | Quantifying and Reducing Biases in Paleogenomic Research | Doctor of Philosophy | Doctorate | Full Time | Mr Adrien Oliva |
| 2018 - 2022 | Co-Supervisor | Reconstructing the Population History of Wallacea and Sahul | Doctor of Philosophy | Doctorate | Full Time | Dr Gludhug Ariyo Purnomo |
| 2017 - 2022 | Co-Supervisor | Exploring the Genetic History of the Ancient Near East through the Bronze and Iron Ages |
Doctor of Philosophy | Doctorate | Full Time | Mr Matthew Peter Williams |