Raymond Tobler
School of Biological Sciences
Faculty of Sciences, Engineering and Technology
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).
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Appointments
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 -
Research Interests
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Journals
Year Citation 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.
Scopus12024 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.
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.
Scopus6 WoS1 Europe PMC52023 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.
Scopus6 Europe PMC42023 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.
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.
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.
Scopus10 WoS3 Europe PMC132021 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.
Scopus64 WoS48 Europe PMC132021 Lan, D., Tobler, R., Souilmi, Y., & Llamas, B. (2021). Genozip - a universal extensible genomic data compressor. Bioinformatics, 37(16), 2225-2230.
Scopus16 WoS5 Europe PMC72021 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.
Scopus26 WoS18 Europe PMC122021 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.
Scopus17 WoS7 Europe PMC52021 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.
Scopus51 WoS42 Europe PMC412021 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.
Scopus17 WoS12 Europe PMC72021 Oliva, A., Tobler, R., Llamas, B., & Souilmi, Y. (2021). BWA-mem is not the best aligner for ancient DNA short reads.
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.
Scopus8 WoS42021 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 PMC62021 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.
Scopus51 WoS32 Europe PMC202021 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 Europe PMC12021 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.
Scopus12021 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.
Scopus8 WoS1 Europe PMC62020 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.
Scopus10 WoS6 Europe PMC72020 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.
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.
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.
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.
Scopus142 WoS116 Europe PMC1002018 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.
Scopus42 WoS32 Europe PMC392018 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.
Scopus57 WoS51 Europe PMC432018 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>.
Europe PMC22017 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 PMC12017 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.
Scopus146 WoS121 Europe PMC442017 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.
Scopus17 WoS17 Europe PMC142017 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.
Scopus26 WoS22 Europe PMC212016 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.
Scopus4 WoS4 Europe PMC62016 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.
Scopus89 WoS82 Europe PMC732016 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.
Scopus18 WoS15 Europe PMC132015 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.
Scopus62 WoS62 Europe PMC532015 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.
Scopus29 WoS27 Europe PMC152015 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.
Scopus173 WoS165 Europe PMC1212014 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.
Scopus500 WoS456 Europe PMC3462014 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.
Scopus103 WoS101 Europe PMC782014 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.
Scopus32 WoS30 Europe PMC252014 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.
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.
Scopus113 WoS100 Europe PMC822010 Tobler, R., Pledger, S., & Linklater, W. (2010). No evidence for ovarian synchrony or asynchrony in hamadryas baboons. Animal Behaviour, 80(5), 829-837.
Scopus9 WoS7 -
Conference Items
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. -
Datasets
Year Citation - Tobler, R., Souilmi, Y., & Huber, C. (n.d.). Supplemental Dataset S57.
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Figures
Year Citation - Tobler, R., Huber, C., & Souilmi, Y. (n.d.). Supplementary data 58-114.
- Tobler, R., Huber, C., & Souilmi, Y. (n.d.). Supplementary data 1-57.
- Tobler, R., Souilmi, Y., & Huber, C. (n.d.). Supplemental Datasets S1-S56.
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Preprint
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.
2024 Purnomo, G., Teixeira, J., Sudoyo, H., Llamas, B., & Tobler, R. (2024). Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context.
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Current Higher Degree by Research Supervision (University of Adelaide)
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 . -
Past Higher Degree by Research Supervision (University of Adelaide)
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 Reconstructing the Population History of Wallacea and Sahul Doctor of Philosophy Doctorate Full Time Dr Gludhug Ariyo Purnomo 2018 - 2022 Co-Supervisor Quantifying and Reducing Biases in Paleogenomic Research Doctor of Philosophy Doctorate Full Time Mr Adrien Oliva 2017 - 2022 Co-Supervisor Exploring the Genetic History of the Ancient Near East through the Bronze
and Iron AgesDoctor of Philosophy Doctorate Full Time Mr Matthew Peter Williams
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