Second-generation DNA sequencing technologies have propelled the modern genomics revolution
DNA capture methods has also boosted ancient genomics. These methods provide our researchers with the potential to measure rates of molecular change and to determine patterns of genomic change over evolutionary time.
This research group has a current focus on the genomic history of the First People of Australasia sensu, Australia, Papua New Guinea, and Aotearoa/New Zealand. We conduct this research in partnership with First Peoples and our long-term goal is to break down the dichotomy between researchers and Indigenous people.
University of Sunshine Coast member:
Dr Sankar Subramanian
Dr Richard O’Rorke, Dr Sally Wasef, Dr Alex Quinn
Ms Jo Wright, Ms Jennifer Leigh Campbell
Ancient DNA sequences from environmental samples
Griffith University has established a second Ancient DNA laboratory. This new facility is specifically aimed at the recovery of ancient DNA sequences from environmental samples such as soils, water, sedimentary cores, scats etc. To do this we will use Liquid Handling Robots to enable automated genome recovery from diverse environmental samples, without contamination risk, together with and a dedicated Illumina NextSeq DNA sequencer. For more than 100 years, environmental scientists have studied diverse organism/environment interactions using a variety of conceptual and technical tools. Recently, studies of ancient and historical DNA have come to complement these tools and to occupy a significant place in environmental studies conducted over serial time. The project will complement the existing Ancient DNA complex facility at Griffith University. The new facility will enable many researchers to have unprecedented access to an ancient DNA facility and a high level of technical support.
2018 Linkage Infrastructure, Equipment and Facilities, $384,671
Genomic library infrastructure for ancient environmental samples
This project aims to enable automated genome recovery from diverse environmental samples, without contamination risk. For more than 100 years, environmental scientists have studied diverse organism / environment interactions using a variety of conceptual and technical tools. Recently, studies of ancient and historical DNA have come to complement these tools and to occupy a significant place in environmental studies conducted over serial time. The project’s addition to the existing dual Ancient DNA complex facility at Griffith University will comprise two liquid handling workstations, each being housed in separate, self-contained, ancient DNA laboratories. The new facility will enable many researchers to have unprecedented access to an ancient DNA facility and a high level of technical support.
Collaborators: Professor David Lambert; Professor Zhihong Xu; Professor Jon Olley; Associate Professor Rebecca Ford; Associate Professor Adam Brumm; Dr Gilbert Price; Professor Leslie Christidis; Dr Subashchandran Sankarasubramanian; Professor Jizheng He
2016-2019 New Zealand Marsden Fund, $767,000 (NZ)
A genomic study of the people of Wairau Bar: Health, history and origins of the first New Zealanders
The settlement of Aotearoa/New Zealand was a result of the last great migration in human history. While Central Polynesia was settled ~1200-1000 BP and Hawaii ~1000 BP, Aotearoa/New Zealand was not settled until ~750 BP. The timing of settlement of Polynesia and Aotearoa/New Zealand has been a topic of much research in recent years. However, the details of the settlement process is still a matter of debate, and the specific island origins of the colonising canoes that landed in Aotearoa/New Zealand have yet to be identified. This project is aimed at complete genomic sequencing of the remains of the First New Zealanders from the Wairau Bar, one of New Zealand’s oldest and most important archaeological sites. We propose to then use these genome data to determine their relationships to other First Peoples from the Pacific and beyond.
Collaborators: Professor David Lambert, Professor Lisa Matisoo-Smith (University of Otago), Associate Professor Craig Millar (University of Auckland).
2015-2019 Australian Research Council, $570,000
Investigating Holocene India—Australia Connections using Ancient Genomics
A number of studies of human migration suggest that after initial colonisation of Australia around 45,000 years ago, these people remained largely isolated until the arrival of Europeans. In contrast, recent studies have suggested a wave of migration from India into Australia occurred approximately 4,230 years ago. However, a major drawback of these studies is that sequence data used was from modern Indigenous Australians who were potentially admixed with Europeans. To address this issue, we will sequence complete genomes from sub-fossils bones of ancient Indian and Australian people and directly investigate this possible India-Australia connection.
Collaborators: Professor David Lambert, Dr Sankar Subramanian, Professor Eske Willerslev (Cambridge and Copenhagen) Dr Kumarasamy Thangaraj (India), Dr Michael Westaway, Dr Ruiqiang Li (Novogene Bioinformatics Technology Pty. Ltd. Beijing).
2015-2018 Australian Research Council Discovery Project, $322,704
Ancient Ecology: Changes in penguin diet over ~30,000 years in Antarctica
The food web of the Antarctic Ocean is a textbook example of energy and nutrient cycling in the marine environment. Although we know a great deal about the current status of this food web, understanding how this complex set of predator-prey relationships have changed over long periods of time is vital to understanding the nature of the system itself. We propose the first direct study of ancient ecology using a combination of second-generation DNA sequencing and targeted gene recovery. We will track changes in the diet of Adélie penguins from serially preserved ancient faecal (guano) remains dating back ~30,000 years. These remains are known to contain microscopic remnants of penguin prey. This would be the first study of its kind.
Collaborators: Professor David Lambert, Professor Eske Willerslev (Cambridge and Copenhagen), Dr Craig Millar (University of Auckland), Professor Carlo Baroni (University of Piza, Italy), Dr Simon Jarman (Australian Antarctic Division).
2014-2017 Australian Research Council Linkage Project, $740,880
Establishing the provenance of Torres Strait Islander remains: genetics, craniometrics and isotopes
The repatriation of Aboriginal and Torres Strait Islander remains has been a focus of Commonwealth and state governments for more than two decades. It remains as a significant social and cultural issue for many Indigenous Australians. One of the main hurdles to repatriation is the fact that hundreds, and possibly thousands, of human remains have very little contextual detail associated with them. A number of techniques have been developed in the field of biological anthropology to reconstruct the history of individual skeletal remains. In this innovative project, we will use advances in the fields of ancient DNA, isotope analysis and craniometrics to resolve the provenance of 113 trophy skulls from the Torres Strait Islands.
Collaborators: Professor David Lambert, Dr Michael Westaway, Dr Duncan Wright (Australian National University), Professor Adrian Miller, Professor Brian Fry, Professor Mark Collard (University of Aberdeen and Simon Fraser University), Dr Sankar Subramanian (University of Sunshine Coast), Professor Eske Willerslev (Cambridge and Copenhagen) Dr Kumarasamy Thangaraj (India), Dr Ruiqiang Li (Novogene Bioinformatics Technology Pty. Ltd. Beijing).
- Subramanian, S. (2016) Europeans have a higher proportion of high-frequency deleterious variants than Africans. Human genetics 135, 1–7
- Malaspinas, A-S, Westaway, M.C… Heupink, T.H. … Subramanian, S., Wright J.L., …Lambert, D.M., Willerslev, E. 2016. The genomic history of Australia. Nature 538, pp. 27-214.
- Wasef, S., Wood, R., Ikram, S., Curtis, C., Holland, B., Willerslev, E., Millar, C., Lambert, D.M., 2015. Radiocarbon dating of Sacred Ibis mummies from ancient Egypt. Journal of Archaeological Science, Reports 4, 355–361.
- Heupink, T.H., Subramanian, S., Wright, J.L., Endicott, P., Westaway, M.C., Huynen, L., Parson, W., Millar, C.D., Willerslev, E., Lambert, D.M. 2015. Ancient mtDNA sequences from the First Australians revisited. Proceedings of the National Academy of Sciences USA 113(25), pp. 6892–6897.
- Seguin-Orlando,A., Korneliussen, T.S., Sikora,M., Malaspinas, A-S, Manica, A., Moltke, I., Albrechtsen, A., Ko, A., Margaryan, A., Moiseyev, V., Goebel, T., Westaway, M., Lambert, D.M., Khartanovich, V., Wall, J.D., Nigst,P.R., Foley,R.A., Lahr, M.M., Nielsen, R., Orlando,L., Willerslev E.. 2014. Genomic structure in Europeans dating back at least 36,200 years. Science 346, 1113-1118.
- Jarvis, E.D., …Subramanian, S.,…Lambert, D.M.,… et al. 2014. Whole Genome Analyses Resolve the Early Branches in the Tree of Life of Modern Birds. Science 346: 1320-1331.
- Rasmussen, M. … Lambert, D.M. … Willerslev. 2011. An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. Science 334: 94-98.
- Huynen, L., Gill, B., Millar, C.D. and Lambert, D.M. 2010. Ancient DNA reveals extreme egg morphology and nesting behaviour in New Zealand’s extinct moa. Proceedings of the National Academy of Sciences USA: 107 (37): 16201-16206.
- Baker, A.J., Huynen, L. Haddrath, O., Millar, C.D. and Lambert, D.M. 2005. Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: the giant moas of New Zealand. Proceedings of the National Academy of Sciences USA 102: 8257-8262.
- Shepherd, L.D., Millar, C.D. Ballard, G. Ainley, D.G., Wilson, P.R., Haynes, G.D., Baroni, C. and Lambert D.M. 2005. Microevolution and mega-icebergs in the Antarctic. Proceedings of the National Academy of Sciences. USA 102: 16717-16722.
- Huynen, C.D., Millar, C.D., Scofield, R.P. and Lambert, D.M. 2003. Nuclear DNA sequences detect species limits in ancient moa. Nature 425: 175-178.