Extracting the past : DNA from ancient aboriginal Australians
Creators: name: Adcock, Gregory John
Publisher: name: The Australian National University
Year: 1997
Subjects: subject: DNA, Fossil
subject: Human remains (Archaeology) Australia
subject: Human remains (Archaeology) Papua New Guinea
subject: Aboriginal Australians

description: DNA was extracted from the skeletal remains of ancient Australian and Papua New Guinean individuals. This DNA was amplified to obtain DNA sequences suitable for determining evolutionary relationships and an individual's sex. The methodology described included acquisition of specimens, DNA extraction, PCR amplification, contamination minimisation procedures and data analysis. A field project was undertaken to understand the requirements for getting permission to use Australian skeletal remains in ancient DNA studies. It was found the researcher must communicate with many groups including Aboriginal people and museum staff, and needs to be aware of their different needs. The extraction and amplification techniques were successful in producing amplified products from less than 0.5g of ancient bone in about 30% of PCR reactions, using primers that targeted the first mitochondrial hypervariable segment (HVS1). A lower rate of success was found for the single copy AMEL gene used for determining sex. Contamination was detected in 3% of HVS1 amplifications but did not prevent complete sequences of ancient HVS1 regions being obtained. The sequence variability together with controls allowed contaminant PCR products to be identified. In experiments designed to assign sex by band differences in PCR products, contamination levels were sufficient to prevent the determination of an individual's sex confidently. DNA was amplified from fifteen ancient individuals, dated from several hundred to more than 30,000 years before present, for 350bp of HVS1. The ancient individuals were from three sites; Kow Swamp (KS) in northern Victoria, the Willandra Lakes (WLH) in western New South Wales and Motupore Island (MOT) off the southeast coast of Papua New Guinea. Statistical tests and genetic distances calculated using a number of pair-wise differences, were used to show that the sequences obtained are unlikely to be derived from contaminating European DNA. The HVS1 data was used to analyse population groups of ancient individuals and phylogenies of the individual mitochondrial lineages. The Kow Swamp population was found to have high HVS1 sequence diversity, suggesting that it was part of a larger regional population. The variation pattern was equivocal concerning the debate over whether the robust morphology of the Kow Swamp people indicates that they derive from a separate migration to the gracile people of the same region. Some of the Kow Swamp lineages clustered together on phylogenetic trees but insufficient data existed to determine whether these lineage groups diversified within or outside Australia. The combined Willandra Lakes and Kow Swamp HVS1 lineages are more diverse than those from the modern population of the same region. Furthermore, some of these ancient lineages are unrelated to any others from a large world-wide data-set. From this, there appears to be many differences between ancient and modern groups that may be an indication that the modern data-base might not contain close relatives of ancient lineages, possibly the result of the recent Aboriginal population losses that followed European colonisation. The HVS1 lineage from WLH3, an individual who was alive possibly more than 30,000 years ago, was not different in any way that demonstrated its antiquity. The closest lineage related to it (WLH15) is from the same site and is of recent origin. In phylogenies the Motupore individuals clustered with one another in two groups and with some Asian and Papua New Guinea lineages in the modem data-set, but not with Polynesian types. They did not cluster with any well defined mitochondrial clans (ie they were not derived with respect to these clans). Since the Motupore individuals were alive 500-1000 years ago, the variation seen and that which is absent, could indicate the timing of arrival of populations carrying certain genotypes. Problems with interpreting HVS1 data and limitations of phylogenetic analyses were encountered. The phylogenetic method of network analysis gave the best results for describing mitochondrial lineage relationships. Future research would be most assisted by improvements in techniques, by more samples of both modern and ancient individuals, with improved control of contamination and by a greater knowledge of molecular genetic variation in modern regional populations so that phylogenetically informative variation can be targeted using PCR.