Australian Centre for Ancient DNA (ACAD)

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https://hdl.handle.net/2440/74194

The Australian Centre for Ancient DNA (ACAD) is one of the leading ancient DNA centres in the world. Established in 2005, it has an international reputation for highly-innovative research and a trans-disciplinary focus. Growing programs include research into Forensics, Genomics, 3rd Generation Sequencing, Human Evolution and Megafaunal Extinctions. ACAD’s key interests include molecular studies of population genetics, paleoenvironments, phylogeny, phylogeopraphy, molecular clocks, and the application of DNA sequences deposited through time.

Interested PhD students should visit the website for possible projects and full contact information http://www.adelaide.edu.au/acad/

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Browsing Australian Centre for Ancient DNA (ACAD) by Author "Adler, C."

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    Ancient DNA from European early Neolithic farmers reveals their near eastern affinities
    (Public Library of Science, 2010) Haak, W.; Balanovsky, O.; Sanchez, J.; Koshel, S.; Zaporozhchenko, V.; Adler, C.; Dersarkissian, C.; Brandt, G.; Schwarz, C.; Nicklisch, N.; Dresely, V.; Fritsch, B.; Balanovska, E.; Villems, R.; Meller, H.; Alt, K.; Cooper, A.; Penny, D.; Genographic Consortium
    In Europe, the Neolithic transition (8,000–4,000 B.C.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 B.C.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500–4,900 calibrated B.C.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500–4,900 calibrated B.C.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major genetic input from this area during the advent of farming in Europe. However, the LBK population also showed unique genetic features including a clearly distinct distribution of mitochondrial haplogroup frequencies, confirming that major demographic events continued to take place in Europe after the early Neolithic.
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    Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans
    (Nature Publishing Group, 2013) Brotherton, P.; Haak, W.; Templeton, J.; Soubrier, J.; Adler, C.; Richards, S.; Dersarkissian, C.; Cooper, A.
    Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this 'real-time' genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.
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    Parallel evolution of genes and languages in the Caucasus region
    (Oxford Univ Press, 2011) Balanovsky, O.; Haak, W.; Adler, C.; Cooper, A.; Dersarkissian, C.
    We analyzed 40 single nucleotide polymorphism and 19 short tandem repeat Y-chromosomal markers in a large sample of 1,525 indigenous individuals from 14 populations in the Caucasus and 254 additional individuals representing potential source populations. We also employed a lexicostatistical approach to reconstruct the history of the languages of the North Caucasian family spoken by the Caucasus populations. We found a different major haplogroup to be prevalent in each of four sets of populations that occupy distinct geographic regions and belong to different linguistic branches. The haplogroup frequencies correlated with geography and, even more strongly, with language. Within haplogroups, a number of haplotype clusters were shown to be specific to individual populations and languages. The data suggested a direct origin of Caucasus male lineages from the Near East, followed by high levels of isolation, differentiation, and genetic drift in situ. Comparison of genetic and linguistic reconstructions covering the last few millennia showed striking correspondences between the topology and dates of the respective gene and language trees and with documented historical events. Overall, in the Caucasus region, unmatched levels of gene–language coevolution occurred within geographically isolated populations, probably due to its mountainous terrain.
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    Survival and recovery of DNA from ancient teeth and bones
    (Academic Press Ltd, 2011) Adler, C.; Haak, W.; Donlon, D.; Cooper, A.; Dersarkissian, C.; Australian Centre for Ancient DNA
    The recovery of genetic material from preserved hard skeletal remains is an essential part of ancient DNA, archaeological and forensic research. However, there is little understanding about the relative concentrations of DNA within different tissues, the impact of sampling methods on extracted DNA, or the role of environmentally-determined degradation rates on DNA survival in specimens. We examine these issues by characterizing the mitochondrial DNA (mtDNA) content of different hard and soft tissues in 42 ancient human and bovid specimens at a range of fragment lengths (77-235 bp) using real-time PCR. Remarkably, the standard drill speeds used to sample skeletal material (c. 1000 RPM) were found to decrease mtDNA yields up to 30 times (by 3.1 × 105 mtDNA copies on average) compared to pulverization in a bone mill. This dramatic negative impact appears to relate to heat damage, and disappeared at very low drill speeds (e.g. 100 RPM). Consequently, many ancient DNA and forensic studies may have obtained false negative results, especially from important specimens which are commonly sampled with drills to minimize signs of damage. The mtDNA content of tooth cementum was found to be five times higher than the commonly used dentine (141 bp, p = 0.01), making the cementum-rich root tip the best sample for ancient human material. Lastly, mtDNA was found to display a consistent pattern of exponential fragmentation across many depositional environments, with different rates for geographic areas and tissue types, improving the ability to predict and understand DNA survival in preserved specimens. © 2010.