Improving access to endogenous DNA in ancient bones and teeth

Poor DNA preservation is the most limiting factor in ancient genomic research. In the majority of ancient bones and teeth, endogenous DNA molecules represent a minor fraction of the whole DNA extract, rendering shot-gun sequencing inefficient for obtaining genomic data. Based on ancient human bone samples from temperate and tropical environments, we show that an EDTA-based enzymatic ‘pre-digestion’ of powdered bone increases the proportion of endogenous DNA several fold. By performing the pre-digestion step between 30 min and 6 hours on five bones, we observe an asymptotic increase in endogenous DNA content, with a 2.7-fold average increase reached at 1 hour. We repeat the experiment using a brief pre-digestion (15 or 30 mins) on 21 ancient bones and teeth from a variety of archaeological contexts and observe an improvement in 16 of these. We here advocate the implementation of a brief pre-digestion step as a standard procedure in ancient DNA extractions. Finally, we demonstrate on 14 ancient teeth that by targeting the outer layer of the roots we obtain up to 14 times more endogenous DNA than when using the inner dentine. Our presented methods are likely to increase the proportion of ancient samples that are suitable for genome-scale characterization.Full Tex

The ancestry and affiliations of Kennewick Man

Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon dated to 8,340-9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans. In order to resolve Kennewick Man's ancestry and affiliations, we have sequenced his genome to ∼1× coverage and compared it to worldwide genomic data including for the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genome-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia

Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.

The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics

An Ancient DNA Study of Four Sympatric Species of Moa (Aves: Dinornithiformes) from Holocene Deposits in North Canterbury, South Island, New Zealand

Ancient DNA (aDNA) was isolated from the bones of 290 individuals and four species of extinct New Zealand moa. All sampled bones had been recovered from a small geographic area (~10 km radius) near Waikari in North Canterbury. A total of 217 specimens were 14C-AMS dated, providing a temporal framework for the genetic analyses and an unprecedented opportunity to study extinct megafauna at the population level. Taxon and sex were determined for each individual, using aDNA technology. This revealed a large excess of females (overall ♂:♀ = 1:5.1), and significant compositional differences for the moa assemblages between fossil sites. Balanced sex ratios were observed among juvenile moa, suggesting that a gender-bias developed as the birds matured, probably as a result of higher male mortality. Female territoriality and ecological niche-separation are discussed in this context. Mitochondrial DNA (mtDNA), amplified using a quantitative PCR procedure, provided a measure of DNA preservation in each radiocarbon-dated fossil. This assessment showed that DNA degrades over thousands of years according to an exponential decay model, and the average molecular half-life for the here targeted DNA fragment was estimated to be 521 years. By using high-throughput sequencing, six polymorphic moa microsatellite markers were identified and characterised. These are the first microsatellite primers developed exclusively for extinct taxa. A high-resolution genetic study of the four sympatric moa populations was carried out, combining information from mtDNA, microsatellites, sex-identification, and radiocarbon age. Genetic diversity, past demography, kinship, and other aspects of moa biology were analysed. The populations showed a remarkable extent of genetic stability throughout the 3000-4000 years preceding their extinction, suggesting that they were large and viable before suddenly disappearing. The results represent significant advances in aDNA research and thanks to the high resolution in microsatellite markers, moa have here been studied, almost as if they were still alive