Daily Archives: December 7, 2016

Ancient DNA: the first three decades

Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19; 370(1660): 20130371.
doi: 10.1098/rstb.2013.0371
PMCID: PMC4275880

Erika Hagelberg,1 Michael Hofreiter,2,3 and Christine Keyser4

When Russell Higuchi, Allan Wilson and co-workers reported the molecular cloning of a small fragment of DNA from a piece of dry tissue of a quagga, an extinct member of the horse family [1], they could hardly imagine that 30 years later several hundred scientists would meet at The Royal Society in London1 to mark the anniversary of the event, and review the astonishing progress of the field of old DNA studies, including the sequencing of whole genomes of extinct megafauna and of our human ancestors. As Alec Jeffreys pointed out in a News and Views written to accompany the 1984 quagga article, his own attempts to recover DNA from a long-dead animal, in his case from preserved mammoth tissue, had not been hopeful: most of the DNA was from recent microbial contamination, and original, elephant-like sequences were present in tiny amounts, highly degraded and altered by post-mortem modifications. While Jeffreys admitted it was too early to give up trying, he argued that the prospects of combining molecular biology and palaeontology ‘into a grand evolutionary synthesis by studying fossil DNA, still look like nothing more than a glorious dream’ [2].

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Ancient DNA and human history

Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):6380-7. doi: 10.1073/pnas.1524306113. Epub 2016 Jun 6.
Slatkin M1, Racimo F2.

Abstract
We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history.

KEYWORDS: Denisovan; Neanderthal; ancient DNA; demography; human history

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Ancient DNA

Eske Willerslev and Alan Cooper*

Abstract
In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.

Keywords: ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair

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