Using Ancient DNA to Understand Evolutionary and Ecological Processes

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Abstract

Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of population genetics have revealed dynamic patterns of change in many large vertebrates, featuring localized extinctions, migrations, and population bottlenecks. The pronounced climate cycles of the Late Pleistocene have played a key role, reducing the taxonomic and genetic diversity of many taxa and shaping modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships in paleoecological systems. In the near future, genome-level surveys of ancient populations will play an increasingly important role in revealing, calibrating, and testing evolutionary processes.

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Kay Prüfer, Fernando Racimo, Nick Patterson … (2014)

We present a high-quality genome sequence of a Neandertal woman from Siberia. We show that her parents were related at the level of half siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neandertal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neandertals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high quality Neandertal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neandertals and Denisovans.

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Matthias Meyer, Martin Kircher, Marie-Theres Gansauge … (2012)

We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.

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Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

Martin Kircher, Susanna Sawyer, Matthias Meyer (2011)

Due to the increasing throughput of current DNA sequencing instruments, sample multiplexing is necessary for making economical use of available sequencing capacities. A widely used multiplexing strategy for the Illumina Genome Analyzer utilizes sample-specific indexes, which are embedded in one of the library adapters. However, this and similar multiplex approaches come with a risk of sample misidentification. By introducing indexes into both library adapters (double indexing), we have developed a method that reveals the rate of sample misidentification within current multiplex sequencing experiments. With ~0.3% these rates are orders of magnitude higher than expected and may severely confound applications in cancer genomics and other fields requiring accurate detection of rare variants. We identified the occurrence of mixed clusters on the flow as the predominant source of error. The accuracy of sample identification is further impaired if indexed oligonucleotides are cross-contaminated or if indexed libraries are amplified in bulk. Double-indexing eliminates these problems and increases both the scope and accuracy of multiplex sequencing on the Illumina platform.