A Metagenomic Analysis of Ancient Sedimentary DNA Across the Pleistocene-Holocene Transition

Abstract

<p>Ancient DNA has the power to elucidate ecological and evolutionary relationships that were previously only quantifiable by proxy. This work details both a metagenetic and a targeted metagenomic study of ancient sedimentary DNA. By using DNA to investigate the plants and animals present in twelve different time points, we describe the nature of the ecological change over the Pleistocene-Holocene transition. We show that as the stability of the habitat degraded due to climate change, the dominant plant communities exhibited a shift from functional groups such as forbs to shrubs and trees. As this cascading change consequently affected the animal communities, we demonstrate the decline, extinction, and replacement of a variety of megafaunal species and mammoths. As well, we provide a proof-ofconcept for the targeted oligonucleotide enrichment for ancient sedimentary DNA. By processing the same DNA extracts with targeted enrichment, we show that metagenomic soil DNA can provide the same taxonomic fingerprint unique to each time period even using different genetic loci. This unique pattern can be used as a reference in future studies. Although the oligonucleotide baits did not yield the composition of taxa that we expected, the oligonucleotide baits did increase the eukaryotic fraction of DNA extracts by up to 50%. Overall, this technique is open to further study and has fantastic potential to redefine the metagenomic work of ancient DNA soil cores.</p>