Analysis of Ancient DNA in Microbial Ecology

Methods in Molecular Biology
Olivier GorgéThierry Grange

Abstract

The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains ...Continue Reading

Citations

May 17, 2019·Journal of Clinical Microbiology·Rebecca J Bennett, Kate S Baker
Sep 14, 2019·Science Advances·E Andrew BennettEva-Maria Geigl
Sep 28, 2017·Annals of Human Biology·Maria Jesus Alvarez-CuberoLuis Javier Martinez-Gonzalez
Oct 23, 2016·BMC Biology·Diyendo MassilaniEva-Maria Geigl
Apr 30, 2017·Science·Pablo LibradoLudovic Orlando
Jul 1, 2020·Microbial Genomics·Nicolas Arning, Daniel J Wilson
Apr 10, 2021·Nature Human Behaviour·William T T TaylorSvetlana Shnaider
Mar 17, 2020·Microbial Pathogenesis·Pamela AfoudaDidier Raoult

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