Beth Shapiro, University of California, Santa Cruz
The scientific field of “ancient DNA” is now nearly three decades old. In this introductory talk, I will describe how the field has evolved over this time, focusing in particular on developments within the last five years. Thanks largely to the advent of next generation sequencing technologies and the consequent plummeting cost of generating DNA sequence data, the last several years has seen tremendous growth in both the range of fossil material from which DNA can be accessed and the scope of evolutionary questions that can be addressed using these data. The field now has not only a better understanding of how, where, and why ancient DNA is preserved, but better techniques for extracting DNA from fossil remains, for isolating target DNA sequences from within the extracted pool of host and environmental DNA, and for making sense of the recovered data using bioinformatics tools.
For many years, ancient DNA analyses were limited mainly to mitochondrial DNA sequences, as mitochondrial genomes are present in much higher numbers in preserved cells than are nuclear genomes and are therefore more likely to be preserved post-mortem than are targeted fragments within the nuclear genome. Despite this limitation, early ancient DNA research provided a variety of new evolutionary insights, including resolving evolutionary relationships between extinct and living species and correlating population size changes over time with climatic events such as ice ages.
With next generation sequencing, it is now feasible to assemble complete nuclear genomes from fossil material, termed “paleogenomes.” Unlike mitochondrial genomes, paleogenomes provide insights into the complete evolutionary history of extinct organisms, species and populations. It is now possible to understand not only that species or populations diverged from each other, but to ask questions about why they diverged, and what the evolutionary consequences of this divergence were. Paleogenomes have provided new and interesting insights into the evolutionary history of our own lineage. These analyses revealed, for example, that all humans with Eurasian ancestry have a small portion of their genomes that derives from admixture with Neandertals, and that the transition to farming in Europe involved the dispersal and admixture of at least three and possibly more groups of Archaic humans. Genome-scale data from species other than humans, including mammoth, horses, and cattle, are revealing the genomic changes that underlie evolutionary processes such as domestication, and raising questions about how genetic data from the past might be used as a tool to conserve living biodiversity.
Finally, in addition to enabling the assembly of paleogenomes, next-generation sequencing technologies have expanded the scope of ancient DNA research to organisms and substrates that were believed to be inaccessible, including microbial and viral pathogens. As technologies for isolating low-abundance DNA sequences continues to improve, this work will make it possible to trace the evolutionary dynamics of pathogens through time, with important potential implications for understanding and controlling infectious diseases in the present day.
Background Review Aritcle:
Shapiro B, Hofreiter M. A paleogenomic perspective on evolution and gene function: New insights from ancient DNA. Science 343: 1236573 (2014).