A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA

Background After three decades of research aimed at recovering DNA from preserved remains, the field of ancient DNA is moving rapidly toward the sequencing and analysis of complete paleogenomes. These data provide a means to better understand evolutionary processes through time, including inference of ancient demography and admixture between lineages, as well as adaptive evolution within populations. The increasing scope of paleogenomics. The proportion of sequence reads that are mappable to a reference genome decreases rapidly with evolutionary distance (blue bars). Recent divergence from a living species is therefore key to successful paleogenomic assembly. Fortunately, most species are diverged from a living relative by <50 million years, so it should in principle be possible to generate paleogenomes for a wide taxonomic variety of organisms. Ma, millions of years ago. Advances Key advances enabling a paleogenomic perspective include improvements in DNA extraction and library preparation, as well as methods to enrich ancient libraries for targeted loci. These methods have made it possible to isolate ancient DNA from a far wider range of preservation environments than has been assumed to be attainable, including extending the temporal reach of ancient DNA back to nearly 1 million years. Outlook Although relatively few paleogenomes have been published to date, their number is rising rapidly, and it is increasingly clear that the range of specimens from which paleogenomes could be produced is much larger than has been assumed previously. As more data become available, including genomic data from living organisms, the capacity to use paleogenomic data to infer evolutionary change through time will continue to expand, particularly with respect to the evolution of populations and the link between genotype and phenotype. The Present of the Past A major goal of evolutionary biology is to understand the process of speciation and the changes that have accompanied and shaped the current distribution of species. Paleogenomics directly addresses these questions through the use of ancient DNA. Shapiro and Hofreiter (10.1126/science.1236573) review the origins and growth of this field and explain how challenges owing to the limited amount of DNA available for analysis and the possibility of contamination by modern material have been overcome. The publication of partial and complete paleogenomes within the last few years has reinvigorated research in ancient DNA. No longer limited to short fragments of mitochondrial DNA, inference of evolutionary processes through time can now be investigated from genome-wide data sampled as far back as 700,000 years. Tremendous insights have been made, in particular regarding the hominin lineage. With rare exception, however, a paleogenomic perspective has been mired by the quality and quantity of recoverable DNA. Though conceptually simple, extracting ancient DNA remains challenging, and sequencing ancient genomes to high coverage remains prohibitively expensive for most laboratories. Still, with improvements in DNA isolation and declining sequencing costs, the taxonomic and geographic purview of paleogenomics is expanding at a rapid pace. With improved capacity to screen large numbers of samples for those with high proportions of endogenous ancient DNA, paleogenomics is poised to become a key technology to better understand recent evolutionary events.