Ancient Biomolecules and Evolutionary Inference

Abstract

Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.

Advancing the understanding of treponemal disease in the past and present

“…Recently, the study of ancient proteins (i.e., paleoproteomics) and lipids has also been applied to questions about health and disease in ancient humans. Such analyses have been used previously to address a range of questions in paleontology and archaeology, and they have the advantage of often obtaining results in environments or time periods that are beyond DNA preservation (Cappellini et al, ). Most proteomic assessments of human pathogens have targeted the oral cavity.…”

Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

“…It has long been realized that performing archaeogenetics research correctly is extremely difficult [38,45,46,[48][49][50]. However, by the same token, during the last three decades the challenging nature of aDNA research has spurred significant technical innovation and rapid deployment of state-ofthe-art genomics and ancillary technologies [46,50,[88][89][90][91][92][93]. Undoubtedly, the most important scientific advance was the introduction of high-throughput sequencing (HTS) to archaeogenetics [94][95][96][97].…”

“…Currently, the dominant commercial HTS technology is based on massively parallel sequencingby-synthesis of relatively short DNA segments [100,101], which is ideally suited to fragmented aDNA molecules extracted from archaeological and museum specimens. In addition, the vast quantities of sequence data generated-literally hundreds of gigabases (Gb) from a single instrument run-can facilitate cost-effective analyses of archaeological specimens containing relatively modest amounts of endogenous aDNA (for technical reviews see [89][90][91][92][93]102]).…”

Toward a clearer view into human prehistory

“…It is worth reminding that the range of sequencing techniques (targeted SNP, whole genome capture and shotgun) differ in terms of required endogamous DNA preversation, costs, and scientific outputs (8). Likewise, different human tissues provide different DNA yields: sampling of the petrous bone has widened the geographical range of aDNA studies, but is of limited use for pathogens (9).…”