title: Ancient human genomics: the methodology behind reconstructing evolutionary pathways.
abstract: High-throughput sequencing (HTS) has radically altered approaches to human evolutionary research. Recent contributions highlight that HTS is able to reach depths of the human lineage previously thought to be impossible. In this paper, we outline the methodological advances afforded by recent developments in DNA recovery, data output, scalability, speed, and resolution of the current sequencing technology. We review and critically evaluate the 'DNA pipeline' for ancient samples: from DNA extraction, to constructing immortalized sequence libraries, to enrichment strategies (e.g., polymerase chain reaction [PCR] and hybridization capture), and finally, to bioinformatic analyses of sequence data. We argue that continued evaluations and improvements to this process are essential to ensure sequence data validity. Also, we highlight the role of contamination and authentication in ancient DNA-HTS, which is particularly relevant to ancient human genomics, since sequencing the genomes of hominins such as Homo erectus and Homo heidelbergensis may soon be within the realm of possibility.
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada. Electronic address: marcis@mcmaster.ca.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Marciniak
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Klunk
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; MYcroarray, Ann Arbor, MI, USA.
authors.forename: Alison
authors.initials: A
authors.lastname: Devault
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada; MYcroarray, Ann Arbor, MI, USA.
authors.forename: Jacob
authors.initials: J
authors.lastname: Enk
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada. Electronic address: poinarh@mcmaster.ca.
authors.forename: Hendrik N
authors.initials: HN
authors.lastname: Poinar
mesh_terms: D000818:Animals; D000885:Anthropology, Physical; D005075:Biological Evolution; D004247:DNA / Q000032:analysis / Q000235:genetics; D005580:Fossils; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D015186:Hominidae / Q000235:genetics*; D006801:Humans
chemical_list: D004247:DNA
keywords: Ancient DNA; High-throughput sequencing; Human evolution