Ancient human genomics: the methodology behind reconstructing evolutionary pathways

Stephanie Marciniak; Jennifer Klunk; Alison Devault; Jacob Enk; Hendrik N Poinar

doi:10.1016/j.jhevol.2014.11.003

Ancient human genomics: the methodology behind reconstructing evolutionary pathways

J Hum Evol. 2015 Feb:79:21-34. doi: 10.1016/j.jhevol.2014.11.003. Epub 2015 Jan 15.

Authors

Stephanie Marciniak¹, Jennifer Klunk², Alison Devault³, Jacob Enk⁴, Hendrik N Poinar⁵

Affiliations

¹ McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada. Electronic address: marcis@mcmaster.ca.
² 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.
³ McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; MYcroarray, Ann Arbor, MI, USA.
⁴ 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.
⁵ 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.

PMID: 25601038
DOI: 10.1016/j.jhevol.2014.11.003

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.

Keywords: Ancient DNA; High-throughput sequencing; Human evolution.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Anthropology, Physical
Biological Evolution*
DNA / analysis
DNA / genetics
Fossils*
Genomics*
High-Throughput Nucleotide Sequencing*
Hominidae / genetics*
Humans

Substances

DNA