title: Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing.
abstract: The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.
authors.forename: Cristina
authors.initials: C
authors.lastname: Gamba
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.
authors.forename: Kristian
authors.initials: K
authors.lastname: Hanghøj
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.
authors.forename: Charleen
authors.initials: C
authors.lastname: Gaunitz
authors.affiliation: Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
authors.forename: Ahmed H
authors.initials: AH
authors.lastname: Alfarhan
authors.affiliation: Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
authors.forename: Saleh A
authors.initials: SA
authors.lastname: Alquraishi
authors.affiliation: Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
authors.forename: Khaled A S
authors.initials: KA
authors.lastname: Al-Rasheid
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, College Green, Dublin 2, Ireland.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Bradley
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.|Université de Toulouse, CNRS UMR 5288, Université Paul Sabatier (UPS), 37 allées Jules Guesde, 31000, Toulouse, France.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
mesh_terms: D000413:Alaska; D001842:Bone and Bones; D004247:DNA / Q000302:isolation & purification*; D005580:Fossils; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008967:Molecular Biology / Q000379:methods*; D013020:South America
chemical_list: D004247:DNA
keywords: DNA extraction; ancient DNA; palaeogenomics; ultrashort fragments