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Comparing the performance of three ancient DNA extraction methods for high‐throughput sequencing
Author(s) -
Gamba Cristina,
Hanghøj Kristian,
Gaunitz Charleen,
Alfarhan Ahmed H.,
Alquraishi Saleh A.,
AlRasheid Khaled A. S.,
Bradley DANIEL G.,
Orlando Ludovic
Publication year - 2016
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12470
Subject(s) - biology , ancient dna , shotgun sequencing , dna , dna sequencing , dna extraction , genome , massive parallel sequencing , computational biology , metagenomics , shotgun , evolutionary biology , genetics , gene , polymerase chain reaction , population , demography , sociology
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.