A rapid column‐based ancient DNA extraction method for increased sample throughput

Abstract

Genetic analyses using museum specimens and ancient DNA from fossil samples are becoming increasingly important in phylogenetic and especially population genetic studies. Recent progress in ancient DNA sequencing technologies has substantially increased DNA sequence yields and, in combination with barcoding methods, has enabled large-scale studies using any type of DNA. Moreover, more and more studies now use nuclear DNA sequences in addition to mitochondrial ones. Unfortunately, nuclear DNA is, due to its much lower copy number in living cells compared to mitochondrial DNA, much more difficult to obtain from low-quality samples. Therefore, a DNA extraction method that optimizes DNA yields from low-quality samples and at the same time allows processing many samples within a short time frame is immediately required. In fact, the major bottleneck in the analysis process using samples containing low amounts of degraded DNA now lies in the extraction of samples, as column-based methods using commercial kits are fast but have proven to give very low yields, while more efficient methods are generally very time-consuming. Here, we present a method that combines the high DNA yield of batch-based silica extraction with the time-efficiency of column-based methods. Our results on Pleistocene cave bear samples show that DNA yields are quantitatively comparable, and in fact even slightly better than with silica batch extraction, while at the same time the number of samples that can conveniently be processed in parallel increases and both bench time and costs decrease using this method. Thus, this method is suited for harvesting the power of high-throughput sequencing using the DNA preserved in the millions of paleontological and museums specimens.

Morphological and genetic evidence for early Holocene cattle management in northeastern China

“…We extracted DNA from two subsamples of the mandible (bone as well as tooth), using standard ancient DNA protocols 17 and precautions 18 . The extracts were built into Illumina sequencing libraries according to the protocol in ref.…”

“…We extracted DNA from one tooth and one bone sample, both obtained from drilling into the original specimen (York laboratory numbers 2458 and 2459, respectively), using a silica-based extraction protocol following ref. 17. All procedures were performed in a dedicated ancient DNA laboratory at the University of York, with appropriate contamination precautions in place 18 .…”

DNA capture reveals transoceanic gene flow in endangered river sharks

“…Glyphis siamensis (NMW 61379) is the holotype specimen, housed at the Naturhistorisches Museum (Vienna, Austria). DNA extraction for the museum samples was performed on dry tissue following an ancient DNA extraction protocol (32,33) regarding the museum and modern samples used in this study, including those derived from the type specimens, are listed in SI Appendix, Table S1. Extracted DNA samples were quantified using a Qubit 2.0 Fluorometer (Life Technologies Corporation).…”

Biotically constrained palaeoenvironmental conditions of a mid-Holocene intertidal lagoon on the southern shore of the Arabian Gulf: evidence associated with a whale skeleton at Musaffah, Abu Dhabi, UAE

“…Alongside with other samples and mock controls, DNA was isolated from the two samples in a clean laboratory dedicated exclusively for ancient DNA (aDNA) work. We used an ancient DNA extraction technique described earlier (Rohland et al, 2010). Samples were tested for DNA preservation in PCR reactions with two different primer pairs, which were specifically designed to amplify parts of the mitochondrial D-loop of grey whales and most other cetaceans (Table 3).…”