Today’s big anthropological headline is based upon this brand new open access PLoS One paper, “Evidence of Authentic DNA from Danish Viking Age Skeletons Untouched by Humans for 1,000 Years.” The paper is written well, has lots of controls, and establishes some protocols on how to recovery ancient DNA. Despite these good things, I think I have found some minor holes in this paper, which I’ll address in this blog post.
The above photo is of the excavation of the skeletal remains sampled in this current study. The remains come from the Gladegil burial site near Otterup, Denmark. Gladegil has yielded 3 males, 4 females, and 3 other individuals whose sex can’t be determined. Carbon-14 dating has revealed that the site is approximately 1,000 years old and is a Christian burial site. As you can see the excavators are in sterile bunny-suits, worn to prevent contamination of modern DNA during the exhuming process. I wonder if this new image of archaeologist will replace the dusty-rugged Indiana Jones type-caricature?
The authors of this paper extracted only mtDNA only from the teeth and associated artifacts, so the title of this paper is misleading, it should have been rewritten “Evidence of Authentic mtDNA…” You may not see this as a significant issue, but I think it is. Other researchers and editors have made sure titles are as accurate as possible, so why then did this one get the green light? While mtDNA is DNA, mtDNA is different from nuclear DNA. First of, there are a lot more copies of the mitochondrial genome compared to the nuclear genome, that’s because cells have one nucleus (for the most part) but many mitochondrion. The mitochondrial genome is much smaller and also is a completely different entity from the nuclear one. It is circular, whereas the nuclear genome is linear. Lastly, the nuclear genome is less stable and that makes extracting and sequencing it from any sample, ancient or not, a much more challenging task.
Anyways, mtDNA was isolated in a clean room by grinding the teeth and what not into a pulp. The highest quality reagents and kits were used, according to the authors. Another misleading aspect of this study is that the entire mtDNA genome was not sequenced, only a portion of the genome, the hyper-variable region 1 (HVR-1) was amplified by quantitative PCR. The HVR-1 is a pretty informative region of the mitochondrial genome, some haplogroups can be identified but it is by no means a high-resolution indicator. If the authors extracted the HVR-2, a region with a lot more haplogroups, the analysis woulda been much more thorough.
I didn’t find any discussion on how the samples were sequenced. Given that the HVR-1 is small, roughly 560 base pairs, I’m thinking a standard dideoxy chain terminated method was used. I guess it is so common nowadays that people don’t even write it in their preliminary publication. I didn’t check the supporting materials. The HVR-1 sequences from the skeletal were aligned based upon known Inuit mtDNA.
The DNA of everyone who was involved with the excavation, extraction, sequencing was also sequenced, to screen for any possible contamination. I give the team kudos for including that in their study. It is critical for anyone doing ancient DNA work, also forensic DNA work, to not only keep track of everyone that handled the samples but also include their DNA in the sequence analysis.
Based upon the haplogroup distribution, the samples were attributed to be of Viking ancestry. To clarify, the presence of haplogroup I and G6 have also been seen relatively higher frequencies in other Viking populations. Hg I is not observed in any ancient Italian, Spanish, British, and central European populations. Again, if HVR-2 was included, this woulda been a more robust association of ancestry…
In general this was a graceful little paper. But after reading it, I don’t see what and where the big umph of this paper is to warrant so much play in the press. There have been much more challenging successes in ancient DNA work that didn’t get as much attention as this paper has gotten. And like I said, it is ultimately a report of an isolation and sequence comparison of only 500 base pairs… which is much easier to do than a nuclear one. I’d like to have seen at least the HVR-2, that woulda given me more of a meal-deal. Perhaps more will be done is a good template for ancient DNA work? At the very least it is an effective template for how to excavated ancient-but-recent DNA and what controls to include in the analysis.
- Melchior, L., Kivisild, T., Lynnerup, N., Dissing, J., Ahmed, N. (2008). Evidence of Authentic DNA from Danish Viking Age Skeletons Untouched by Humans for 1,000 Years. PLoS ONE, 3(5), e2214. DOI: 10.1371/journal.pone.0002214