Microsat allele calls for D. robustus

Microsat allele calls for the extinct South Island giant moa (Dinornis robustus), genotyped in six microsatellite loci

Layer1_3_6_Shotgun_sequences

Layer1_3_6_Shotgun_sequence

Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum

<div><p>Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively) than parietal skull bone (average of 2.2%). Despite sample-to-sample variation, petrous bone overall performs better than tooth cementum (p = 0.001). This difference, however, is driven largely by a cluster of viking skeletons from one particular locality, showing relatively poor molecular tooth preservation (<10% endogenous DNA). In the remaining skeletons there is no systematic difference between the two substrates. A crude preservation (good/bad) applied to each sample prior to DNA-extraction predicted the above/below 10% endogenous DNA threshold in 80% of the cases. Interestingly, we observe signficantly higher levels of cytosine to thymine deamination damage and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to tooth cementum. Lastly, we show that petrous bones from ancient cremated individuals contain no measurable levels of authentic human DNA. Based on these findings we discuss the <i>pros</i> and <i>cons</i> of sampling the different elements.</p></div

Endogenous DNA content and visual preservation.

<p>A complete overview of the endogenous DNA content and the visual state of preservation (as defined in the method section) for each of the non-cremated samples. Sample names: T = tooth, P = petrous bone, S = parietal (skull) bone. WP, well-preserved. PP, poorly preserved.</p

Endogenous DNA content.

<p>Each data point represent the relationship between endogenous DNA content in tooth cementum and petrous bones from the same skeleton. Red datapoints represent skeletons in which visual tooth preservation was considered to be poor (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170940#pone.0170940.g001" target="_blank">Fig 1</a>).</p

Sample overview.

<p>An overview of the 34 sampled skeletons included in this study.</p

DNA sequence length peridiocity.

<p>A signal of 10 bp peridiocity in the length distribution of the human DNA sequences was generally observed more pronounced in the tooth cementum (A) compared to the petrous bone (B). Here this differential signal is shown for skeleton H1 as example. Such 10 bp peridiocity has been observed previously for ancient samples and is believed to reflect preferential cleavage of the DNA strand at positions where the DNA face away from the nucleosome [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170940#pone.0170940.ref042" target="_blank">42</a>].</p

Visual tooth preservation.

<p>Examples of poor and good tooth preservation as recorded from simple visual inspection during the sample processing. The upper (poor preservation) teeth display a root with a brittle and "chalky" appearance and the cementum layer is either fragmentary or completely gone. This in contrast to a thick, hard and compact cementum layer observed in the two lower teeth (good preservation).</p

Endogenous DNA content using tooth preservation as reference.

<p>Paired endogenous DNA contents in tooth cementum, petrous bone and parietal bone from the same skeleton, using molecular tooth preservation as condition. A) Poor molecular tooth preservation (<10% endogenous DNA), and B) Good molecular tooth preservation (>10% endogenous DNA) respectively.</p

Pacioni_etal_data

Data associated with Pacioni, C., Hunt, H., Allentoft, M.E., Vaughan, T.G., Wayne, A.F., Baynes, A., Haouchar, D., Dortch, J., Bunce, M., in press. Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial. Molecular Ecology. Please refer to ReadMe.txt (within the zipped folder) for additional information