Biology Faculty Articles
Title
Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments
Document Type
Article
Publication Date
8-14-2018
Publication Title
American Journal of Physical Anthropology
Keywords
ancient DNA, DNA extraction, next-generation sequencing, skeletal remains, tropics
ISSN
0002-9483
Volume
166
First Page
824
Last Page
836
Abstract
Objectives
The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi‐tropical sites in Tanzania, Mexico, and Puerto Rico (N = 12).
Materials and Methods
All samples were extracted twice, built into double‐stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step.
Results
No significant difference was found in overall ancient DNA yields or post‐mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality‐filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments.
Discussion
Both methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.
NSUWorks Citation
Nieves-Colon, Maria A.; Andrew T. Ozga; William J. Pestle; Andrea Cucina; Vera Tiesler; Travis W. Stanton; and Anne C. Stone. 2018. "Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments." American Journal of Physical Anthropology 166, (): 824-836. doi:10.1002/ajpa.23472.
Supporting Information S1
ajpa23472-sup-0002-suppinfos2.xlsx (53 kB)
Supporting Information S2
ajpa23472-sup-0003-suppinfos3.pdf (1886 kB)
ORCID ID
0000-0003-4540-7106
ResearcherID
D-1147-2018
DOI
10.1002/ajpa.23472
