Ms Nihan Dilsad Dagtas1,2,3, Dr. Viviane Slon1,2,3
1Department of Anatomy and Anthropology, Tel Aviv University, Tel Aviv, Israel, 2Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel, 3The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
Biography:
Nihan Dagtas graduated from the Middle East Technical University’s Department of Biology in Ankara. Wanting to combine genetics and archaeology, she decided to pursue a career in archaeogenomics, focusing on the mitochondrial genetic diversity of ancient sheep in Anatolia for her master thesis. Following graduation, she continued working in the field of ancient DNA, as a graduate student and later as a research assistant at the University of Oklahoma. She contributed to various studies over the years, from extinct short-faced bears to Neolithic peoples of Anatolia, illuminating one mystery from the past at a time. Now, she is working towards a PhD degree at Tel Aviv University under Dr. Viviane Slon, with her dissertation revolving around the application of novel methods to sedimentary ancient DNA.
Abstract:
Ancient DNA fragments tend to be highly fragmented, making ancient DNA datasets particularly vulnerable to contamination by modern DNA introduced during sampling, handling or laboratory procedures. One notable characteristic that differentiates ancient from present-day DNA is the size of fragments, which tend to be far shorter in ancient DNA due to post-mortem degradation. This study explores the potential of leveraging semi-permeable capsule technology to conduct a size-based separation of DNA fragments prior to library preparation, as a decontamination procedure in ancient DNA research. The protocol was tested on 10 sediment samples and 12 skeletal remains, that differed spatiotemporally. Following either lysis or DNA extraction, semi-permeable capsules with a size cutoff of 100 base pairs were used to physically separate shorter from longer DNA fragments. DNA library preparation was followed by shallow shotgun sequencing, as well as by two rounds of targeted enrichment for either mammalian or human mitochondrial DNA (mtDNA) prior to sequencing, for sediment and skeletal remains, respectively. The procedure's performance was evaluated by analyzing fragment size distribution, percentage of mapped sequences, ancient DNA damage, and extent of present-day DNA contamination in the libraries. Results from our experiments were varied. While some skeletal remains showed a mild improvement in the recovery of short fragments following encapsulation, others exhibited higher contamination levels compared to controls that underwent standard extraction. In sediment samples, although the average size of identifiable mammalian mtDNA fragments was shorter after encapsulation, this did not result in the detection of additional ancient taxa. Pending future improvements to the protocol, given the extra handling steps and associated costs, we suggest reserving the encapsulation strategy for highly contaminated samples, where it may offer a valuable solution when other decontamination methods have been exhausted.