Abstract

The investigation of DNA preservation in archaeological human remains has opened up unprecedented opportunities for understanding the genetic history of our ancestors. This article explores the methods employed to preserve and extract DNA from ancient samples, along with the challenges and limitations encountered in the process. Various preservation techniques, such as cold storage and desiccation, are utilized to maximize DNA preservation. However, DNA degradation and contamination remain significant challenges. The extraction and analysis of ancient DNA involve specialized techniques such as PCR and whole-genome sequencing. The insights gained from ancient DNA analysis have revolutionized our understanding of migration patterns, genetic diversity, and the origins of specific traits. As technology advances, new methods offer the potential for even more detailed genetic information. Interdisciplinary collaborations and continued research hold promise for further unraveling the mysteries of our collective human history.

Keywords

DNA degradation; bone remains; ancient DNA; real-time qPCR; mitochondrial DNA; nuclear DNA

Introduction

Archaeology has long been a window into our ancient past, revealing the fascinating stories and lifestyles of those who came before us. Over the years, researchers have made incredible advancements in the field, revolutionizing our understanding of history. One such breakthrough is the ability to extract and analyze ancient DNA from archaeological human remains. Investigating DNA preservation in these ancient samples has opened up new avenues for exploring human evolution, migration patterns, and genetic diversity. In this article, we delve into the methods used to preserve and extract DNA from archaeological human remains, the challenges encountered, and the remarkable insights gained from this cutting-edge research.

he evolution of molecular genetic techniques has allowed the amplification in PCR and qPCR and also of degraded DNA; double-strand breaks and many other forms of DNA damage block the extension step of PCR, so as the damage increases and the size of amplifiable fragments will decrease; by determining the maximum amplifiable fragment size in different samples, a relative quantification of DNA degradation can be obtained. Considering degradation as a random event, in damaged samples, the amount of amplifiable fragments will decrease exponentially with increasing amplicon size, and the frequency of DNA damage can be estimated by determining the rate of decline. Furthermore, it is possible to evaluate the quality of the DNA through the quantitative ratios of fragments of different sizes.

Until now, nearly all genetic studies performed on ancient remains have targeted mitochondrial DNA genes. The mitochondrial genome is present in multiple copies in the cell and is inherited from the mother; consequently, mutations are transmitted clonally across generations and can be used to trace maternal lineages.

However, recent studies have shown that nuclear DNA seems less subject to degradation and damage over time, probably because nuclear DNA is better protected by proteins so it is possible to amplify longer strands.

Our study aims to establish an index of DNA damage useful for identifying samples that can potentially be amplified and sequenced, reducing failures and research costs. We considered a human mitochondrial gene, mitochondrially encoded 12s RNA, and a human nuclear gene, 18s ribosomal RNA, in order to evaluate the extent of the damage in the two DNAs. The design of the experiments carried out to study the degradation involved the construction of pairs of primers that would allow the amplification of fragments of increasing size on the same gene and similar in size between the two genes.

Preservation Methods

Preserving DNA in ancient human remains is a complex process that requires meticulous care and specialized techniques. Various factors affect DNA preservation, including the burial environment, temperature, humidity, and the presence of damaging enzymes. Researchers employ a combination of strategies to maximize DNA preservation, such as cold storage, desiccation, and the addition of preservatives like silica gel or ethanol. Additionally, proper excavation techniques and handling procedures are crucial to minimize contamination from modern DNA sources.

Challenges and Limitations

Despite advancements in DNA preservation techniques, the process is not without its challenges. DNA degradation is an inevitable process, and over time, DNA molecules break down into smaller fragments, making it more difficult to obtain complete genetic information. Environmental conditions, such as high temperatures and humidity, can accelerate degradation, leading to further challenges in DNA recovery. Contamination from external sources, including researchers, equipment, and bacterial or fungal DNA, is another significant concern that must be carefully addressed through strict laboratory protocols.

Extraction and Analysis

Once a sample is obtained from an archaeological human remain, the DNA extraction process begins. Several methods, including silica-based column purification, organic extraction, and enzymatic digestion, are employed to isolate DNA from the bone or tooth material. The extracted DNA is then subjected to various sequencing techniques, such as PCR (polymerase chain reaction) or whole-genome sequencing, to obtain genetic information.

Insights Gained

Studying ancient DNA has provided invaluable insights into human history. By comparing the genomes of ancient populations with present-day individuals, researchers can uncover migration patterns, genetic admixture events, and the origins of specific genetic traits. For example, ancient DNA analysis has shed light on the peopling of the Americas, revealing the complex interactions between indigenous populations and migrants from Asia. Similarly, DNA analysis of European remains has helped trace the spread of agriculture and the movements of ancient populations across the continent.

Future Directions

As technology continues to advance, so too does the field of ancient DNA research. New methods, such as single-cell sequencing and ultra-deep sequencing, hold promise for recovering even more detailed genetic information from ancient remains. Additionally, interdisciplinary collaborations with fields like anthropology, archaeology, and history will enhance our understanding of the genetic and cultural aspects of human populations throughout time.

Conclusion

Investigating DNA preservation in archaeological human remains has revolutionized our understanding of human history. Through careful preservation techniques, meticulous laboratory protocols, and advanced sequencing methods, scientists have unlocked fascinating insights into ancient populations and their interactions. The study of ancient DNA continues to provide a bridge between the past and the present, helping us trace our ancestral roots and unravel the mysteries of our collective human story.

References

1. Ammerman NT. (2007). Introduction: Observing Religious Modern lives.InEveryday religion: Observing modern religious lives.Edited by Ammerman, N. T. 3-18. Oxford: Oxford University Press.

Indexed at, Google Scholar, Crossref

2. Levitt P. (2008).Religion as a path to civic engagement.Ethnic and Racial Studies, 31(4), 766-791.

Indexed at, Google Scholar, Crossref

3. Ammerman NT. (2014).Finding religion in everyday Life. Sociology of Religion,75(2), 189-207.

Indexed at, Google Scholar, Crossref

4. Ammerman NT. (2020).Rethinking Religion: Toward a Practice Approach.The American Journal of Sociology, 126(1), 6-51.

Indexed at, Google Scholar, Crossref

5. Banderker, A. M. (n.d.).Animal Abuse and Welfare in Islam.

Google Scholar

6. Bardakoglu, A. (n.d.).Kopek Islam Ansiklopedisi.ISAM. Istanbul.

Indexed at, Google Scholar

7. Baysa, H. (2021).Ev ve Sus Hayvanu Edinma Saiklerinin Fikhi Acidan Tahlili.Islam Hukuku Arastirmalari Dergisi, 235-262.

Google Scholar

8. Bender, C. (2012). "Practicing Religion," In the Cambridge Companion to Religious Studies. Robert Orsi, (ed.).Cambridge University Press.

Google Scholar

9. Berglund, J. (2014).Princely Companion or Object of Offense? The Dog's Ambiguous Status in Islam.Society & Animals, 22(6), 545-559.

Indexed at, Google Scholar, Crossref

10. Buhârî, (1987),Muhammed b. İsmâîl Ebû Abdillâh, el-Câmiʿu’s-sahîh, Beyrut: Dâru İbn Kesîr,Hadith, 538.

Indexed at, Google Scholar