Implications of aDNA in Modern Archeology

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Implications of aDNA in Modern Archeology

Introduction

Archeological studies have witnessed a significant positive trend in developing scientifically-backed studies over the past decades. Some of the scientific archeological techniques include soil analysis, x-ray scanning, CT scanning, radio carbon dating, and ancient DNA. The ancient D.N.A. techniques of the biological relationship of the bones and teeth remain samples have contributed to the development and acceptance of archeological results. As indicated by Kistler et al., 2020, pg 613, the advent of aDNA analysis from dead tissues dates back to 1984. However, the gradual developments of the aDNA technologies, including the PCR evolution, aDNA preservation, aDNA fragmentation, and application of molecular genetics, have advanced the growth of aDNA in archeology.

Some of the examples where aDNA have been applied in archelogy include Tarim Mummies, Cheddar man and Kennewick man. Although the development in aDNA technologies could have positive implications in the current archeological interests, other negative implications, including the politicization of aDNA use, have arisen. In this regard, this paper illustrates the significant concerns surrounding aDNA, such as the challenge of preserving the aDNA and the possibility of contaminating aDNA data. The paper also delves into the statistical analysis of aDNA, the role of aDNA, and the implications of politicization of the aDNA results. Finally, the paper illustrates how aDNA relates to cultural archeological data.

Modern Scientific archeological Techniques

Over the last centuries, archeologists have continued to invent modern scientific archeological techniques that have characterized a shift from the old techniques. Compared to the historical tools of archeology, such as cultural identification of populations, modern scientific archeological techniques such as aDNA, soil analysis, lidar scanning, X-ray scanning, C.T. scanning, and radiocarbon dating could be a more effective tool for archeologists for identifying artifacts because they are scientifically backed. For example, since the soil analysis of the sediments of Kennewick man were not conclusive to provide radiocarbon dating of the specimen, the C.T. scans and careful analysis of the lithic object in the right pelvic were used to study it (McManamonn, 2018, pg.6). aDNA archeological technique is the most scientifically efficient methodology used by archeologists currently.

Definition of D.N.A.

D.N.A. refers to the molecule that carries the genetic characteristics of an individual, which are unique and cannot be changed.

Issues and Arguments Arising from the Use of D.N.A. in Archeology

Challenges of preserving aDNA

Ancient D.N.A. (aDNA) is one of the vital tools and techniques that archeologists utilize to do archeological works. However, one of the main issues surrounding the acceptability of aDNA is the challenge of preserving aDNA. The challenges associated with preserving and depositing aDNA data and biases resulting from PCR primers are significant issues with using aDNA (Balint et al. Pg 950, 2018). However, further research has established that aDNA preservation issues could be solved by making genome data more available. Also, the biases of PCR primers could be reduced through availing more data during metabarcoding.

Ethical Handling of Ancestral Remains for aDNA Research

Another concern of aDNA is the ethical handling of archeological research, especially regarding the handling of human remains. A significant number of molecular characteristics of aDNA could be lost through erosion since geographic and climatic conditions limit the preservation of D.N.A. samples for future use. Therefore, excavation of human remains is necessary to preserve the aDNA in labs. However, the Tarim Mummies are surprisingly preserved despite the extremely arid and cold climate of Tarim Basin (Peyrot, 2017, pg.17). The efforts to preserve the samples could be limited by the ethical issues involved in handling and excavating ancestral remains. Bioethicists and other indigenous scientists doing paleogenomics research should adhere to ethical handling of the ancestral remains (Bardil et al. 2018, pg1).

Consequently, archeologists should seek consent from the community when handling the human remains. Also, the sampling and destruction of humans remain to perform aDNA research should consider cultural, social, and political implications (Orlando et al. 2020, pg 6). Therefore, communication and conceptualization of the aDNA research should bring everyone on board to avoid conflicts.

Contamination of aDNA

Contamination of aDNA is a significant challenge that arises from handling the samples by contaminating with modern genomes D.N.A. According to, Nakatsuka, 2020, pg. 90, some samples might be contaminated due to non-compliance with the ethical standards for handling samples. Since contamination of aDNA has resulted in controversies surrounding the authenticity of the aDNA analysis results, modern technology has lessened the challenge. For instance, although the Egyptian mummies were in a degraded state and had a low copy of aDNA, NGS technology was used taxonomically to classify the remains (Gad et al. 2021, pg. 2). Further, Orlando et al. 2020, pg 7 indicate that handling aDNA should be done in a cleaner environment immediately after excavation to minimize contamination with modern D.N.A. by handling staff. However, to remedy the contamination challenges, archeologists have come up with methods of estimating contamination by modern nuclear D.N.A. in the specimen. One of the methods is the linkage disequilibrium method (L.D.) of estimating contamination. The technique suggests that if the sequences of the contaminating individuals are contained in the sample, the L.D. should be diminishing since the contaminant D.N.A. and authentic D.N.A. have different haplotypes (Nakatsuka, pg 90, 2020). The method could be challenging because the data of the contaminating individuals or the genotype data of the uncontaminated sample may not be available. Considering that contamination of the aDNA specimen samples could negatively affect the authenticity of the use of aDNA for archeological studies, the issue could reverse the acceptability of the technique in the modern archeological areas of interest.

Statistical analysis of aDNA

One of the applications of aDNA analysis in archeology is determining the possibility of kinship relationships between individuals. According to Vai et al., 2020, pg. 5, understanding past societies using aDNA data analysis and archeological data analysis to create a fine population structure showing kinship relationships requires the creation of a pedigree diagram.

Figure 1. Pedigree diagram showing the relationships of selected individuals and the inbreeding coefficients (Vai et al. pg 5, 2020)

Table 1: The relationships of selected individuals and the inbreeding coefficients (Vai et al. pg 5, 2020)

The K₀, K₁, and K₂ represent the probability of finding zero, one, or two alleles between individuals indicated in the diagram. For example, the probability of finding two similar alleles between identical twins is one compared to first cousins, which is zero. An example of applying aDNA genomic analysis to solve the kinship relationship disputes in archeology is the Egyptian mummies. The aDNA genomic relationship disputes between the Egyptians two brother mummies named Nakh-Ank and Khnum-Nakht in the 12^th century, which suggested they belonged to the same maternal relationship (Gad, 2021, pg. 3). Therefore, the implication of the aDNA analysis in determining the kinships relationship could increase the acceptability of using aDNA as a study tool for archeology.

Significant Roles of aDNA in Archeology

Ancient D.N.A. plays an essential role in archeological studies considering that the aDNA has gained popularity over time as an efficient tool of acquiring the archeological evidence of ancient specimens. First, the aDNA is utilized in identifying the archeological remains to analyze how diverse the remains’ genetics were and reconstruct their physical appearance. The aDNA genome-wide analysis on the Cheddar Man indicated similarities with the Mesolithic samples from Britain. On rebuilding physical appearance, it was concluded that it was dark-skinned, had dark hair, and had light eyes (Sointula, 2020, pg. 12). The reconstruction of the Cheddar Man using the aDNA analysis is shown below in figure 2

Figure 2: The reconstruction of the Cheddar Man using the aDNA (Sointula, 2020, pg. 12)

While determining the features of the human remains, it is necessary to carry out mutation analysis of the samples to determine the links to different genotype bases. For example, the haplotype mutation analysis done on Cheddar Man tested positive for the 6 SNPs using the adenine, guanine, thiamine, and cytosine (Debuele, 2020, pg. 23). The Cheddar aDNA reads of the 6 SNPs are shown in table 1 below, indicating ancestral negative and derived positive.

Table 2: Results of aDNA reads for the six SNPs of the I2a-L38 branch Cheddar Man Tested derived (+) (Debuele, 2020, pg. 23)

Key for the “letters” to the bases

• Guanine (G)

• Adenine (A)

• Thymine (T)

• Cytosine (C)

Also, aDNA could reveal the social, ecological, and environmental characteristics of the ancient people. According to Brunson and Reich, 2019, pg. 319, the ancient D.N.A. aids in understanding the human historical past by providing access to genomic data for thousands of years ago hence revealing ecological, social, and environmental human evolution patterns. Also, the aDNA analysis of the Tarim Mummies and comparison with the modern Central Asian and East Asian people suggest a relationship with the contemporary Sardinian while the later iron age samples from Northern Tarim are related with the Uighur and Kazak mtDNA samples. (Thompton and Schurr, 2004, pg. 94) In this case, aDNA analysis is used to link the archeological remains with cultural, political, and social relationships to show biological continuity.

Additionally, archeologists could use an aDNA analysis to establish the migration patterns of ancient populations. For instance, when the genetic materials were extracted from ancient skeletons in European archeological history, aDNA analysis revealed a break between the hunter-gatherers and Neolithic people when the results were compared with the present-day people (Frieman and Hofmann, 2019, pg. 533). An example is the aDNA sample analysis of archeological remains from Spain, England, France, and Hungary, as shown in Table 2. Below

Table 3: aDNA samples that are closest to Cheddar Man from an Autosomal perspective (Debeule, 2020, pg. 19)

The table above illustrates that the aDNA samples from the European regions of England, France, Spain, and Hungary have genetic proximity to Cheddar man suggesting the hunter-gatherers migrated to Northwestern Europe from Southeastern Europe 14,000 years ago (Debeule, 2020, pg. 19). Also, the genomic studies of the European samples and the focus on Y-chromosomes sequences suggested migrations of male individuals into Western Europe that coincided with the Yamaya culture (Hakenbeck, 2019, pg 6). However, using aDNA to offer migration in Europe has become a politically contested issue, with some disputing the idea for political issues

Implications of Politicization of aDNA for Archeologists

The use of aDNA as a tool for archeology research has attracted divergent views, including politicians, over the past years. The politicization of the issue could have far-reaching implications on modern archeological interests. The genetic reconstruction of the Kennewick Man as a Palaeoamerican has sparked political differences and repatriations and reburial of the human remains to ancient Americans after an aDNA analysis (Kakaliouras, 2019, pg. 84). For example, while ethnicity and genetics are different aspects, politicians have used archeological data for political interests to advance race arguments and ethnicity. The radical individuals may also utilize the genetic data and results to promote their political and personal plans (Wolinsky, 2019, pg 1). Thus, scientists should not acknowledge the usage of their data for radical reasons.

Although the aDNA has effectively destabilized the old notions and myths resulting from older archeological tools, the results have also been used for political reasons by people who interpret the aDNA data to suit their arguments. The Kennewick Man case is a crucial example where the genetic analysis results of the 9000-year-old remains of Kennewick attracted political debate, which enhanced recognition of tribal rights of native Americans through the use of human remains as tribe identical symbols (Rogers, 2019, pg. 2349) However, the results elicited controversy on whether the modern tribe could claim possession of the remains (Rogers, 2019, pg 2375). Additionally, the modern genomic results of aDNA have triggered political debates in Israel, of which Prime Minister Netanyahu weighed in on the issue. Netanyahu dismissed the aDNA findings that suggested that the bones found in a graveside in Askeleton indicated that the Philistines originated from the area 3,000 years ago Wolinsky 2019. Pg. 2). Considering that the Israeli politicization of the aDNA findings where the Philistines used the results to claim the land ownership and Netanyahu’s dismissal of the results, the implications of aDNA on archeologists include discrediting the archeological findings for political reasons. The age of the bones was one of the contentious issues in the disputed aDNA analysis results. The aDNA analysis suggest that the ages of the specimen have a direct correlation with the number of different NCPs and the climate where the samples from the colder site showed the highest complexity found in the specimen (Wadsworth, 2017, pg. 3), as shown in figure 3 below

Figure 3. Number of NCP’s identified versus the Asx DL ratio in the 69 bone samples (Wadsworth, 2017, pg. 4)

The triangular shapes represent teeth specimens, while circular shapes are bone samples. The colors represented are; green = Lerna, black = El Portalón, red = Asine, blue = Saxony. Also, the variation in the complexity of proteome is noted across different archeological locations (Wadsworth, 2017, pg. 3), as shown below in fig 4

From the figure above, the 69 samples of proteome matched are specific to the archeological sites and degradation levels.

Archeological Relationship between Biological and Cultural Identity

Archeological studies utilize diverse biological and cultural tools to identify and arrive at conclusive and verifiable findings. Therefore, understanding the archeological relationship between biological and cultural identity is vital for palaeogeneticists and archeologists. Considering those cultural archeological techniques and aDNA tools are distinct, conflict could arise on the acceptability of either of the two. Therefore nature-culture binary opposition is a significant issue as aDNA is taken as nature (Crellin and Harris, 2020 pg 37). For instance, while aDNA is dependent on scientific genetic analysis that reveals sequences such as the sex of the remains and ancestry relationships, cultural tools only create simple identities of past populations. Thus, the archeologists’ implications of the use of D.N.A. for areas of interest such as determining the sex of the specimen could be made more accessible by studying the genomes of the specimen using the aDNA.

Although D.N.A. and cultural archeology have conflicting opinions, there are areas where the two are linked together. First, aDNA depends on cultural archeology in aspects such as genetic clustering. Eisenmann et al. 2018, Pg 9 indicate that modern genetic studies utilize archeological cultural designations to create genetic clusters and groups, especially the mixed naming systems. Besides using archeological cultural data in mixed systems of genetic clustering, aDNA helps develop and identify cultural relationships. The ancient D.N.A. focuses on understanding human culture using biological means to dig into the history of humans by analyzing human remains, specifically bones and teeth.

An example is the case study on how the recent aDNA illustrates the European massive migrations history of the third Millennium. While using the aDNA analysis, a sample in the central German suggested the cultural migration from the East as indicated by the genetic influx, which is connected to the Yamaya cultures (Fuholt, pg 162, 2018). However, using aDNA to link human populations with archeological cultures could create conflicts if people seek material proximity based on the results. For example, if used by different actors, the findings may result in changing aspects of social interactions (Fuholt, pg, 163, 2020). Therefore, the use of aDNA to justify cultural events may result in conflicting debates.

Conclusion

Archeological studies depend mainly on the aDNA studies of the ancient samples to achieve authentic and more conclusive results. The use of aDNA analysis for archeological studies has had positive implications on the acceptability and growth of archeology. Consequently, aDNA has been applied in archeology in areas such as establishing kinship relationships between individuals. Despite the positive impact of aDNA in archeology, the challenges such as contamination of aDNA samples by modern D.N.A. through handling and preservation challenges have characterized the slow acceptability of aDNA as an archeological tool. Also, the politicization of aDNA applications in archeology has had negative implications on aDNA development. Nonetheless, the aDNA research has helped the development of archeology in many ways, such as the application of genomic data in areas such as tracking migration patterns, cultural origins of the human beings, establishing kinship relationships and understanding cultural linkages.

References

Balint, M., Pfenninger, M., Grossart, H.P., Taberlet, P., Vellend, M., Leibold, M.A., Englund, G. and Bowler, D., 2018. Environmental D.N.A. time series in ecology. Trends in Ecology & Evolution, 33(12), pp.945-957.

Bardill J et al. 2018. Advancing the ethics of paleogenomics. Science, 360(6387): 384-5

Brunson, K. and Reich, D., 2019. The promise of paleogenomics beyond our species. Trends in Genetics, 35(5), pp.319-329.

Crellin, R.J. and Harris, O.J., 2020. Beyond binaries. Interrogating ancient D.N.A. Archaeological Dialogues, 27(1), pp.37-56.

DE BEULE, H.A.N.S., 2020. Cheddar Man a Y-Chromosomal Perspective.

Eisenmann, S., Bánffy, E., van Dommelen, P., Hofmann, K.P., Maran, J., Lazaridis, I., Mittnik, A., McCormick, M., Krause, J., Reich, D. and Stockhammer, P.W., 2018. Reconciling material cultures in archaeology with genetic data: The nomenclature of clusters emerging from archaeogenomic analysis. SCIentIfIC REpoRTS, 8, p.13003.

Frieman, C.J. and Hofmann, D., 2019. Present pasts in the archaeology of genetics, identity, and migration in Europe: a critical essay. World Archaeology, 51(4), pp.528-545.

Furholt, M., 2018. Massive migrations? The impact of recent aDNA studies on our view of third millennium Europe. European journal of archaeology, 21(2), pp.159-191.

Gad, Y.Z., Hassan, N.A.M., Mousa, D.M., Fouad, F.A., El-Sayed, S.G., Abdelazeem, M.A., Mahdy, S.M., Othman, H.Y., Ibrahim, D.W., Khairat, R. and Ismail, S., 2021. Insights from ancient D.N.A. analysis of Egyptian human mummies: clues to disease and kinship. Human Molecular Genetics, 30(R1), pp.R24-R28.

Hakenbeck, S.E., 2019. Genetics, archaeology and the far right: an unholy Trinity. World Archaeology, 51(4), pp.517-527.

Kakaliouras, A.M., 2019. The repatriation of the Palaeoamericans: Kennewick Man/The Ancient One and the end of a non-Indian ancient North America. B.J.H.S. Themes, 4, pp.79-98.

Kistler, L., Bieker, V.C., Martin, M.D., Pedersen, M.W., Ramos Madrigal, J. and Wales, N., 2020. Ancient plant genomics in archaeology, herbaria, and the environment. Annual review of plant biology, 71, pp.605-629.

McManamon, F.P., 2018. Kennewick Man Case: Tribal Consultation, Scientific Studies, and Legal Issues. Encyclopedia of Global Archaeology.

Nakatsuka, N., 2020. Estimating contamination in ancient nuclear D.N.A. using linkage disequilibrium. Integrating Ancient and Modern D.N.A. To Study Human History in South Asia and the Americas, p.90.

Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P.W., Ávila-Arcos, M.C., Fu, Q., Krause, J., Willerslev, E., Stone, A.C. and Warinner, C., 2021. Ancient D.N.A. analysis. Nature Reviews Methods Primers, 1(1), pp.1-26.

Peyrot, M., Kelder, J.M., de Jong, S.P.L. and Mouret, A., 2017. Tocharian: An Indo-European language from China. Aspects of globalisation. Mobility, exchange and the development of multi-cultural states, pp.12-17.

Rogers, A., 2019. Owning Geronimo but Not Elmer McCurdy: The Unique Property Status of Native American Remains. B.C.L. Rev., 60, p.2347.

Sointula, A., 2020. Ancient Human Reconstructions and aDNA: Is there an ethical dilemma?

Vai, S., Amorim, C.E.G., Lari, M. and Caramelli, D., 2020. Kinship determination in archeological contexts through D.N.A. analysis. Frontiers in Ecology and Evolution, 8, p.83.

Wadsworth, C., Procopio, N., Anderung, C., Carretero, J.M., Iriarte, E., Valdiosera, C., Elburg, R., Penkman, K. and Buckley, M., 2017. Comparing ancient D.N.A. survival and proteome content in 69 archaeological cattle tooth and bone samples from multiple European sites. Journal of proteomics, 158, pp.1-8.

Wolinsky, H., 2019. Ancient D.N.A. and contemporary politics: The analysis of ancient D.N.A. challenges long‐held beliefs about identity and history with potential for political abuse. E.M.B.O. reports 20(12), p.e49507.