Our history through the lens of ancient sedimentary DNA: adding color to the picture

The Power of Ancient DNA to Uncover Our History

How did we get here? Why are we the way we are?

Ancient DNA (aDNA) offers a window into our past, revealing pivotal moments that shaped our genetic landscape. Yet, traditional methods reliant on ancient skeletal remains only provide discrete data points that are few and far between, limiting our ability to gain a full perspective of our history. Pioneering the use of DNA from sediments, which are readily available at any archaeological site, presents an exciting opportunity to bridge these gaps and paint a comprehensive picture of human evolution, like switching from black & white photos to color.

To fully leverage these new opportunities, one must develop novel sophisticated approaches to recover and analyze sedimentary aDNA data. Our project rises to this challenge.

Our project aims to lay the groundwork for addressing key questions about human history and behavior through innovative approaches to sedimentary ancient DNA (aDNA) analysis.

1. Identity: By recovering and analyzing ancient human DNA from sediment samples, we can map the presence of past human groups across time and space, shedding light on their technical abilities, cultural practices, and social structures.

2. Community: Our methods will enable a detailed examination of ancient communities, including their organization, population size, and genetic diversity. This will provide insights into communal behavior and the dynamics of ancient societies.

3. Environment: Co-analyzing ancient human DNA with environmental DNA in sediment samples will help reconstruct the environments in which ancient groups lived and their interactions with natural resources. This can illuminate changes over time in human-environment interactions and their impact.

Through the advancement of sedimentary aDNA analysis, we aim to unravel significant historical events and their impact on human history and genetics. This innovative approach promises to enrich our understanding of the past and inform present-day research endeavors.

Challenges and Open Questions

While sediments offer an abundant source of genetic material, sedimentary ancient DNA datasets pose unique challenges. They contain a mixture of DNA from various organisms and individuals, and are often contaminated. We propose to develop this technology so that it can become ubiquitous in field research, which will bring about qualitative changes in our understanding of our history and of the process that have brought about our current gene pool. In particular, we propose to improve both the sample collection/preparation and the analytical workflow to enable robust and broad dissemination of this technology.

Additionally, current techniques analyze single data points without considering their context, potentially missing crucial information. We propose to develop a holistic approach to sedimentary ancient DNA analysis, leveraging the complementary strengths of the two PIs–expertise in aDNA data and in mathematical algorithms–who will work in synergy to come up with appropriate mathematical and algorithmic tools to analyze data recovered from sediments. Together, we envision an algorithm that would co-analyze all data originating from the same site through its various layers, with the outcome explaining the history of the groups who lived at that location. Moreover, we will develop strategies to improve the sample collection and preparation techniques, aiming to add as many data points as possible to this holistic analysis.

In summary, our goal is to make ancient sedimentary DNA analysis a standard practice in archaeological research, allowing for the tracking of human presence, populations, and behaviors over time. This innovative approach will enable new insights into our genetic past that are unattainable with existing methodologies, ultimately leading to exciting scientific discoveries.

Main Aims of This Project

1. Develop a novel, holistic, and comprehensive mathematical framework for the analysis of sedimentary ancient DNA–maximizing the usability of all extracted DNA fragments;

2. Propose innovative field sampling and laboratory techniques to improve the success rates of ancient DNA recovery from sediment samples, and improve the speed and efficiency of screening samples for aDNA;

3. Disseminate this approach as a standard, widely-used tool within the scientific community through a user-friendly, broadly-applicable, and reproducible laboratory and analytical pipeline, thereby taking the analysis of past populations based on sedimentary ancient DNA to the next level.

Overall, we envision that developments achieved here will transform sampling for sedimentary aDNA analyses into a ubiquitous tool in field archaeology, anthropology, evolutionary ecology, paleogenetics and other related disciplines.

Future Research Directions

Future work may also be channeled in other directions, which would require further developments in addition to the ones planned within the scope of this project - thereby addressing new types of questions.

1. Ancient Epigenetics: Our epigenome carries signatures of our interaction with the environment in ways that cannot be obtained from genetic data. Future research may explore ancient epigenetic signals in sediment samples, providing insights into the phenotype of ancient individuals and their interaction with the environment.

2. Evolution of Diseases: Leveraging sedimentary DNA to study the evolution of diseases could offer insights into genetic changes over time in disease agents and their impact on human communities. This could inform strategies for disease prevention and treatment.

Funding

This project was made possible through the support of grant 62571 from the John Templeton Foundation.

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