Tracing Indigenous American genomic history, subsistence strategies, health and their interplay through time using DNA from ancient masticated plant fibres

Project Information

QUIDS

Grant agreement ID: 101078151

DOI

10.3030/101078151

EC signature date 14 December 2022

Start date 1 April 2023

End date 31 March 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 491 174,00

EU contribution

€ 1 491 174,00

Coordinated by

KOBENHAVNS UNIVERSITET
Denmark

Periodic Reporting for period 1 - QUIDS (Tracing Indigenous American genomic history, subsistence strategies, health and their interplay through time using DNA from ancient masticated plant fibres)

Reporting period: 2023-04-01 to 2025-09-30

Summary of the context and overall objectives of the project

Palaeogenomics has revolutionised our understanding of human population history by analysing thousands of human genomes from skeletal remains. Unfortunately, this requires destructive sampling of such remains and can conflict with descendant communities' values and heritage conservation policies. To circumvent these limitations, we are using a novel DNA source: ancient quids. Quids are archaeological wads of chewed plant fibres that, like a buccal swab, contain the chewer's, their oral microbiome's and the chewer's meals' DNA, and that of the plants used for their elaboration. Thus, quids can simultaneously track human population history, dietary, cultural and microbiome shifts, pathogens and their interplay over time.

We are analysing quids from the Americas, where evolutionary history is understudied, skeletal remains are rare and destructive sampling is limited. In contrast to skeletal remains, quids are abundant in the American archaeological record and span from the Late Pleistocene to the Holocene and recent centuries. Through ancient quid DNA, we are reconstructing the genomic history of Indigenous Americans, their past lifeways and subsistence strategies, their health, and how these influenced each other throughout the three major historical transitions in the continent: the initial rapid peopling by hunter-gatherers, the emergence of complex agricultural societies and their demise during European colonisation.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We are still at the data production stage of the project. We started this project based on limited low-depth pilot data from three samples, suggesting that retrieving human, floral, faunal and microbial DNA from ancient quids was possible. So far, we have carried out groundwork at the wet and dry labs to optimise retrieval and analysis of quid DNA.

We have developed a subsampling strategy and a sample preparation procedure that has allowed us to automate DNA extraction and sequencing. Thanks to these, we have already processed ~100 quid samples. To extract knowledge from the large volumes of sequencing data we are producing, we have developed and implemented a bioinformatic workflow that is tailored to the species taxonomic diversity we have observed in different quids so far, i.e. quids contain DNA from multiple species but not as many as those in other environmental samples such as sediments. This workflow includes initial species identification and DNA sequence assignment steps, followed by more dedicated population genomics analyses.

With these two key advancements in hand, we have already moved towards the applied research portion of the project, where we aim to trace the genomic history, subsistence strategies and health of Indigenous Americans through time in different key regions of the continent.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Based on our work so far, we are confident that quids are a good source of 'endogenous' DNA that allows for genomic studies and contributes to minimising destructive sampling of ancestral human remains. Unfortunately, the 'endogenous' human DNA that quids yield is not comparable with DNA retrieved from human tissue in quality and quantity. However, the favourable tradeoff is that quid DNA allows us to connect genomic ancestries with subsistence strategies and health directly. In addition to moving the field towards more integrative views of the evolutionary history of human populations, our system can generate knowledge—that might have been affected through 500 years of colonialism—which is readily useful for Indigenous communities regarding their cultural past, traditional diets and their health.