Periodic Reporting for period 2 - COREX (From correlations to explanations: towards a new European prehistory)
Periodo di rendicontazione: 2022-11-01 al 2024-04-30
The possibility to study ancient genomic DNA has created a major revolution not just in archaeology but in public perceptions of prehistory. These major advances in understanding the genetic history of western Eurasia exceed our current ability to relate them to the empirical archaeological record beyond the vaguest and most general of terms. The most important challenge in archaeology today is to be able to handle, integrate and interpret all the new genetic data with archaeological and environmental data, including detailed environmental DNA reconstructions so that we can compare the archaeological evidence for cultural relationships and past social and adaptive strategies with the evidence from the ancient genomes.
Thus, the overall goal of COREX is to explain the key processes that formed the genetic and cultural diversity of Europe north of the Mediterranean from the beginning of farming c. 6000 BCE to the end of the Bronze Age c. 500 BCE. At the same time as the explosion in ancient genome research there has been major growth in the collection of large databases of radiocarbon dates and their use to infer past population size changes. These have been accompanied by statistical methods to evaluate the validity of the inferences being made and to correlate them with other proxies, such as anthropogenic impacts on the environment. All these methods are adopted, and correlated with changes in subsistence, diet and diseases to create a multi-proxy foundation for explaining the complex processes of population change throughout later prehistory.
The unique combination of complementary disciplinary backgrounds and skills of the COREX team is creating novel methodological approaches combined with the collection and integration of data sets never previously brought together. This will allow us to rewrite the big history of western Eurasia, by exploring how small-scale processes generate large-scale patterns in genetic and cultural data, and considering how the two interact. Doing so will allow us to move from correlations to explanations of how changes have been shaped by the dynamic interaction of cultural innovation, migration, admixture, population growth and collapse, dietary change, biological adaptation, social structure, and the emergence of new diseases.
Our work is important for society because it throws new light on the processes that have shaped European identities over the course of prehistory.
Thus, the overall goal of COREX is to explain the key processes that formed the genetic and cultural diversity of Europe north of the Mediterranean from the beginning of farming c. 6000 BCE to the end of the Bronze Age c. 500 BCE. At the same time as the explosion in ancient genome research there has been major growth in the collection of large databases of radiocarbon dates and their use to infer past population size changes. These have been accompanied by statistical methods to evaluate the validity of the inferences being made and to correlate them with other proxies, such as anthropogenic impacts on the environment. All these methods are adopted, and correlated with changes in subsistence, diet and diseases to create a multi-proxy foundation for explaining the complex processes of population change throughout later prehistory.
The unique combination of complementary disciplinary backgrounds and skills of the COREX team is creating novel methodological approaches combined with the collection and integration of data sets never previously brought together. This will allow us to rewrite the big history of western Eurasia, by exploring how small-scale processes generate large-scale patterns in genetic and cultural data, and considering how the two interact. Doing so will allow us to move from correlations to explanations of how changes have been shaped by the dynamic interaction of cultural innovation, migration, admixture, population growth and collapse, dietary change, biological adaptation, social structure, and the emergence of new diseases.
Our work is important for society because it throws new light on the processes that have shaped European identities over the course of prehistory.
The first two years of the project have been devoted to starting up and consolidating the various actions within the project’s different working packages (WP), including hiring staff, data acquisition, and fieldwork organization. No major problems have been encountered except for travel problems due to the COVID-19 pandemic, which limited the possibility to meet and to a certain extent also of sampling.
The biggest challenge has been represented by creating, organizing, and managing the Big Interdisciplinary Archaeological Database (BIAD) for WP1. The database is now operational, with users both inputting and analysing data on a daily basis. Database development and structural improvements are ongoing. A workflow has been designed for data mining and entry into BIAD in a systematic manner, ensuring that errors are minimised, data quality maintained, and that all data can be traced to a source. One of the major goals of the project is the BIAD to be able to serve as an open access source once for future research as well once the project is finalized. This will be the first of its kind in archaeology. We have therefore presented the principles of the database at international conferences, and it raised considerable interest.
Regarding fieldwork and environmental DNA (WP2), archeological sediment samples were selected from 11 sites (c. 80 samples from diverse contexts including: ditches, middens, graves, pits and accreted surfaces) ranging from the terminal Mesolithic to the Early Iron Age (Hallstatt) in France, Croatia, the Czech Republic, Sweden, Denmark and the Netherlands. These have been extracted, libraries have been built and the preliminary bioinformatic analysis is complete.
WP3 consists of the PI, a PhD student trained in evolutionary genetics and a postdoctoral fellow specializing in paleoecology and computational inference. We have begun agglomerating different types of archaeobotanical, archaeozoological and environmental data collected in BIAD and developing models that can connect these disparate sources of data to population turnovers and mobility transitions. WP3 is also involved in connecting ancient DNA datasets with the archaeological datasets (over 5,000 ancient DNA records), in order to connect measures of ancestry changes and genetic connectivity with existing archaeological proxies already present in the database.
The WP4 according to plan has not started yet.
The biggest challenge has been represented by creating, organizing, and managing the Big Interdisciplinary Archaeological Database (BIAD) for WP1. The database is now operational, with users both inputting and analysing data on a daily basis. Database development and structural improvements are ongoing. A workflow has been designed for data mining and entry into BIAD in a systematic manner, ensuring that errors are minimised, data quality maintained, and that all data can be traced to a source. One of the major goals of the project is the BIAD to be able to serve as an open access source once for future research as well once the project is finalized. This will be the first of its kind in archaeology. We have therefore presented the principles of the database at international conferences, and it raised considerable interest.
Regarding fieldwork and environmental DNA (WP2), archeological sediment samples were selected from 11 sites (c. 80 samples from diverse contexts including: ditches, middens, graves, pits and accreted surfaces) ranging from the terminal Mesolithic to the Early Iron Age (Hallstatt) in France, Croatia, the Czech Republic, Sweden, Denmark and the Netherlands. These have been extracted, libraries have been built and the preliminary bioinformatic analysis is complete.
WP3 consists of the PI, a PhD student trained in evolutionary genetics and a postdoctoral fellow specializing in paleoecology and computational inference. We have begun agglomerating different types of archaeobotanical, archaeozoological and environmental data collected in BIAD and developing models that can connect these disparate sources of data to population turnovers and mobility transitions. WP3 is also involved in connecting ancient DNA datasets with the archaeological datasets (over 5,000 ancient DNA records), in order to connect measures of ancestry changes and genetic connectivity with existing archaeological proxies already present in the database.
The WP4 according to plan has not started yet.
The project has been focusing, according to plan, on several different scientific fields/questions and the development of novel approaches to fully address them:
BIAD
We have developed a new type of integrated archaeological database, BIAD (Big Interdisciplinary Archaeological Database), with the potential to revolutionize future archaeological research. BIAD is already extending beyond COREX, with new data being provided by several independent projects. The database will shortly be made public access.
One of the major problems in our data collection has been to identify an appropriate way to include fundamental archaeological data such as the arrangement of a body in human burials and info about pottery shape and decoration. Current approaches to recording these data are largely qualitative, or categorical at best. We have developed a novel method of recording all possible physical positioning of human bodies as continuous numerical data, allowing a rich analysis of variance. This will add a significant layer of culturally informative data to BIAD. As to pottery shape and decoration, we have devised a novel algorithm to automatically process images of pots to generate a numerical vector description of the pot shape, and generate c. 100 descriptive statistics, permitting a rich analysis of variance. Extension work is currently investigating the more challenging problem of encoding pottery decoration in a similar manner.
eDNA
Our preliminary ancient environmental DNA results have yielded intriguing botanical results, but so far given the absence of fauna has pushed us to develop novel protocols to increase ancient DNA extraction yields. This can potentially expand the impact of eDNA research in the project, as well as for future research. We expect the outcome of eDNA development to have a tremendous scientific impact.
Genomic ancestry
We are combining proxies for adaptation and mobility with archaeological and environmental data from BIAD, to better understand the drivers of evolutionary processes during different periods of the Holocene. We are attempting innovative ways to model paleo-vegetation, archaeobotanical and archaeozoological records, to understand how humans modified the niche of various cultivated/domesticated species in Europe across prehistory, and how these niche changes related to population turnovers. We expect to shed new light on the processes that have shaped European subsistence and organization modes over the course of prehistory.
BIAD
We have developed a new type of integrated archaeological database, BIAD (Big Interdisciplinary Archaeological Database), with the potential to revolutionize future archaeological research. BIAD is already extending beyond COREX, with new data being provided by several independent projects. The database will shortly be made public access.
One of the major problems in our data collection has been to identify an appropriate way to include fundamental archaeological data such as the arrangement of a body in human burials and info about pottery shape and decoration. Current approaches to recording these data are largely qualitative, or categorical at best. We have developed a novel method of recording all possible physical positioning of human bodies as continuous numerical data, allowing a rich analysis of variance. This will add a significant layer of culturally informative data to BIAD. As to pottery shape and decoration, we have devised a novel algorithm to automatically process images of pots to generate a numerical vector description of the pot shape, and generate c. 100 descriptive statistics, permitting a rich analysis of variance. Extension work is currently investigating the more challenging problem of encoding pottery decoration in a similar manner.
eDNA
Our preliminary ancient environmental DNA results have yielded intriguing botanical results, but so far given the absence of fauna has pushed us to develop novel protocols to increase ancient DNA extraction yields. This can potentially expand the impact of eDNA research in the project, as well as for future research. We expect the outcome of eDNA development to have a tremendous scientific impact.
Genomic ancestry
We are combining proxies for adaptation and mobility with archaeological and environmental data from BIAD, to better understand the drivers of evolutionary processes during different periods of the Holocene. We are attempting innovative ways to model paleo-vegetation, archaeobotanical and archaeozoological records, to understand how humans modified the niche of various cultivated/domesticated species in Europe across prehistory, and how these niche changes related to population turnovers. We expect to shed new light on the processes that have shaped European subsistence and organization modes over the course of prehistory.