Ancient genomic reconstruction of convergent evolution to agriculture

Project Information

AGRICON

Grant agreement ID: 852558

DOI

10.3030/852558

Project closed

EC signature date 30 October 2019

Start date 1 November 2019

End date 30 April 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 500 000,00

EU contribution

€ 1 500 000,00

Coordinated by

THE FRANCIS CRICK INSTITUTE LIMITED
United Kingdom

Periodic Reporting for period 3 - AGRICON (Ancient genomic reconstruction of convergent evolution to agriculture)

Reporting period: 2022-11-01 to 2024-04-30

Summary of the context and overall objectives of the project

By the advent of the warmer Holocene period, approximately 11,000 years ago, human populations had expanded out of their African origin to populate all major continents except for Antarctica, over a period of 40 thousand years. As the climates warmed came a remarkable convergent transformation of human lifestyles that occurred independently in multiple continents and human populations. This transition from a hunter-gatherer subsistence, for which only small group sizes could be sustained, to food production lifestyles such as animal herding and crop agriculture, fundamentally shaped the human condition and global biodiversity today. It catalysed large-scale population growth, offering the opportunity for increased rates of adaptation, but also rapidly presented a great number of human populations with a new evolutionary challenge.

This project aims to understand how convergent adaptation to new food-producing lifestyles impacted the genomes of human populations and accompanying domestic dog populations, and to which extent phenotypic convergence was driven by the same underlying genetic architecture. This will include gaining a deepening understanding of the genetic history and demography that preceded agriculture and unfolded during its expansion. It includes understanding the geographic origin of the first domestic animal: the domestic dog, which may have ushered in later developments in managing livestock and food production, and how the dog continued to adapt to agriculture alongside humans.

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

Work has focused on ancient DNA retrieval, sequencing, and analysis, for both canid and human skeletal material from across the past 10,000 years. In collaboration with archaeologists, we have sequenced and published genomes from over 100 ancient dogs and wolves from across the world. We have also retrieved ancient DNA from dozens of ancient humans from multiple regions, which are currently undergoing sequencing and analysis. We have developed new methods to study adaptation and genetic history using these ancient DNA data sets.

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)

The project has achieved a breakthrough on the origin of domestic dogs, which until now has been largely unknown. By sequencing a large number of wolf and dog genomes, we have discovered evidence for dual wolf ancestry of dogs. This suggests that dogs may have been domesticated independently both in west- and east Eurasia. This breakthrough paves the way for pinpointing the origins of dogs further, and understanding the process behind domestication and how it relates to the later advent of agriculture. We have also shown that dogs followed human agricultural groups as they expanded into Europe and Africa, but revealed exceptions to this pattern in cases where dogs did not expand alongside human groups. Finally, we have shown evidence that genetic adaptations in dogs associated with starch metabolism were present in early agricultural dogs, but had a complex evolution and were still absent thousands of years after agriculture in many dogs.