Periodic Reporting for period 3 - PALAEOFARM (Linking livestock genetic diversity with three thousand years of agricultural crises and resilience)
Okres sprawozdawczy: 2023-09-01 do 2025-02-28
Over the last 50 years, chicken production has increased fivefold, chicken growth rate has tripled, and milk production per cow has doubled. Yet, many of the biotechnological tools responsible for these trends are now under threat of becoming obsolete. While the causes for this are numerous, one significant driver is a dramatic reduction of genetic diversity in livestock populations.
Cycles of agricultural productivity growth and decline have occurred throughout European history, spurred by major historical forces such as the spread of empires and continent-wide epidemics. For example, productivity crashed between the 4th and 13th centuries, only to rebound in the period leading to the Agricultural Revolution of the 18th century. Fluctuating levels of genetic diversity were likely both cause and remedy to these cycles. Genetic diversity acts as a fuel for selection: the lower it is, the more difficult it is to improve traits, and the more likely that epidemics will develop and spread. Given this importance, maintaining diversity amongst livestock is recognised as one of the UN’s Sustainable Development Goals. Despite this, we lack any understanding of how much genetic variability was present, and subsequently lost, before, during, and after either the Green or Agricultural Revolutions, and nor do we understand how efficiently it was utilised.
PALAEOFARM will assess the long-term sustainability of modern breeding practices by unravelling how genetic variability was leveraged across major agricultural transitions in European history. Using an innovative combination of ancient DNA, archaeozoology, and experimental immunology, I will explore how livestock populations withstood epidemics and selective breeding in a world without antibiotics or quantitative genetic techniques. This will provide a novel perspective on how a multi-billion euro industry, responsible for feeding billions of people, can be sustained in the face of major biotechnological obsolescence.
Cycles of agricultural productivity growth and decline have occurred throughout European history, spurred by major historical forces such as the spread of empires and continent-wide epidemics. For example, productivity crashed between the 4th and 13th centuries, only to rebound in the period leading to the Agricultural Revolution of the 18th century. Fluctuating levels of genetic diversity were likely both cause and remedy to these cycles. Genetic diversity acts as a fuel for selection: the lower it is, the more difficult it is to improve traits, and the more likely that epidemics will develop and spread. Given this importance, maintaining diversity amongst livestock is recognised as one of the UN’s Sustainable Development Goals. Despite this, we lack any understanding of how much genetic variability was present, and subsequently lost, before, during, and after either the Green or Agricultural Revolutions, and nor do we understand how efficiently it was utilised.
PALAEOFARM will assess the long-term sustainability of modern breeding practices by unravelling how genetic variability was leveraged across major agricultural transitions in European history. Using an innovative combination of ancient DNA, archaeozoology, and experimental immunology, I will explore how livestock populations withstood epidemics and selective breeding in a world without antibiotics or quantitative genetic techniques. This will provide a novel perspective on how a multi-billion euro industry, responsible for feeding billions of people, can be sustained in the face of major biotechnological obsolescence.
We have sequenced and analyzed the genome of 15 ancient Marek disease virus (MDV) derived from archaeological chickens. We showed that this deadly virus has been circulating for at least 1000 years, i.e. over 900 years prior to the first description of the disease. Today, MDV infections kill >90% of unvaccinated birds and controlling it costs >US$1bn annually yet we do not have samples prior to the 1960s. As a result, the genetic changes that contributed to the increase in virulence of MDV infection prior to the 1960s remain unknown. Armed with our ancient genomes we were able to pinpoint which part in the genome of MDV has evolved faster in the last 100 years. We then developed a cell-based assay to functionally test ancient MDV in-vitro, demonstrating that ancient MDV were likely incapable of driving tumor formation. This allowed us to identify sequence changes in MDV that drove tumor formation in birds.
The historical perspective that our results provide can form the basis on which to rationally improve modern vaccines, and track or even predict future virulence changes. Lastly, our results highlight the utility of functional paleogenomics to generate insights into the evolution and fundamental biological workings of pathogen virulence.
We have also collected and screened for endogenous DNA over 300 chickens since the start of the project and generated 40 ancient chicken genomes from European samples dating back to the last 2,000 years. We are currently in the process of generating an additional 60-120 chicken genomes before the summer 2023, which will be analysed together with modern genomes before the end of 2023.
Lastly, we have also collected and screened archeological pig samples from Europe. These samples are now being processed, and on our preliminary results we have identified multiple pig samples which possess traces of pathogenic species that can infect both pigs in human.
The historical perspective that our results provide can form the basis on which to rationally improve modern vaccines, and track or even predict future virulence changes. Lastly, our results highlight the utility of functional paleogenomics to generate insights into the evolution and fundamental biological workings of pathogen virulence.
We have also collected and screened for endogenous DNA over 300 chickens since the start of the project and generated 40 ancient chicken genomes from European samples dating back to the last 2,000 years. We are currently in the process of generating an additional 60-120 chicken genomes before the summer 2023, which will be analysed together with modern genomes before the end of 2023.
Lastly, we have also collected and screened archeological pig samples from Europe. These samples are now being processed, and on our preliminary results we have identified multiple pig samples which possess traces of pathogenic species that can infect both pigs in human.