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Cultures of dairying: gene-culture-microbiome evolution and the ancient invention of dairy foods

Periodic Reporting for period 3 - DAIRYCULTURES (Cultures of dairying: gene-culture-microbiome evolution and the ancient invention of dairy foods)

Reporting period: 2021-11-01 to 2023-04-30

Global milk production exceeds 697 million metric tons – the volume equivalent of 278,800 Olympic size swimming pools – enough for every person on earth to consume a quarter litre of milk every single day. And yet, three quarters of the world’s population is genetically lactose intolerant. Milk is a fraught food, deeply entangled with politics, culture, economics, and history. At once celebrated as a super-food, vilified as unnatural, promoted as a cultural value, and decried as a danger, milk is a food whose history reflects the uneasy relationship between humans and food in the modern world. The DAIRYCULTURES project seeks to enrich scientific and public understanding of dairy foods by systematically investigating the deep history of the biological and cultural relationships between humans, livestock, and microbes in a “gene-culture-microbiome coevolution” framework.

The prehistory of dairying presents a puzzling problem, a “milk paradox,” for archaeology. How and why did ancient peoples develop a staple food that is apparently poorly digested by most adult humans? And, once developed, how did this food spread on a continental scale? How are the Bronze Age steppe migrations of humans and their livestock related to the spread of dairying across Eurasia, and can we accurately trace the spread of dairying in the archaeological record? Is lactase persistence (LP) really the only important biological factor in the gene-culture co-evolution of dairying – or should we also be focusing on microbes? The DAIRYCULTURES project focuses its attention on Mongolia, a country with a rich dairying history and where half of the population still leads a nomadic pastoralist lifestyle. This combination of a rich dairy prehistory and a robust contemporary dairy tradition makes Mongolia an ideal context in which to investigate “gene-culture-microbiome” coevolution.

There are three outstanding problems regarding our understanding of animal milk-based subsistence in traditional dairying societies like Mongolia. First, the origin of dairy domesticates and the time depth of dairying is poorly understood. Second, although recent advances have been made in the detection of milk proteins from dental calculus and archaeological food containers, current databases are patchy and incomplete in their coverage of milk protein sequences from various dairy species, making the identification of archaeological milk proteins challenging. Third, relatively little is known regarding the relationship between the gut microbiome and dairy digestion in traditional dairying societies, like Mongolia. The DAIRYCULTURES project aims to address these problems by (1) establishing a genetic framework for domesticated sheep, goat, cattle, and yak ancestry lineages and the detection of past human and animal breed migrations, (2) establishing better tools, protocols, and resources for milk detection and characterization from archaeological materials, and (3) evaluating the role of the human gut microbiome in milk digestion and dairy gene-culture-microbiome coevolution in contemporary Mongolia.
The DAIRYCULTURES project has made significant progress towards project goals in several areas. All project staff have been hired, including students and postdocs in Germany as well as our fieldwork coordination team in Mongolia.

We have identified the relevant regulatory agencies and ethical commissions for conducting work on modern animal and human genetics. We have established memoranda of understanding with partner Mongolian and Russian institutions and our study protocols have been approved.

We have reconstructed the time depth of dairying in Mongolia, including the dairying history of five of Mongolia's seven dairy livestock. This work has included the development of new approaches for authenticating ancient milk proteins, as well as a systematic evaluation and optimization of of protein extraction protocols.

We have begun laboratory work on characterizing genetic diversity in ancient dairy livestock breeds. We are currently analyzing the genetic variation and diversity of these ancient animals across time and space. Through this initial work, we have identified the earliest known domesticated sheep in Central Asia. We are currently developing an in-solution capture assay to enrich for animal genome DNA, which will allow us to improve the quality of our ancient animal genome sequences. We have also acquired saliva swabs from a representative set of dairy livestock in Mongolia that will allow us to better characterize local genetic diversity in present-day Mongolia for comparison to our ancient samples.

The DAIRYCULTURES project has contributed to reconstructing the population history of ancient Mongolia, which allows us to contextualize major dairy technologies within a broader cultural and societal context. We have reconstructed trends in lactase persistence genotypes in ancient Mongolian populations spanning 6,000 years. We have shown that the lactase persistence phenotype has never been present at a frequency higher than 10% in Mongolian populations, despite this genetic trait being introduced multiple times by migrating groups in prehistory. We found no selection on the phenotype in Mongolia over the past 6,000 years. We have collected buccal swab samples from present-day study participants to determine the frequency of lactase persistence today in rural and urban settings.

To refine our understanding of dairy subsistence and milk intake in current Mongolian diets, we have empirically measured the macronutrient (including lactose) and micronutrient content of 15 major dairy foods consumed in Mongolia, and an additional 15 are currently undergoing analysis. With this dataset, we are able to accurately measure and predict lactose intake in contemporary nomadic herder diets.

We are currently characterizing lactose tolerance phenotypes and analyzing the microbial structure of the human gut microbiome in urban and rural communities in Mongolia.

We created a public website for the project, and we have completed a searchable database of ethnographic photos and videos related to Mongolian dairying practices that is embedded in the website.

We hosted two major conferences related to the project in Central Asia (Mongolia and Kyrgyzstan) and Portugal, as well as an interactive workshop to disseminate information about the project to potential study participants and members of the public in Mongolia. We have presented our interim findings at more than two dozen conferences, workshops, and invited seminars. We produced a short documentary film, a photobook, two folksong soundtracks, and discussed our research on both radio and television programs.

To facilitate improved public education and accessibility within our partner country, Mongolia, we produced full Mongolian translations of two major research articles, and we partnered with the scientific journals to link them to the main publication. We also produced a coloring book aimed at K-12 education that we made available in relevant partner country languages: Mongolian, Kazakh, Buryad, and Russian.
Future anticipated results include the characterization and systematic comparison of the gut microbiome in Mongolian nomadic herders and urban dwellers, and the completion of genetic analysis of modern and archaeological dairy livestock.
Traditional yak milking in northern Mongolia