Characterizing Adaptation and Migration Events with Modern and Ancient Genomes

In this project we are trying to better understand how humans peopled the world and how they adapted to the new environments they encountered during their dispersal. To work towards those objectives we plan to generate and analyze snapshots of DNA through time from both ancient and modern human populations. We then compare the DNA data we generate alongside publically available data and we infer the demographic history of those populations. Moreover, we look for signature of selection at the molecular level.

To do this work, and to better account for the specific challenges of ancient DNA data, we use existing population genetic tools but we also develop new methodology. Our results should have a societal impact as we can reconstruct the human past thanks to DNA data but also raise awareness about indigenous groups as we are particularly interested in understanding the movements of people who settled first around the globe.

Throughout the grant, we characterized the migration of humans across several regions in the world, including the Americas and Polynesia (our primary focus) but also Oceania and Europe. To do this work, we have developed methodology to tackle challenges specific to ancient DNA research, including the parsing of large and messy datasets generated through several years of work and varying protocols, typical of ancient DNA research project but also to measure contamination, and overcome the large amounts of missingness in the data through imputation strategies.

To reach our empirical aims, we have worked with representatives of indigenous communities and anthropologists to sample ancient human remains and generate ancient genomes and isotopic data to study the human past.

In the Americas, we have been able to show that the first migrants moved quickly from North to South in mostly one migration wave. We were also able to show that South American populations have a special relationship to Oceanian populations, as if the population that first entered the Americas was deeply structured. Our data also suggests that contemporary indigenous groups in Chile/Patagonia are likely the direct descendants of the ancient groups living there thousands of years ago. Furthermore, we have been able to show that most of the 19th century Brazilian populations we studied do not carry any evidence of Polynesian ancestry - unlike some indidivuls we studies in previous work of fully Polynesian ancestry. Instead, our latest results suggest a strong genetic link between our sequenced Brazilian individuals and Indigenous groups from South America and more specifically Brazil. Furthermore, we have recovered evidence of South American gene flow in Polynesian populations, which could well indicate that Polynesians reached the Americas before Columbus. In Oceania, we have found that there is a strong genetic affinity between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Finally, in Europe, we have found evidence of Steppe-like ancestry reaching Greece later than most of the rest of Europe, i.e. after the Neolithic Bronze age transition.

In terms of dissemination, we reached out to indigenous groups to collaborate and present ongoing results across the project. We also presented our work in a number of conferences. Furthermore, our for our results that are being either finalised for publication (selection in the Americas and ancient microbes), or submitted (peopling of Polynesia and Brazil) or have already appeared (method development and peopling of Europe, Oceania and the Americas).

Once our publications are accepted, especially for the empirical work, we also plan to reach out and communicate more final results, in the form of written summaries translated into several languages as well as some input into museum exhibit and social media. Early in the project we also developped a specific outreach startegy that we plan to continue in the future, specifically we developped early on the Project Genome Odyssey: a multi-disciplinary science communication project related to the scientific publication “A genomic history of Aboriginal Australia” with several publications and events. Our role was to produce the play and the related videos, to co-write the play, to organize and manage all related events such as the exhibit and the “cafés scientifiques”.

• A theatre play: “Génome Odyssée Chapitre 1, l’Australie, Quand la science devient Théâtre »
Script: https://wp.unil.ch/egg/key-publications-for-tenure-track-package-as-malapinas
Video recording of the play:
Trailer: https://vimeo.com/477212780
Full play: https://vimeo.com/273343483

Shows took place in Geneva, Switzerland (Musée d’ethnographie) and Paris, France (Musée de l’Homme) from October 2017 to January 2018. The play was seen by about 2’000 children and families.

• An exhibit: “Draw me a scientist” - An exhibit of drawings made by children before and after the play, Genopode, University of Lausanne – May/June 2018
• “Cafes scientifiques”: organization of events where scientists meet classes (middle school children) to discuss genomes, population genetics and human evolution, at the Middle School Sécheron, Geneva, Switzerland, May 2017
• Videos: “Australia”, “Aboriginal Australians”, “Scientist”, “Genome” – videos made to advertise the play and to understand the target audience prior to the play
https://vimeo.com/genomeodyssey
• A twitter account: https://twitter.com/GenomeOdyssey to advertise the play and inform the public

Traditionally, the human past was studied with paleoanthropological data. We show here that by using state of the art methodology, we can generate DNA data from both modern and ancient humans. By doing so, we can complement paleoanthropological data to refine the story of our humanity.

Periodic Reporting for period 5 - CAMERA (Characterizing Adaptation and Migration Events with Modern and Ancient Genomes)

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