Project

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Characterizing migrations with modern and ancient genomic data: the limits of the Polynesian expansion

Applicant Malaspinas Anna Sapfo
Number 154717
Funding scheme Ambizione
Research institution Institut für Ökologie und Evolution Universität Bern
Institution of higher education University of Berne - BE
Main discipline Genetics
Start/End 01.03.2015 - 28.02.2019
Approved amount 496'507.00
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All Disciplines (3)

Discipline
Genetics
Molecular Biology
Anthropology, Primatology

Keywords (5)

molecular evolution; Americas; population genomics; ancient DNA; Polynesia

Lay Summary (French)

Lead
L´hypothèse d´un contact entre les populations humaines d´Amériques et de Polynésie date du début du XXème siècle. Bien que cette question soit encore largement débattue, elle n’a été que peu abordée avec des données génomiques. L’utilisation de ce genre de données dans le cadre de ce projet devrait permettre d’élucider divers aspects telle que la temporalité ou le nombre d’individus impliqués dans un contact potentiel entre ces populations éloignées.
Lay summary

Titre

Caractérisation des migrations humaines avec des données anciennes et modernes ou les limites de l’expansion Polynésienne dans l’océan pacifique

Contenu et objectifs du travail de recherche 

La colonisation des Amériques fait l’objet de nombreuses études depuis plus d’un siècle. Il est aujourd’hui accepté que les humains aient colonisé les Amériques il y a 15 à 30 mille ans. Des contacts secondaires pré historiques ou historiques ont également été proposés, notamment avec la Polynésie. Mais beaucoup reste encore à découvrir quand à ce contact secondaire potentiel.

Ce projet porte sur l’étude de ce contact secondaire encore mal élucidé à travers la génération et l’analyse de données génomiques humaines pour des populations humaines encore peu ou pas caractérisées génétiquement.

Dans un premier temps, nous irons collecter des échantillons modernes et anciens en Polynésie française et dans divers musées au Brésil et sur l’ile de paques. Nous développerons en parallèle des modèles de génétique des populations applicables aux données collectées. Puis nous génèrerons les données génomiques que nous analyserons dans la phase finale du projet.  

Nos recherches aideront à mieux comprendre les mouvements des Polynésiens dans le temps et l’espace au cours de leurs voyages à travers l’océan pacifique.  

Contexte scientifique et social du projet de recherche

L’émergence de données génomiques permet ces dernières années de réévaluer les théories concernant le mode et tempo de colonisation du monde par les humains depuis leur apparition jusqu’à nos jours. Pour mieux comprendre nos origines il est donc important à la fois de collecter des données génomiques mais aussi de développer de modèles permettant d’inférer des paramètres démographiques qui relatent les populations entre elles dans le temps et l’espace.

Mots-clés

Génétique des populations, AND ancien, Polynésie, Ameriques, évolution moléculaire

Direct link to Lay Summary Last update: 29.04.2015

Responsible applicant and co-applicants

Employees

Publications

Publication
In-solution Y-chromosome capture-enrichment on ancient DNA libraries
Cruz-Dávalos Diana I., Nieves-Colón María A., Sockell Alexandra, Poznik G. David, Schroeder Hannes, Stone Anne C., Bustamante Carlos D., Malaspinas Anna-Sapfo, Ávila-Arcos María C. (2018), In-solution Y-chromosome capture-enrichment on ancient DNA libraries, in BMC Genomics, 19(1), 608-608.
In-solution Y-chromosome capture-enrichment on ancient DNA libraries
Cruz-Dávalos Diana I., Nieves-Colón María A., Sockell Alexandra, Poznik G. David, Schroeder Hannes, Stone Anne C., Bustamante Carlos D., Malaspinas Anna-Sapfo, Ávila-Arcos María C. (2018), In-solution Y-chromosome capture-enrichment on ancient DNA libraries, in BMC Genomics, 19(1), 608-608.
The prehistoric peopling of Southeast Asia
McColl Hugh, Racimo Fernando, Vinner Lasse, Demeter Fabrice, Gakuhari Takashi, Moreno-Mayar J. Víctor, van Driem George, Gram Wilken Uffe, Seguin-Orlando Andaine, de la Fuente Castro Constanza, Wasef Sally, Shoocongdej Rasmi, Souksavatdy Viengkeo, Sayavongkhamdy Thongsa, Saidin Mohd Mokhtar, Allentoft Morten E., Sato Takehiro, Malaspinas Anna-Sapfo, Aghakhanian Farhang A., Korneliussen Thorfinn, Prohaska Ana, Margaryan Ashot, de Barros Damgaard Peter, Kaewsutthi Supannee, et al. (2018), The prehistoric peopling of Southeast Asia, in Science, 361(6397), 88-92.
Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia
de la Fuente Constanza, Ávila-Arcos María C., Galimany Jacqueline, Carpenter Meredith L., Homburger Julian R., Blanco Alejandro, Contreras Paloma, Cruz Dávalos Diana, Reyes Omar, San Roman Manuel, Moreno-Estrada Andrés, Campos Paula F., Eng Celeste, Huntsman Scott, Burchard Esteban G., Malaspinas Anna-Sapfo, Bustamante Carlos D., Willerslev Eske, Llop Elena, Verdugo Ricardo A., Moraga Mauricio (2018), Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia, in Proceedings of the National Academy of Sciences, 115(17), E4006-E4012.
Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia
de la Fuente Constanza, Ávila-Arcos María C., Galimany Jacqueline, Carpenter Meredith L., Homburger Julian R., Blanco Alejandro, Contreras Paloma, Cruz Dávalos Diana, Reyes Omar, San Roman Manuel, Moreno-Estrada Andrés, Campos Paula F., Eng Celeste, Huntsman Scott, Burchard Esteban G., Malaspinas Anna-Sapfo, Bustamante Carlos D., Willerslev Eske, Llop Elena, Verdugo Ricardo A., Moraga Mauricio (2018), Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia, in Proceedings of the National Academy of Sciences, 115(17), E4006-E4012.
Human bony labyrinth is an indicator of population history and dispersal from Africa
Ponce de León Marcia S., Koesbardiati Toetik, Weissmann John David, Milella Marco, Reyna-Blanco Carlos S., Suwa Gen, Kondo Osamu, Malaspinas Anna-Sapfo, White Tim D., Zollikofer Christoph P. E. (2018), Human bony labyrinth is an indicator of population history and dispersal from Africa, in Proceedings of the National Academy of Sciences, 115(16), 4128-4133.
Human bony labyrinth is an indicator of population history and dispersal from Africa
Ponce de León Marcia S., Koesbardiati Toetik, Weissmann John David, Milella Marco, Reyna-Blanco Carlos S., Suwa Gen, Kondo Osamu, Malaspinas Anna-Sapfo, White Tim D., Zollikofer Christoph P. E. (2018), Human bony labyrinth is an indicator of population history and dispersal from Africa, in Proceedings of the National Academy of Sciences, 115(16), 4128-4133.
Decline of genetic diversity in ancient domestic stallions in Europe
Wutke Saskia, Sandoval-Castellanos Edson, Benecke Norbert, Döhle Hans-Jürgen, Friederich Susanne, Gonzalez Javier, Hofreiter Michael, Lõugas Lembi, Magnell Ola, Malaspinas Anna-Sapfo, Morales-Muñiz Arturo, Orlando Ludovic, Reissmann Monika, Trinks Alexandra, Ludwig Arne (2018), Decline of genetic diversity in ancient domestic stallions in Europe, in Science Advances, 4(4), eaap9691-eaap9691.
Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans
Moreno-Mayar J. Víctor, Potter Ben A., Vinner Lasse, Steinrücken Matthias, Rasmussen Simon, Terhorst Jonathan, Kamm John A., Albrechtsen Anders, Malaspinas Anna-Sapfo, Sikora Martin, Reuther Joshua D., Irish Joel D., Malhi Ripan S., Orlando Ludovic, Song Yun S., Nielsen Rasmus, Meltzer David J., Willerslev Eske (2018), Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans, in Nature, 553(7687), 203-207.
Madjedbebe and genomic histories of Aboriginal Australia
Dortch Joe, Malaspinas Anna-Sapfo (2017), Madjedbebe and genomic histories of Aboriginal Australia, in Australian Archaeology, 83(3), 174-177.
A genomic history of Aboriginal Australia
Malaspinas Anna-Sapfo, Westaway Michael C., Muller Craig, Sousa Vitor C., Lao Oscar, Alves Isabel, Bergström Anders, Athanasiadis Georgios, Cheng Jade Y., Crawford Jacob E., Heupink Tim H., Macholdt Enrico, Peischl Stephan, Rasmussen Simon, Schiffels Stephan, Subramanian Sankar, Wright Joanne L., Albrechtsen Anders, Barbieri Chiara, Dupanloup Isabelle, Eriksson Anders, Margaryan Ashot, Moltke Ida, Pugach Irina, et al. (2016), A genomic history of Aboriginal Australia, in Nature, 538(7624), 207-214.
Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective
Malaspinas Anna-Sapfo (2016), Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective, in Molecular Ecology, 25(1), 24-41.
Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries
Ávila-Arcos María C., Sandoval-Velasco Marcela, Schroeder Hannes, Carpenter Meredith L., Malaspinas Anna-Sapfo, Wales Nathan, Peñaloza Fernando, Bustamante Carlos D., Gilbert M. Thomas P. (2015), Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries, in Methods in Ecology and Evolution, 6(6), 725-734.
Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean
Schroeder Hannes, Ávila-Arcos María C., Malaspinas Anna-Sapfo, Poznik G. David, Sandoval-Velasco Marcela, Carpenter Meredith L., Moreno-Mayar José Víctor, Sikora Martin, Johnson Philip L. F., Allentoft Morten Erik, Samaniego José Alfredo, Haviser Jay B., Dee Michael W., Stafford Thomas W., Salas Antonio, Orlando Ludovic, Willerslev Eske, Bustamante Carlos D., Gilbert M. Thomas P. (2015), Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean, in Proceedings of the National Academy of Sciences, 201421784-201421784.
Genomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan Maanasa, Steinrücken Matthias, Harris Kelley, Schiffels Stephan, Rasmussen Simon, DeGiorgio Michael, Albrechtsen Anders, Valdiosera Cristina, Ávila-Arcos María C., Malaspinas Anna-Sapfo, Eriksson Anders, Moltke Ida, Metspalu Mait, Homburger Julian R., Wall Jeff, Cornejo Omar E., Moreno-Mayar J. Víctor, Korneliussen Thorfinn S., Pierre Tracey, Rasmussen Morten, Campos Paula F., Damgaard Peter de Barros, Allentoft Morten E., Lindo John, Metspalu Ene (2015), Genomic evidence for the Pleistocene and recent population history of Native Americans, in Science, 349(6250), 3884-3884.
Population genomics of Bronze Age Eurasia
Allentoft Morten E., Sikora Martin, Sjögren Karl-Göran, Rasmussen Simon, Rasmussen Morten, Stenderup Jesper, Damgaard Peter B., Schroeder Hannes, Ahlström Torbjörn, Vinner Lasse, Malaspinas Anna-Sapfo, Margaryan Ashot, Higham Tom, Chivall David, Lynnerup Niels, Harvig Lise, Baron Justyna, Casa Philippe Della, Dąbrowski Paweł, Duffy Paul R., Ebel Alexander V., Epimakhov Andrey, Frei Karin, Furmanek Mirosław, Gralak Tomasz (2015), Population genomics of Bronze Age Eurasia, in Nature, 522(7555), 167-172.

Collaboration

Group / person Country
Types of collaboration
Eske Willerslev, Centre for GeoGenetics, Denmark Denmark (Europe)
- Publication
Claudia Rodrigues Carvalho, National Museum, Rio de Janeiro, Brazil Brazil (South America)
- Publication

Communication with the public

Communication Title Media Place Year
Other activities Genome Odyssée; Chapitre 1, l'Australie International 2018
New media (web, blogs, podcasts, news feeds etc.) Genome Odyssey website International 2017

Associated projects

Number Title Start Funding scheme
171636 Genome Odyssey. To the heart of Aboriginal Australian genes. 01.02.2017 Agora

Abstract

BACKGROUND: The mode and tempo of the colonization of the Americas before it was discovered by Europeans remains unresolved. After more than a century of study the majority of available genetic, archaeological and linguistic evidence supports one or more pre-Columbian migration event(s) from Siberia to North America around 15-30 thousand years before present, followed by an expansion into South America. Prehistoric or historic connections between South America and Southeast Asia/Oceania have been noted including similarities in culture, human skull morphology and domestic breeds, but so far no genetic evidence from humans has been found to support such contact. We recently found that skeletal remains from Brazil belonging to two indigenous Botocudos presented a combination of mitochondrial DNA variants common in present day Oceanian populations. AIMS: I propose to investigate the question of a Polynesian-South American contact with genomic data. Specifically, we aim to (I) infer the colonization of Polynesia using genetic data from present-day Polynesians, (II) infer the structure of the indigenous Botocudo of Brazil, (III) characterize the Polynesian-South American contact considering ancient and modern data jointly. The main questions I seek to answer are: (I) What was the mode and tempo of the colonization of Polynesia? Does the genetic data fit the archeological data? Which Polynesian populations exhibit a Native American signal? (II) What is the structure within the Botocudo population? How do they relate to other Native American populations? Is there more than two individuals with a Polynesian signal? How strong is the Polynesian signal? (III) When did the Polynesian and South American populations first began admixing? Was it before or after European contact with South America/Polynesia? What was the direction of the gene flow? RELEVANCE: The results will contribute to deepen our understanding of the peopling of the world, ultimately having relevance to enduring questions such as: Where do we all come from? Who are our ancestors? The statistical methods will be applicable to any migration/admixture event across the tree of life. They will also benefit the growing field of ancient genomics and other fields where data are collected at several time points, such as experimental evolution and epidemiology. The generated data will be of general interest to investigate other population genetics aspect, including related human migration events and the impact of a range expansion in terms of genetic load. Finally, by the end of the project, we should have all the pieces necessary to solve the decades-old puzzle concerning the colonization of the Americas.
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