Historical genomics of long-term PEople-Palm Interactions in the NeotrOpics (PEPINO)

Programme : LabEx CEBA
Durée : 2019 - 2020

Mots clés

Oenocarpus, adaptation, domestication, Amazonia, genomics

Résumé

Recent discoveries suggest that humans have more intensively transformed Amazonia than previously thought, and that the contemporary biodiversity of Amazonian rainforests contains legacies of pre-Colombian societies. The present-day distribution of genomic diversity of hyperdominant food crops in Amazonian forest landscapes -and their underlying biogeographic history- are thus expected to result from complex interactions between natural and human-mediated evolutionary processes. However, the degree to which pre-Columbian human societies affected the contemporary distribution of functional genomic diversity in Amazonian food crops is largely unknown. The goal of this project is to evaluate how long-term interactions between people and a hyperdominant food-producing palm (Oenocarpus bataua Mart.) acted together with natural evolutionary processes to create the present-day distribution of functional genomic diversity across Amazonia through a continental-scale biogeographic study. We will analyze retrospectively the effects of global (land use and climate) changes on population evolution and evaluate the resilience of populations after anthropogenic disturbance in ancient agro-ecosystems of Amazonia. Analyzing the simultaneous effects of natural and human-mediated pressures is of major interest, because these two processes are ongoing and are likely to intensify in the current context of global change.

We will address the following question: How have natural (gene flow, demography, climate adaptation) and human-mediated (dissemination, selection, resultant inbreeding) evolutionary processes interacted together to create the present-day distribution of genomic diversity of O. bataua across Amazonia? This question will be tackled through an original sampling design (combining sites close to ancient villages with archaeological evidence of strong human activity and sites with no nearby evidence of pre-Colombian occupation) and modern evolutionary genomics (setting-up a genome-wide capture experiment to sequence the coding regions of thousands of candidate genes for adaptation and domestication). The originality of this project lies in: (1) the integration of past anthropogenic-disturbance knowledge to understand the biogeographic history of a hyperdominant food-producing palm across Amazonia; (2) the use of a custom capture kit composed of 20’000 molecular probes to target the exons of thousands of candidate genes for adaptation and domestication; (3) the development of innovative analytic procedures, including specific bioinformatics pipelines and custom Bayesian models of evolutionary genomics.

Collaborations

  • UMSR LEEISA (‘Laboratoire Ecologie, Evolution et Interactions des Systèmes Amazoniens’), Cayenne, Guyane Française
  • UMR AGAP (‘Genetic Improvement and Adaptation of Mediterranean and Tropical Plants’), Montpellier, France
  • INPA (Instituto Nacional de Pesquisas da Amazônia), Manaus, Brazil
  • University of California, Berkeley, USA
  • UFOPA (Federal University of Western Pará), Santarém, Brazil
  • IDSM (Instituto de Desenvolvimento Sustentável Mamirauá, Laboratório de Arqueologia), Tefé, Brazil
  • UMR BioGeCo (‘Biodiversity, Genes and Communities’), Bordeaux, France

Galerie d'images