Da Silva O. auteur aut IRD Ayata S. D. auteur aut IRD Ser-Giacomi E. auteur aut IRD Leconte J. auteur aut IRD Pelletier E. auteur aut IRD Fauvelot Cécile auteur aut IRD Madoui M. A. auteur aut IRD Guidi L. auteur aut IRD Lombard F. auteur aut IRD Bittner L. auteur aut IRD text journalArticle eng text/pdf reformatted digital access For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-by-environment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies. specialized MEDITERRANEE 034 020 [Early access] [14 p.] 2022 1462-2912 https://www.documentation.ird.fr/hor/fdi:010086011 10.1111/1462-2920.16171 1462-2912 [F B010086011] https://www.documentation.ird.fr/hor/fdi:010086011 https://horizon.documentation.ird.fr/exl-doc/pleins_textes/2022-10/010086011.pdf IRD - Base Horizon / Pleins textes 2022-10-07 2025-02-24 fdi:010086011 fre