| Summary: | This repository contains all the scripts and most of the intermediary files necessary to replicate the analyses of the preprint "The antique genetic plight of the Mediterranean monk seal ( Monachus monachus )" available at: https://biorxiv.org/cgi/content/short/2021.12.23.473149v2 This version of the data has been revised according to two reviewers' comments and suggestions during a submission process at Proceedings of the Royal Society B. Within each of the different zipped folders a readme.txt file briefly explains how the analyses are organized. We thank all the collectors and museums listed in Table S1 for providing access to genetic samples. We are grateful to P. Kyritsis [Archipelagos], for his logistic help, to Sophie Courjal and the staff of the “Plateau technique - Biologie moléculaire et microbiologie” at EDB for their assistance during lab work, I. Carvalho for early comments on the manuscript and two anonymous reviewers who significantly helped improving the manuscript. This work was funded by the Fondation Prince Albert II de Monaco (project “Génétique de la conservation du phoque moine de Méditerranée”). The Genotoul bioinformatics (Bioinfo Genotoul) platforms provided computing resources. JS was supported by PANGO-GO (ANR-17-CE02-0001), and LABEX TULIP (ANR-10-LABX-0041). Abstract Disentangling the impact of Late Quaternary climate change from human activities can have crucial implications on the conservation of endangered species. We investigated the population genetics and demography of the Mediterranean monk seal (Monachus monachus), one of the world's most endangered marine mammals, through an unprecedented dataset encompassing historical (extinct) and extant populations from the eastern North Atlantic to the entire Mediterranean Basin. We show that Western-Sahara/Mauritania (Cabo Blanco), Madeira, Western Mediterranean (historical range) and Eastern Mediterranean regions segregate in four populations. This structure is likely the consequence of recent drift, combined with long-term ...
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