The antique genetic plight of the Mediterranean monk seal (Monachus monachus)

• Main Authors: Jordi Salmona, Julia Dayon, Emilie Lecompte, Alexandros A. Karamanlidis, Alex Aguilar, Pablo Fernandez de Larrinoa, Rosa Pires, Giulia Mo, Sabrina Agnesi, Asunción Borrell, Erdem Danyer, Bayram Öztürk, Arda M. Tonay, Luis M. Gonzalez, Panagiotis Dendrinos, Philippe Gaubert
• Format: Dataset
• Language: English
• Published: 2021
• Subjects: Mediterranean monk seals; Population decline; Demographic history; Marine mammals; Genetic diversity; Isolation by distance; Blanco; North Atlantic
• Online Access: https://zenodo.org/record/5796262; https://doi.org/10.5281/zenodo.5796262

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/2021.12.23.473149v1 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 Sophie Courjal and the staff of the “Plateau technique - Biologie moléculaire et microbiologie” at EDB for their assistance during lab work. 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, and the LABEX TULIP (ANR-10-LABX-0041) contributed to JS’ salary. 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 isolation by distance (R2 = 0.7), resulting from prevailing short-distance (< 500 km) and infrequent long-distance dispersal (< 1,500 km). All populations (Madeira especially), show high levels of inbreeding and low levels of genetic diversity, seemingly declining since historical time, but surprisingly not being impacted by the 1997 massive die-off in Cabo Blanco. ...