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 Cabo Blanco (Western Sahara/Mauritania), Madeira, Western Mediterranean (historical range) and Eastern Mediterranean regions segregate into four populations. This structure is probably the consequence of recent drift, combined with long-term isolation by distance ( R ² = 0.7), resulting from prevailing short-distance (less than 500 km) and infrequent long-distance dispersal (less than 1500 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. Approximate Bayesian Computation analyses support scenarios combining local extinctions and a major effective population size decline in all populations during Antiquity. Our results suggest that the early densification of human populations around the Mediterranean Basin coupled with the development of seafaring techniques were the main drivers of the decline of Mediterranean monk seals.

From August 2021 to December 2023, one adult male Mediterranean monk seal was repeatedly registered, through a systematic monitoring camera system, frequenting a marine cave in southern Kefalonia Island, central Ionian Sea, Greece. The presence of the same adult seal in a series of caves and overhangs in a bay in northwestern Zakynthos, southern Ionian Sea, in September 2023 and May 2024 was verified through opportunistic surveys and citizen science. The two locations are ca. 15 km apart and each is located in a different marine NATURA 2000 site. Appropriate conservation measures need to take into consideration the fact that seals do move between Kefalonia and Zakynthos (and possibly also other Ionian islands) and that the entire area has to be considered as a single “conservation unit” rather than elaborating protection measures on a small scale around a couple of resting and pupping caves alone. A full network of marine caves under strict protection surrounded by a buffer zone, taking into account at least the species’ home range, is needed in order to substantially cover the monk seal’s critical terrestrial habitats throughout the Ionian Sea.

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 Cabo Blanco (Western Sahara/Mauritania), Madeira, Western Mediterranean (historical range), and Eastern Mediterranean regions segregate into four populations. This structure is likely the consequence of recent drift, combined with long-term isolation by distance ( R ² = 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. Approximate Bayesian Computation analyses support scenarios combining local extinctions and a major effective population size decline in all populations during Antiquity. Our results suggest that the early densification of human populations around the Mediterranean Basin coupled with the development of seafaring techniques were the main drivers of the decline of Mediterranean monk seals.