Mitochondrial DNA haplotypes reveal a fine-scale population structure in sperm whales (Physeter macrocephalus) around Sao Miguel Island (Azores)

Abstract

The sperm whale is an emblematic species of the Azores archipelago. After a century of intensive whaling, the species has become a focal point for ecotourism since the late 1980s, enabling collaborative research during tourism activities. This study assessed the feasibility of using a citizen science based non-invasive sampling approach to evaluate the genetic diversity of local sperm whales. Seven local whale-watching companies contributed to collect 70 fecal samples and 34 sloughed skin fragments between 2019 and 2024. A 588-bp fragment of mitochondrial DNA Control Region (MCR) was successfully sequenced from 56 fecal samples and all skin fragments, yielding 90 MCR sequences assigned to 79 individual sperm whales. MCR sequences from both sources of the same individuals were in perfect agreement, validating the use of fecal samples for mitochondrial haplotype analysis - the first study to do so in sperm whales. Four MCR haplotypes, including a newly determined one, evidenced different maternal lineages within the Macaronesia population. Haplotypes showed a clear geographic pattern around Sao Miguel Island: one was restricted almost exclusively to the south coast, while the other three occurred predominantly on the north. This contrasted distribution is likely correlated to different matrilineal groups.