Unravelling Taxonomic Complexity in Elusive Cetaceans: Mitogenome Insights into Evolutionary History and Cryptic Diversity of Bryde's Whales

Abstract

ABSTRACT Cetaceans, despite their ability to cross wide distances, enabling mostly high levels of gene flow, can develop unique genetic lineages driven by variations in life‐history traits, diverse migratory routes and local adaptation, complicating taxonomy and delineation of conservation units. Comprehensive genetic data are essential to overcome the challenges of obtaining suitable sample sizes from wild cetaceans while untangling cryptic species diversity. The Bryde's whale ( Balaenoptera edeni ) has a complicated discovery and taxonomic history that hinders accurate conservation assessments. In southern Africa, two populations are recognised: the inshore (SAi) and the offshore southeast Atlantic population (SEA). This study examines their phylogenetic relationships and evolutionary history relative to global populations and other balaenopterids. Complete mitochondrial genomes from SAi and SEA individuals were analysed alongside mitogenomes from the Arabian/Persian Gulf (United Arab Emirates, UAE, this study), North Pacific offshore ecotypes (GenBank), coastal Japan's inshore ecotype (GenBank) and five additional balaenopterid species (GenBank). Phylogenomic analyses revealed that each population forms a distinct lineage. SAi and SEA individuals grouped with the subspecies B. edeni brydei (offshore ecotype), despite the SAi occurring inshore, whereas the UAE individual was more closely related to B. edeni edeni and B. ricei . Divergence dating estimates suggest that the southern African, UAE and North Pacific populations shared a most recent common ancestor approximately 4–5 million years ago. These findings emphasise the need to reassess conservation units, population estimates and potentially reclassify new subspecies or species among Bryde's whales. This study demonstrates how mitogenome data can detect cryptic diversity in elusive cetaceans, directing more effective conservation of unique genetic lineages.