Unravelling taxonomic complexity in elusive cetaceans : mitogenome insights into evolutionary history and cryptic diversity of Bryde's whales
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Wiley
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
Description
DATA AVAILABILITY STATEMENT : The mitogenomic data of additional balaenopterid species and Bryde's whales from Japan are accessible from GenBank under the listed accession numbers provided in Table 1. Newly generated mitogenomes from the South African inshore population (SAi), the Southeast Atlantic population (SEA), and the United Arab Emirates population (UAE) are publicly available on GenBank under accession numbers provided.
SUPPLEMENTARY MATERIAL :
FIGURE S1: A Bayesian inference phylogenetic tree generated by MrBayes of the balaenopterid dataset based on full mitogenome data and 1 million MCMCs. The posterior probabilities are indicated at each node.
FIGURE S2: Maximum likelihood tree of the balaenopterid dataset based on the amino acid sequences of 13 mitochondrial protein-coding genes computed with 10,000 bootstrap replicates. The maximum likelihood bootstrap support is indicated by numbers along branches and at nodes.
FIGURE S3: Maximum likelihood tree of the Bryde's-Rice's dataset based on the amino acid sequences of 13 mitochondrial protein-coding genes computed with 10,000 bootstrap replicates. The maximum likelihood bootstrap support is indicated by numbers along branches and at nodes.
Keywords
Bryde's whale (Balaenoptera edeni), Cetaceans, Conservation unit, Cryptic diversity, Mitogenome, Phylogenomics, Taxonomy
Sustainable Development Goals
SDG-14: Life below water
Citation
Paynee, D., Bloomer, P., Penry, G. et al. 2026. “Unravelling Taxonomic Complexity in Elusive Cetaceans: Mitogenome Insights into Evolutionary History and Cryptic Diversity of Bryde's Whales.” Ecology and Evolution, vol. 16, no. 5, art. e73614, pp. 1-11. https://doi.org/10.1002/ece3.73614.