Navigating Cetacean Mitochondrial Genome Data: Identifying Coverage and Deficiencies in Public Repositories.

Abstract

Genetic reference databases underpin a wide range of molecular approaches used to study cetacean biodiversity, including environmental DNA (eDNA), yet their reliability depends critically on data completeness, taxonomic accuracy, and metadata quality. Here, we present the first global assessment of mitochondrial sequence availability for cetaceans, evaluating taxonomic coverage, geographic representation, metadata completeness, and the distribution of five commonly targeted mitochondrial markers (12S rRNA, 16S rRNA, D-loop, cytochrome oxidase I, and cytochrome b). We retrieved 17,569 cetacean accessions from the NCBI Nucleotide database and an additional 259 COI-only records from BOLD Systems. Sequence availability was strongly biased toward Delphinidae and Balaenopteridae, whereas several families, notably Ziphiidae, were markedly underrepresented. We also identified discrepancies between database records and currently accepted cetacean taxonomy (e.g., outdated genera, non-accepted species, and collapsed higher-level taxa). Among markers, the D-loop dominated database representation, largely as standalone sequences (12,437 records), reflecting historical and current sequencing priorities and underscoring its continued relevance for population-level studies and eDNA marker development. Only 38% of accessions included geographic metadata, with georeferenced records concentrated primarily in the Americas and the Northwest Pacific, while large regions, including much of Africa, remained poorly represented. Although broad geographic patterns mirrored known family distributions, pronounced regional and taxonomic gaps persist. Our results highlight critical deficiencies in mitochondrial reference databases for cetaceans and emphasise the need for improved metadata standards, targeted sequencing of underrepresented taxa and regions, and open data sharing to enhance the effectiveness and global applicability of eDNA-based cetacean monitoring.