Finless porpoises are among the most unusual of the roughly 98 living cetacean species. Unlike most whales and dolphins, they lack a dorsal fin entirely; instead, a broad, low ridge of tubercles runs along the middle of the back, and its width has long been used to separate the wide-ridged N. phocaenoides from its narrow-ridged relatives. First described by Georges Cuvier in 1829, the genus Neophocaena was for decades treated as a single species spanning the Indo-Pacific, but molecular and morphological work eventually split it into the wide-ridged form and the narrow-ridged N. asiaeorientalis, the latter of which includes the only porpoise population in the world that lives entirely in freshwater, in China’s Yangtze River. While the narrow-ridged subspecies have attracted intense research and conservation attention, the wide-ridged species, listed as Vulnerable by the IUCN, has remained comparatively neglected, particularly the Indian Ocean populations whose genetic makeup has been almost entirely unexamined at the whole-genome level.

The Kozhikode specimen gave the team a chance to close part of that gap. Morphologically, the animal matched the diagnostic profile of N. phocaenoides: a blunt, beakless head, spade-shaped teeth, a short and broad rostrum deflected downward, and a total body length of 144 centimeters, all within the known ranges for the species. After two months of burial in salted alluvial soil, the researchers exhumed a fully articulated skeleton, now deposited as a reference specimen in the National Zoological Collections of the Zoological Survey of India’s Western Ghat Regional Centre. The skeletal preparation preserved the complete vertebral column, paired limb bones, and a skull with a condylobasal length of 185 millimeters, providing a rare anatomical voucher for a species whose remains are seldom recovered intact along the Indian coast.

The mitochondrial genome extracted from the specimen proved to be 16,386 base pairs long, with the canonical vertebrate arrangement of 37 genes: 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. Most genes are transcribed from the heavy strand, with ND6 and eight tRNAs on the light strand, as is typical for mammals. The team documented the start and stop codons for every protein-coding gene and compared them with published mitogenomes of the narrow-ridged subspecies, finding lineage-specific variation in termination signals, including AGA and AGG stop codons in some genes. Comparative analyses across all available Neophocaena mitogenomes showed the genomes are AT-rich, that codon usage favors amino acids such as leucine, arginine, and serine, and that pairwise ratios of nonsynonymous to synonymous substitutions fall well below one for all 13 protein-coding genes, a signature of strong purifying selection that has kept these mitochondrial genes functionally stable across the genus.

The phylogenetic story proved more tangled than the tidy taxonomy might suggest. Drawing on 88 complete mitochondrial genomes from GenBank plus the new sequence, and using the harbour porpoise and Dall’s porpoise as outgroups, the researchers built a Bayesian tree that confirmed the monophyly of the porpoise family Phocoenidae with strong support. Yet the three nominal Neophocaena taxa did not sort into cleanly reciprocally monophyletic groups; instead, sequences assigned to N. phocaenoides and the two N. asiaeorientalis subspecies intermixed across the tree, with soft polytomies and extremely short branches hinting at rapid, recent diversification. Two automated species-delimitation methods, ABGD and ASAP, consistently parsed the mitogenomes into six operational taxonomic units, more than the three names currently recognized, underscoring how incomplete the genus’s classification remains.

The most striking result concerned the Arabian Sea. The newly sequenced Indian mitogenome clustered tightly with a single previously reported Arabian Sea genome, and the two together shared the highest number of segregating sites, 166, relative to their nearest neighbors of any haplotypes in the analysis. Both were assigned to the same distinct OTU by both delimitation methods. The authors suggest this reflects genuine regional genetic structuring, plausibly shaped by the Arabian Sea’s distinctive oceanography, where monsoon-driven upwelling, seasonal reversal of currents, and historically volatile glacial-age climates could have isolated porpoise populations from their Pacific counterparts. They caution, however, that sampling from the region remains thin, and that confirming the Arabian Sea porpoises as an evolutionarily significant unit will require broader population-level sampling, particularly from the Bay of Bengal, ideally using nuclear markers such as genome-wide SNPs rather than maternally inherited mitochondrial DNA alone.

To translate the genetics into conservation geography, the team built an ensemble species distribution model combining five algorithms, boosted regression trees, multivariate adaptive regression splines, generalized linear models, maximum entropy, and random forests, trained on 103 spatially rarefied occurrence records and ten uncorrelated environmental layers from the Bio-ORACLE database. The ensemble performed strongly, with training AUC values between 0.885 and 0.955 and cross-validation values between 0.862 and 0.895. One variable towered over the rest: bathymetry, which contributed nearly 62 percent of predictive power on average, reflecting the porpoise’s strict confinement to shallow coastal waters. Iron concentration, a micronutrient that fuels phytoplankton growth, contributed almost 12 percent, followed by seafloor slope, chlorophyll, and aspect. Temperature, salinity, and current velocity, by contrast, barely registered, indicating that the species’ distribution is governed primarily by depth and nutrient-driven productivity, proxies for the prey-rich coastal zones the animals depend on.

The model’s output was sobering. Within the IUCN-assessed range of roughly 2.95 million square kilometers, only about 256,742 square kilometers, or 8.71 percent, was predicted as suitable habitat, with the largest strongholds in Indonesia and China, and moderate extents in Myanmar, Malaysia, India, Vietnam, and Thailand. Worse, only 23.38 percent of the suitable area falls within existing marine protected areas or Important Marine Mammal Areas, leaving vast stretches of high-quality habitat effectively unprotected. The threat assessment layered a cumulative human impact index over the suitable habitat and found the heaviest pressures in the South China Sea region, around Singapore, China, and Taiwan, and in the Persian/Arabian Gulf, where Iraq, Kuwait, Qatar, and Iran showed substantial overlap between porpoise habitat and pollution, shipping, and coastal development. These are precisely the stressors, habitat loss to ports and aquaculture, vessel strikes in high-speed ferry corridors, and underwater noise that disrupts echolocation and foraging, that have driven the species’ decline.

The authors argue that the combination of a distinct Arabian Sea lineage and a fragmented, heavily pressured habitat portfolio demands both expanded spatial protection and smarter management. They advocate dynamic ocean management, in which protection measures shift in space and time using real-time data from remote sensing, animal tracking, and habitat models, and they call for intensified genomic sampling across the western half of the species’ range to resolve its population structure before it can inform formal taxonomic revision. The study has its limits, as the authors acknowledge: the genetic and morphological data come from a single stranded individual, and the distribution model rests on public occurrence records that capture broad patterns but not seasonal variability. Even so, the message is clear. A porpoise that slipped ashore on a Kerala beach has revealed a hidden branch of the finless porpoise family tree, and a map showing that the species’ future hangs on a sliver of shallow, productive sea that humanity has barely begun to protect.

Subject of Research: Mitogenomics and habitat suitability modeling of the Indo-Pacific finless porpoise Neophocaena phocaenoides

Article Title: Mitogenomic and Ecological Perspectives on the Wide‐Ridged Indo‐Pacific Finless Porpoise Neophocaena phocaenoides: Toward Emerging Conservation Strategies

Article References: Kamalakannan, M., Abedin, I., Putra, A., Hegde, V. D., Banerjee, D., Choi, J. H., Kim, H.-W., & Kundu, S. (2026). Mitogenomic and Ecological Perspectives on the Wide‐Ridged Indo‐Pacific Finless Porpoise Neophocaena phocaenoides : Toward Emerging Conservation Strategies. Ecology and Evolution, 16(9), Article e74249. https://doi.org/10.1002/ece3.74249

Image Credits: AI Generated

DOI: 10.1002/ece3.74249

Keywords: finless porpoise, Neophocaena phocaenoides, mitogenome, Arabian Sea, phylogenetics, species distribution model, marine conservation, habitat suitability, purifying selection, marine protected areas, cetacean genetics, IUCN Vulnerable