Temporal variation of the underwater soundscape in Jiaotou Bay,an Indo-Pacific humpback dolphin (Sousa chinensis) habitat off Hainan Island,China

The underwater soundscape is an important ecological element affecting numerous aquatic animals, in particular dolphins, which must identify salient cues from ambient ocean noise. In this study, temporal variations in the soundscape of Jiaotou Bay were monitored from February 2016 to January 2017, where a population of Indo-Pacific humpback dolphins (Sousa chinensis) has recently been a regular sighting. An autonomous acoustic recorder was deployed in shallow waters, and 1/3-octave band sound pressure levels (SPLs) were calculated with central frequencies ranging from 25 Hz to 40 kHz, then were grouped into 3 subdivided bands via cluster analysis. SPLs at each major band showed significant differences on a diel, fishing-related period, seasonal, and tidal phase scale. Anthropogenic noise generated by passing ships and underwater explosions were recorded in the study area. The fish and dolphin acoustic activities both exhibited diel and seasonal variations, but no tidal cycle patterns. A negative significant relationship between anthropogenic sound detection rates and dolphin detection rates were observed, and fish detection rates showed no effect on dolphin detection rates, indicating anthropogenic activity avoidance and no forced foraging in dolphins in the study area. The results provide fundamental insight into the acoustic dynamics of an important Indo-Pacific humpback dolphin habitat within a coastal area affected by a rapid increase in human activity, and demonstrate the need to protect animal habitat from anthropogenic noises.     

Whistle signal variations among three Indo-Pacific humpback dolphin populations in the South China Sea: a combined effect of the Qiongzhou Strait's geographical barrier function and local ambient noise?

Geographic variations in the dolphin whistles could be useful in assessing association and isolation among populations. Whistle of free-ranging Indo-Pacific humpback dolphins (Sousa chinensis) among the Pearl River Estuary (PRE), Leizhou Bei (LZB) and Sanniang Bay (SNB) populations were investigated. A total of 2850 whistles with legible fundamental contour were extracted and 15 acoustic parameters were measured. Contrary to SNB, PRE and LZB had the same relative proportion of tonal type compositions with flat and sine representing the most frequent types. The generalized linear model analysis showed significant acoustic difference among populations and tonal types. All frequency parameters in SNB were significantly higher than those in PRE and LZB, where no significant variation was observed in most of the parameters either at the population level or within each tonal type. Canonical discriminant functions analysis showed a smaller difference between PRE and LZB than between PRE and SNB and between LZB and SNB. Compared with previous recordings, recent recordings demonstrated a consistent pattern of becoming higher in whistle frequency parameters in both LZB and SNB populations, suggesting that noise pollution in LZB and SNB increasing with time according to the acoustic niche hypothesis. Dolphin whistle's geographic variations could be shaped by the combined function of the geographical barrier function of the Qiongzhou strait and local ambient noise. Considering the isolated condition and the relatively smaller population size of the humpback dolphin in the SNB, more effective and proactive conservation actions should be taken to prevent the extinction of small populations.     

A pioneering survey of deep-diving and off-shore cetaceans in the northern South China Sea

A pioneering boat-based survey was conducted in 2019, to gather baseline information regarding the presence, composition, relative abundance, and spatial distribution of deep-diving and off-shore cetaceans in the northern South China Sea (SCS). A total of 27 sightings comprising at least 8 cetacean species were recorded during the 13-day survey, including 5 deep-diving species (i.e. Risso's dolphin [Grampus griseus], short-finned pilot whale [Globicephala macrorhynchus], sperm whale [Physeter macrocephalus], Cuvier's beaked whale [Ziphius cavirostris], and an unidentified beaked whale [either the ginkgo-toothed beaked whale, Mesoplodon ginkgodens, or Deraniyagala's beaked whale, Mesoplodon hotaula]), as well as 3 off-shore dolphins (i.e. pantropical spotted dolphin [Stenella attenuate], striped dolphin [Stenella coeruleoalba], and Fraser's dolphin [Lagenodelphis hosei]). With the exception of pantropical spotted dolphins, all other species were sighted and recorded at sea in the northern SCS for the first time. The pantropical spotted dolphin was the most frequently sighted species, comprising 30% of the total sightings. Deep-diving cetaceans were mainly sighted in the northern Xisha Archipelago, whereas off-shore dolphins were distributed across the survey area. The pantropical spotted dolphin was observed in aggregations of more than 100 individuals and nearly all encountered species included calves; these findings suggested that the survey area functions as an important feeding and calving ground for various cetacean species. This pioneering survey provides fundamental information regarding cetacean fauna in the northern SCS and highlights the need to strengthen research and conservation efforts concerning these species.     

Bartonella species detection in captive, stranded and free-ranging cetaceans

We present prevalence of Bartonella spp. for multiple cohorts of wild and captive cetaceans. One hundred and six cetaceans including 86 bottlenose dolphins (71 free-ranging, 14 captive in a facility with a dolphin experiencing debility of unknown origin, 1 stranded), 11 striped dolphins, 4 harbor porpoises, 3 Risso's dolphins, 1 dwarf sperm whale and 1 pygmy sperm whale (all stranded) were sampled. Whole blood (n = 95 live animals) and tissues (n = 15 freshly dead animals) were screened by PCR (n = 106 animals), PCR of enrichment cultures (n = 50 animals), and subcultures (n = 50 animals). Bartonella spp. were detected from 17 cetaceans, including 12 by direct extraction PCR of blood or tissues, 6 by PCR of enrichment cultures, and 4 by subculture isolation. Bartonella spp. were more commonly detected from the captive (6/14, 43%) than from free-ranging (2/71, 2.8%) bottlenose dolphins, and were commonly detected from the stranded animals (9/21, 43%; 3/11 striped dolphins, 3/4 harbor porpoises, 2/3 Risso's dolphins, 1/1 pygmy sperm whale, 0/1 dwarf sperm whale, 0/1 bottlenose dolphin). Sequencing identified a Bartonella spp. most similar to B. henselae San Antonio 2 in eight cases (4 bottlenose dolphins, 2 striped dolphins, 2 harbor porpoises), B. henselae Houston 1 in three cases (2 Risso's dolphins, 1 harbor porpoise), and untyped in six cases (4 bottlenose dolphins, 1 striped dolphin, 1 pygmy sperm whale). Although disease causation has not been established, Bartonella species were detected more commonly from cetaceans that were overtly debilitated or were cohabiting in captivity with a debilitated animal than from free-ranging animals. The detection of Bartonella spp. from cetaceans may be of pathophysiological concern.     

An insight into the epidemiology of dolphin morbillivirus worldwide

Serum samples from 288 cetaceans representing 25 species and originating from 11 different countries were collected between 1995 and 1999 and examined for the presence of dolphin morbillivirus (DMV)-specific antibodies by an indirect ELISA (iELISA) (N = 267) or a plaque reduction assay (N = 21). A total of 35 odontocetes were seropositive: three harbour porpoises (Phocoena phocoena) and a common dolphin (Delphinus delphis) from the Northeastern (NE) Atlantic, a bottlenose dolphin (Tursiops truncatus) from Kent (England), three striped dolphins (Stenella coeruleoalba), two Risso's dolphins (Grampus griseus) and a bottlenose dolphin from the Mediterranean Sea, one common dolphin from the Southwest (SW) Indian Ocean, three Fraser's dolphins (Lagenodelphis hosei) from the SW Atlantic, 18 long-finned pilot whales (Globicephala melas) and a bottlenose dolphin from the SW Pacific as well as a captive bottlenose dolphin (Tursiops aduncus) originally from Taiwan. The presence of morbillivirus antibodies in 17 of these animals was further examined in other iELISAs and virus neutralization tests. Our results indicate that DMV infects cetaceans worldwide. This is the first report of DMV-seropositive animals from the SW Indian, SW Atlantic and West Pacific Oceans. Prevalence of DMV-seropositives was 85.7% in 21 pilot whales from the SW Pacific and both sexually mature and immature individuals were infected. This indicates that DMV is endemic in these animals. The same situation may occur among Fraser's dolphins from the SW Atlantic. The prevalence of DMV-seropositives was 5.26% and 5.36% in 19 common dolphins and 56 harbour porpoise from the NE Atlantic, respectively, and 18.75% in 16 striped dolphins from the Mediterranean. Prevalence varied significantly with sexual maturity in harbour porpoises and striped dolphins; all DMV-seropositives being mature animals. The prevalence of seropositive harbour porpoise and striped dolphins appeared to have decreased since previous studies. These data suggest that DMV is not endemic within these populations, that they are losing their humoral immunity against the virus and that they may be vulnerable to new epidemics.     

Malignant seminoma with metastasis, Sertoli cell tumor, and pheochromocytoma in a spotted dolphin (Stenella frontalis) and malignant seminoma with metastasis in a bottlenose dolphin (Tursiops truncatus)

Seminoma with metastasis was diagnosed in a spotted dolphin (Stenella frontalis) and an Atlantic bottlenose dolphin (Tursiops truncatus). Sertoli cell tumor and pheochromocytoma were also diagnosed in the spotted dolphin. The spotted and bottlenose dolphins were adult males that stranded and died on the coasts of northwest Florida and southeast North Carolina, respectively. Neoplasia is infrequently reported in cetaceans. This is the first report of seminoma, Sertoli cell tumor, and pheochromocytoma in a dolphin, the first report of three distinct neoplasms in a dolphin, and one of the few reports of malignant neoplasia in dolphins.     

Dermatitis with invasive ciliated protozoa in dolphins that died during the 1987-1988 Atlantic Bottlenose Dolphin morbilliviral epizootic

Dermatitis with intradermal cilated protozoa was identified in 18 of 95 (19%) Atlantic Bottlenose Dolphins (Tursiops truncatus) that died during the 1987-1988 Atlantic-dolphin morbillivirus epizootic. The lesions were characterized by focally extensive suppurative and histiocytic dermatitis and cellulitis with ulceration and variable numbers of dermal and hypodermal ciliates. Vasculitis, thrombosis, and/or intravascular ciliates were rarely present. In one dolphin, there was an associated lymphadenitis with ciliates, and in another, bronchopneumonia with rare intrabronchiolar ciliates. Ten of the dolphins were female, and eight were male. The animals ranged in length from 148 to 260 cm. Eleven were from Virginia, four were from New Jersey, and three were from Florida. In 13 dolphins, results of immunohistochemical and/or polymerase chain reaction (PCR) tests were positive for morbillivirus infection. Results of immunohistochemical tests were negative in four dolphins that were not also tested with PCR. Results were also negative in one dolphin tested using both methods. Nine dolphins had concomitant bacterial, fungal, and/or other protozoal infections. Fourteen other dolphins with ciliate-associated dermatitis were identified from 414 Atlantic bottlenose dolphin cases (3%) archived at the Armed Forces Institute of Pathology. The incidence of dermatitis with invasive ciliates is much greater in dolphins that died during the 1987-1988 epizootic.     

Pathologic and immunocytochemical studies of morbillivirus infection in striped dolphins (Stenella coeruleoalba).

Hundreds of striped dolphins (Stenella coeruleoalba) died along the Spanish Mediterranean coast during the second half of 1990. We necropsied 58 dolphins. Partial collapse of the lungs with patchy atelectasis, subcutaneous edema, icterus, and stomatitis were the most prominent gross morphologic changes. Histologically, a bronchiolo-interstitial pneumonia was the most frequent lesion (72% of the animals). It was characterized by hyperplasia of alveolar epithelial type II cells and formation of multinucleate syncytia in alveolar and bronchiolar lumina. Other prominent lesions were encephalitis (69%), lymphoid depletion, and formation of multinucleate syncytia in the cortex of lymph nodes. The distribution of morbillivirus antigen was investigated in 23 well-preserved dolphins using a monoclonal antibody against the hemagglutinin glycoprotein of phocine distemper virus. Positive immunostaining was found in brain (77%), in lung (70%), and in mesenteric (61%), mediastinal (47%), and prescapular (45%) lymph nodes. Phocine distemper virus antigen was demonstrated less frequently in trachea, stomach, biliary epithelium, intestine, kidney, and mammary gland. Necrotizing-hemorrhagic pneumonia and encephalitis due to Aspergillus fumigatus were seen in three dolphins, whereas two animals had lesions of toxoplasmosis. Changes in our dolphins were similar to those caused by distemper in seals and porpoises. The origin of the dolphin virus and the relationships among dolphin, seal, and porpoise morbilli viruses are unknown.     

Development and validation of monoclonal and polyclonal antibodies for the detection of immunoglobulin G of bottlenose dolphins (Tursiops truncatus).

Antibodies directed against species-specific immunoglobulin G (IgG) have a broad range of applications in serologic and immunologic research and in the development of clinical assays. Validated anti-IgG antibodies for marine mammal species are in short supply. The objective of this study was to produce and validate antibodies with specificity for IgG of the common bottlenose dolphin (Tursiops truncatus). Bottlenose dolphin IgG was purified using protein G. Two mouse monoclonal antibodies and a rabbit polyclonal antibody were developed from mice and rabbits immunized with bottlenose dolphin IgG. The specificity of the monoclonal antibodies and the polyclonal antibody for bottlenose dolphin IgG was first verified by Western blot analysis and enzyme-linked immunosorbent assay (ELISA). For further validation, both monoclonal antibodies and the polyclonal antibody were incorporated in an indirect ELISA for the detection of the immune response of bottlenose dolphins to a vaccine antigen. Three bottlenose dolphins were immunized with a commercial Erysipelothrix rhusiopathiae vaccine, and serial blood samples were collected from all dolphins for measurement of levels of circulating antibodies. Seroconversion was observed in all 3 dolphins by use of both monoclonal antibodies and the polyclonal antibody. Circulating antibodies were detectable as early as 6 days after immunization in 1 dolphin. Peak antibody levels were detected 14 days after the immunization. The ability to detect seroconversion in all 3 immunized bottlenose dolphins firmly establishes the specificity of the monoclonal antibodies and the polyclonal antibody for IgG of the common bottlenose dolphin.     

Evaluation of two-dimensional and three-dimensional ultrasound in the assessment of thyroid volume of the Indo-Pacific bottlenose dolphin (Tursiops aduncus)

The assessment of thyroid volume plays an indispensable role in the diagnosis and management of different thyroid diseases. The present study evaluates the accuracy of dolphin thyroid volume measurement as determined by four two-dimensional (2D) ultrasound methods (A-D), with a standard of reference using three-dimensional (3D) ultrasound. The measurement accuracy for different recognized thyroid configuration is also evaluated. Inter- and intraoperator variability of the measurement methods was determined. Thyroid ultrasound examinations were conducted in 16 apparently healthy Indo-Pacific bottlenose dolphins (Tursiops aduncus) with 2D and 3D ultrasound under identical scanning conditions. All 2D ultrasound measurement methods yielded high accuracies (79.9-81.3%) when compared with the 3D ultrasound measurement, and had high measurement reproducibility (77.6-86.2%) and repeatability (78.1-99.7%). For 2D ultrasound measurements, Methods A and B were more accurate and reliable than Methods C and D, regardless of thyroid configuration. Ultrasound is useful in the measurement of thyroid volume in bottlenose dolphins. For the first time, a reliable ultrasound scanning protocol for measuring dolphin thyroid volume was developed, which provides a means to establish a normative reference for the diagnosis of thyroid pathologies and to monitor the thyroid volume during the course of treatment in living dolphins. Key words: 3D ultrasound, Indo-Pacific bottlenose dolphin, thyroid volume measurement, Tursiops aduncus.     

Staphylococcus aureus infections of captive dolphins (Tursiops truncatus) and oceanarium personnel.

Samples from blowhole and pharynx of 1 dolphin ill with a respiratory tract infection and 31 healthy dolphins at 2 oceanariums were examined by bacteriologic cultural technique. During the same period, nasal and volar forearm skin samples were collected from 32 healthy personnel and from a furuncle on the forearm of 1 attendant. Coagulase-positive staphylococci were isolated from 8 dolphins (including the ill dolphin) and from 14 persons. Antibiotic sensitivity patterns (8 drugs were tested) differed markedly for the staphylococcal isolates recovered from dolphins, as compared with those from persons. Staphylocci from the dolphins were totally or partially sensitive to every antibiotic, whereas almost all of the isolates from persons were resistant to penicillin and ampicillin, as well as to certain other antibiotics. Staphylococcus bacteriophage typing revealed that only 1 isolate from a dolphin could be typed (type D11). Six of the isolates from persons were typable, but no isolate was sensitive to only type D11. It was concluded that, although Staphylococcus aureus could be isolated commonly from captive dolphins, there was no evidence of cross infection between the dolphins and the oceanarium personnel.     

Multilocus DNA metabarcoding diet analyses of small cetaceans: a case study on highly vulnerable humpback dolphins and finless porpoises from the Pearl River Estuary,China

Accurate diet identification of top predators is crucial to fully understand their ecological roles. Compared to terrestrial animals, gathering dietary information from cetaceans is notoriously difficult. Here, we applied a multilocus metabarcoding approach to investigate the diet of vulnerable Indo-Pacific humpback dolphins and Indo-Pacific finless porpoises from the Pearl River Estuary (PRE), China. Our analyses identified 21 prey fish species from the 42 humpback dolphin stomachs, as well as 10 species of fish and 1 species of cephalopod from the 13 finless porpoise stomachs. All of the taxa were assigned to the species level, highlighting that the multimarker approach could facilitate species identification. Most of the prey species were small- and medium-sized fishes that primarily fed on zooplankton. The calculated similarity index revealed a moderated dietary overlap between the 2 cetaceans, presumably due to the feeding of the 2 predators in association with fishing vessels in the PRE. A more diverse diet was observed in humpback dolphins in the closed fishing season compared to the fishing season, implying the influence on the dolphin diet due to the availability of commercial fishery resources. However, according to the results of species rarefaction curves, our findings on the feeding habits of the 2 cetaceans are still limited by insufficient sample size and therefore should be interpreted with caution. This study represents a first attempt to apply the multilocus DNA metabarcoding technique in the diet analysis of small cetaceans, although more efforts are needed to improve this type of analysis.     

Echocardiographic evaluation of the bottlenose dolphin (Tursiops truncatus).

Safe and effective echocardiography would represent a valuable tool for marine mammal veterinarians and physiologists evaluating the dolphin heart. Unfortunately, conventional ultrasound technology (transthoracic echocardiography) has been limited by logistic, anatomic, and behavioral challenges. Five mature male Atlantic bottlenose dolphins (Tursiops truncatus) were trained for echocardiographic imaging (four for both transthoracic and transesophageal imaging, and one for only transthoracic imaging). It was noted that transesophageal image quality transiently improved when the dolphins spontaneously exhaled. Subsequently, dolphins were conditioned to hold their breath following forced exhalation, and imaging proceeded during such behavioral breath holds. Over 25 transthoracic and 100 transesophageal echocardiographic studies were performed, including both two-dimensional imaging and color flow mapping. Transthoracic imaging yielded poor-quality images of only small portions of the heart. In contrast, transesophageal imaging, which improved dramatically with behavioral breath holding following exhalation, yielded consistently high-quality images of the entire heart (mitral, tricuspid, aortic, and pulmonary valves, atrial and ventricular septa, left and right atria, left and right ventricles, and ascending aorta and main pulmonary artery). Color flow mapping demonstrated mild tricuspid regurgitation in all dolphins, and mild aortic regurgitation in one dolphin found to have a pedunculated mass arising from the sinutubular junction just above the aortic valve. There were no complications in nonsedated dolphins. The heart of the bottlenose dolphin can be safely, effectively, and reproducibly evaluated with the use of transesophageal echocardiography in conjunction with behavioral breath holding following forced exhalation. This approach, and the normative echocardiographic data generated from this work, lays the foundation for future echocardiographic studies of cetaceans.     

Characterization of the immunoglobulin A heavy chain gene of the Atlantic bottlenose dolphin (Tursiops truncatus)

Immunoglobulin constant region heavy chain genes of the dolphin (Tursiops truncatus) have been described for IgM and IgG but not for IgA. Here, the heavy chain sequence of dolphin IgA has been cloned and sequenced as cDNA. RT-PCR amplification from blood peripheral lymphocytes was carried out using degenerate primers and a single sequence was detected. The inferred heavy chain structure shows conserved features typical of mammalian IgA heavy chains, including three constant (C) regions, a hinge region between constant region domain 1 (C1) and constant region domain 2 (C2), and conserved residues for interaction with the Fc alpha R1 and N-glycosylation sites. Comparisons of the deduced amino acid sequences of the IgA heavy chain for the dolphin and the evolutionarily related artiodactyl species showed high similarity. In cattle and sheep, as in dolphins, a single IgA subclass has been identified. Southern blot analysis as well as genomic PCR confirmed the presence of multiple IGHA sequences suggesting that IGHA pseudogenes may be present in the dolphin genome.     

Brucella-induced abortions and infection in bottlenose dolphins (Tursiops truncatus).

Two bottlenose dolphins (Tursiops truncatus) aborted fetuses that died as a result of Brucella infection. Brucella placentitis occurred in both cases. Infected placenta and vaginal/uterine fluids may transmit Brucella species to other cetaceans. In a third case, an identical organism was cultured from lung necropsy tissue of an adult female T. truncatus. Microbiology, specific polymerase chain reaction, and pulsed-field gel electrophoresis results supported the designation of an additional genomic group(s), Brucella delphini, for isolates adapted to T. truncatus. Current serologic diagnostic tests reliable for known Brucella species are unreliable in detecting dolphin brucellosis. Our findings, together with previous reports, suggest that dolphin brucellosis is a naturally occurring disease that can adversely impact reproduction in cetaceans. The zoonotic significance of cetacean brucellosis is unknown, although the disease has not been reported in people who have frequent contact with dolphins. Further studies on the zoonotic aspects, distribution, prevalence, virulence, and impact of this disease in cetaceans and other marine mammal species are needed.     

Near-shore distribution of Heaviside’s (Cephalorhynchus heavisidii) and dusky dolphins (Lagenorhynchus obscurus) at the southern limit of their range in South Africa

Photo-identification surveys over three years along 390 km of coastline north of Cape Town, revealed that Heaviside’s dolphin distribution was consistent between years and higher in areas more exposed to swells and with greater long-term availability of small hake Merluccius capensis (their principal prey). Dusky dolphin sighting rates varied considerably between years, but were generally higher in areas with lower hake availability and sandier shores (mostly straighter coastline). Large groups of 50–200 dusky dolphins were only seen in St Helena Bay, the site of a wind-driven upwelling zone. Heaviside’s dolphins were found in shallower, cooler water than dusky dolphins and were more likely to be seen during brighter phases of the moon (when nocturnal light conditions may influence the vertical migration patterns of prey) and in areas of high hake abundance. Near-shore fishing activity was higher in the northern half of the study area and clustered around harbours. Set netting occurred only at Yzerfontein and St Helena Bay, but due to changes in the industry is currently thought to be a low threat to the population. Interactions between Heaviside’s and dusky dolphins were usually neutral and sympatry appears to be mediated by differences in overall range and the type and size of prey species taken.     

Relationship between plasma iron concentration and gastric pH in captive adult bottlenose dolphins (Tursiops truncatus)

OBJECTIVE: To determine the correlation between plasma iron concentrations and gastric pH in a population of captive Atlantic bottlenose dolphins (Tursiops truncatus). ANIMALS: 6 adult female dolphins that ranged from 16 to 30 years of age. PROCEDURES: Blood and gastric samples were collected from each dolphin to allow measurement of plasma iron concentrations and gastric pH, respectively. Samples were collected each month for 12 months. RESULTS: Within each dolphin, plasma iron concentrations and gastric pH did not differ significantly over time. There was a strong negative correlation (r = -0.85) between plasma iron concentration and gastric pH, which suggested that dolphins with a lower gastric pH had a higher plasma iron concentration. CONCLUSIONS AND CLINICAL RELEVANCE: Analysis of results reported here suggested that gastric pH may play an important role in iron absorption in dolphins.     

Early divergence and differential population histories of the Indo-Pacific humpback dolphin in the Pacific and Indian Oceans

The currently recognized Indo-Pacific humpback dolphin occurs in estuaries and surrounding shallow waters from the South China Sea to the Asian coast of the Indian Ocean. However, a recent study suggested that the humpback dolphin from the Bay of Bengal may represent a distinct phylogenetic species. In this study, we sequenced 915-bp mtDNA segments from five geographic populations in both Chinese and Thai waters; together with previously published sequences, these data revealed that the ancestral Indo-Pacific humpback dolphin might have split during the transition from the Oligocene to Miocene (23.45 Mya, 95% HPD: 16.65–26.55 Mya), and then dispersed along the Pacific and Indian Ocean coasts of Asia. Genetic differentiation was detected between most of the examined populations, except for only a few pairwise populations in the northern South China Sea. Genetic differentiation/distance between the humpback dolphins from the northern and southern South China Sea met the sub-species threshold value proposed for marine mammals, whereas that between the humpback dolphins in the Pacific and the Indian Ocean was above the species threshold. Bayesian inference of historic gene flow indicated low but constant northward gene flow along the Indian Ocean coast; however, there was a recent abrupt increase in gene flow in the Pacific region, likely due to the shortening coastline at the low stand of sea level. Our results revealed that the current taxonomic classification of Indo-Pacific humpback dolphins may not reflect their phylogeography.