Cultural transmission of tool use combined with habitat specializations leads to fine-scale genetic structure in bottlenose dolphins

Socially learned behaviours leading to genetic population structure have rarely been described outside humans. Here, we provide evidence of fine-scale genetic structure that has probably arisen based on socially transmitted behaviours in bottlenose dolphins (Tursiops sp.) in western Shark Bay, Western Australia. We argue that vertical social transmission in different habitats has led to significant geographical genetic structure of mitochondrial DNA (mtDNA) haplotypes. Dolphins with mtDNA haplotypes E or F are found predominantly in deep (more than 10 m) channel habitat, while dolphins with a third haplotype (H) are found predominantly in shallow habitat (less than 10 m), indicating a strong haplotype–habitat correlation. Some dolphins in the deep habitat engage in a foraging strategy using tools. These ‘sponging’ dolphins are members of one matriline, carrying haplotype E. This pattern is consistent with what had been demonstrated previously at another research site in Shark Bay, where vertical social transmission of sponging had been shown using multiple lines of evidence. Using an individual-based model, we found support that in western Shark Bay, socially transmitted specializations may have led to the observed genetic structure. The reported genetic structure appears to present an example of cultural hitchhiking of mtDNA haplotypes on socially transmitted foraging strategies, suggesting that, as in humans, genetic structure can be shaped through cultural transmission.     

Cultural transmission of tool use by Indo-Pacific bottlenose dolphins (Tursiops sp.) provides access to a novel foraging niche

Culturally transmitted tool use has important ecological and evolutionary consequences and has been proposed as a significant driver of human evolution. Such evidence is still scarce in other animals. In cetaceans, tool use has been inferred using indirect evidence in one population of Indo-Pacific bottlenose dolphins (Tursiops sp.), where particular dolphins (‘spongers’) use marine sponges during foraging. To date, evidence of whether this foraging tactic actually provides access to novel food items is lacking. We used fatty acid (FA) signature analysis to identify dietary differences between spongers and non-spongers, analysing data from 11 spongers and 27 non-spongers from two different study sites. Both univariate and multivariate analyses revealed significant differences in FA profiles between spongers and non-spongers between and within study sites. Moreover, FA profiles differed significantly between spongers and non-spongers foraging within the same deep channel habitat, whereas the profiles of non-spongers from deep channel and shallow habitats at this site could not be distinguished. Our results indicate that sponge use by bottlenose dolphins is linked to significant differences in diet. It appears that cultural transmission of tool use in dolphins, as in humans, allows the exploitation of an otherwise unused niche.     

Why Do Dolphins Carry Sponges?

Tool use is rare in wild animals, but of widespread interest because of its relationship to animal cognition, social learning and culture. Despite such attention, quantifying the costs and benefits of tool use has been difficult, largely because if tool use occurs, all population members typically exhibit the behavior. In Shark Bay, Australia, only a subset of the bottlenose dolphin population uses marine sponges as tools, providing an opportunity to assess both proximate and ultimate costs and benefits and document patterns of transmission. We compared sponge-carrying (sponger) females to non-sponge-carrying (non-sponger) females and show that spongers were more solitary, spent more time in deep water channel habitats, dived for longer durations, and devoted more time to foraging than non-spongers; and, even with these potential proximate costs, calving success of sponger females was not significantly different from non-spongers. We also show a clear female-bias in the ontogeny of sponging. With a solitary lifestyle, specialization, and high foraging demands, spongers used tools more than any non-human animal. We suggest that the ecological, social, and developmental mechanisms involved likely (1) help explain the high intrapopulation variation in female behaviour, (2) indicate tradeoffs (e.g., time allocation) between ecological and social factors and, (3) constrain the spread of this innovation to primarily vertical transmission.     

Sponge Carrying by Dolphins (Delphinidae,Tursiops sp.): A Foraging Specialization Involving Tool Use?

During long-term research on bottlenose dolphins (Tursiops sp.) in Shark Bay, Western Australia, several individuals were observed carrying sponges, Echinodictyum mesenterinum, on their rostra. Over multiple years, five regularly sighted individuals were usually carrying sponges when encountered (67–100% of encounters). Four additional regularly sighted individuals were observed with sponges just one time each. All five individuals that routinely carried sponges were female. Two of the anomalous, one-time carriers were female, one was likely female, and one was male. Most observations of sponge carrying occurred within a restricted area, a relatively deep water channel (8–10 m deep). Surface observations of sponge carrying, including focal animal observations, revealed a stereotyped surfacing and diving pattern, and occasional indications of prey consumption. Three hypotheses are considered regarding the function of sponge carrying: 1. dolphins were playing with the sponges; 2. the sponges contain some compound of use to the dolphins (e.g. for medicinal purposes); and 3. the sponges were used as a tool to aid in foraging. The foraging tool hypothesis is best supported, but the exact manner in which sponges are used remains to be discovered. Sponge carrying is a behavioural specialization, probably involving foraging, and regularly engaged in by only a small proportion of female dolphins in Shark Bay.     

SHARK ATTACKS ON BOTTLENOSE DOLPHINS (TURSIOPS ADUNCUS) IN SHARK BAY, WESTERN AUSTRALIA: ATTACK RATE, BITE SCAR FREQUENCIES, AND ATTACK SEASONALITY

Shark predation may have been a central factor influencing the evolution of sociality in dolphins, as well as a determinant of dolphin habitat use and behavior. To understand the role of predation in driving interpopulation differences in behavior and sociality, it is important to quantify differences in predation risk among populations. This study describes the frequency of shark-inflicted scars and estimates the shark attack rate on bottlenose dolphins ( Tursiops aduncus ) in Shark Bay, Western Australia. Shark bite scars were found on 74.2% (95 of 128) of non-calves, and most of these scars were inflicted by tiger sharks ( Galeocerdo cuvier ). Although there were no differences among age/sex classes in the frequency of scarring, significantly more adult males than adult females bore multiple scars. The rate of unsuccessful shark attack was estimated to be between 11% and 13% of dolphins attacked each year. Large sharks (>3 m) were responsible for a disproportionate number of attacks. However, bites from small carcharhinid sharks on 6.2% of dolphins suggest that some of these small sharks may be dolphin ectoparasites. Both the scar frequencies and attack rate suggest that Shark Bay dolphins face a greater risk of predation than bottlenose dolphins in other locations.     

Does tiger shark predation risk influence foraging habitat use by bottlenose dolphins at multiple spatial scales?

Prey availability and predation risk are important determinants of habitat use, but their importance may vary across spatial scales. In many marine systems, predator and prey distributions covary at large spatial scales, but do no coincide at small spatial scales. We investigated the influences of prey abundance and tiger shark ( Galeocerdo cuvier ) predation risk on Indian Ocean bottlenose dolphin ( Tursiops aduncus ) habitat use across multiple spatial scales, in Shark Bay, Western Australia. Dolphins were distributed between deep and shallow habitats and across microhabitats within patches approximately proportional to prey density when shark abundance was low. When shark abundance was high, foraging dolphins greatly reduced their use of dangerous, but productive, shallow patches relative to safer deep ones. Also, dolphins reduced their use of interior portions of shallow patches relative to their edges, which have higher predator density but lower intrinsic risk (i.e. a higher probability of escape in an encounter situation). These results suggest that predation risk and prey availability influence dolphin habitat use at multiple spatial scales, but intrinsic habitat risk, and not just predator encounter rate, is important in shaping dolphin space use decisions. Therefore, studies of habitat use at multiple spatial scales can benefit from integrating data on prey availability and the subcomponents of predation risk.     

Where to catch a fish? The influence of foraging tactics on the ecology of bottlenose dolphins (Tursiops truncatus) in Florida Bay,Florida

Observations of bottlenose dolphins ( Tursiops truncatus ) in Florida Bay, Florida, between 2002 and 2005 revealed the use of three distinct foraging tactics. The goal of this study was to identify ecological correlates with tactic use and describe the impact of foraging specializations on the overall habitat use and distribution patterns of this dolphin population. Foraging tactics showed strong association with contrasting environmental characteristics, primarily depth. Locations of two of these tactic groups were spatially repulsed. Analyses of sighting histories of individual dolphins observed at foraging events determined that dolphins which employed one tactic never employed the other, and vice versa . Although bottlenose dolphins have plastic foraging behaviors, dolphins in Florida Bay appear to specialize in one tactic and subsequently limit their overall distribution patterns to coincide with habitats that facilitate success using that foraging tactic. This study demonstrates how foraging behavior can be an ecological determinant of overall dolphin habitat use patterns and works to create spatial structure within a population due to consistent mapping of tactics onto environmental variation. These foraging specializations potentially impact the social and demographic patterns of this dolphin population. The possible evolutionary mechanisms behind this intraspecific variation, including resource limitation and social learning, are considered.     

Bottlenose dolphins that forage with artisanal fishermen whistle differently

Acoustic communication is a taxonomically widespread phenomenon, crucial for social animals. We evaluate social sounds from bottlenose dolphins (Tursiops truncatus) of Laguna, southern Brazil, whose social structure is organized around a cooperative foraging tactic with artisanal fishermen. This tactic involves stereotyped and coordinated behaviour by dolphins and fishermen and is performed by a subset of the dolphin population, splitting it into two distinct social communities. We compared the acoustic parameters and type of whistles emitted by dolphins of the “non‐cooperative” and “cooperative” communities, both during their interactions with fishermen and in times where dolphins were engaged in other types of foraging. Our findings show how dolphins’ social sounds differ between foraging tactics and social communities. The frequencies of six whistle types (ascending, descending, concave, convex, multiple, flat) were significantly dependent on tactics and communities. Ascending whistles were more common than expected during foraging without fishermen, and among dolphins of the non‐cooperative community. Whistle acoustic parameters (duration, number of inclination changes and inflection points, and initial, final, maximum, minimum frequencies) also varied between social communities. In general, whistles emitted by cooperative dolphins, mainly when not interacting with fishermen, tended to be shorter, had higher frequency and more inflections than those emitted by non‐cooperative dolphins. These results suggest that different whistles may convey specific information among dolphins related to foraging, which we hypothesize promote social cohesion among members of the same social community. These differences in acoustic repertoires add a new dimension of complexity to this unique human–animal interaction.     

A new level of complexity in the male alliance networks of Indian Ocean bottlenose dolphins (Tursiops sp.)

Male bottlenose dolphins in Shark Bay, Western Australia form two levels of alliances; two to three males cooperate to herd individual females and teams of greater than three males compete with other groups for females. Previous observation suggested two alliance tactics: small four to six member teams of relatives that formed stable pairs or trios and unrelated males in a large 14-member second-order alliance that had labile trio formation. Here, we present evidence for a third level of alliance formation, a continuum of second-order alliance sizes and no relationship between first-order alliance stability and second-order alliance size. These findings challenge the 'two alliance tactics' hypothesis and add to the evidence that Shark Bay male bottlenose dolphins engage in alliance formation that likely places considerable demands on their social cognition.     

“Porpicide” in California: Killing of harbor porpoises (Phocoena phocoena) by coastal bottlenose dolphins (Tursiops truncatus)

Between 2007 and 2009, we witnessed three aggressive interactions between harbor porpoises and bottlenose dolphins in Monterey Bay, California. This is the first time such aggression has been documented in the Pacific, and the first time a harbor porpoise was collected immediately after witnessing its death, inflicted by bottlenose dolphins. Of the bottlenose dolphins present, 92% were males either confirmed (61%) or putative (31%). Since 2005, 44 harbor porpoise deaths inflicted by bottlenose dolphins were documented in California. Aberrant behavior was rejected as a cause of aggression, based on widespread documentation of similar behaviors in other populations of free‐ranging bottlenose dolphins. The evidence for interspecies territoriality as a form of competition for prey was weak: there is little dietary overlap and there are differences in bottlenose dolphin and harbor porpoise distribution patterns in California. Object‐oriented play was plausible as a form of practice to maintain intraspecific infanticidal skills or a form of play to maintain fighting skills between male associates. Contributing factors could be high‐testosterone levels, as attacks occurred at the height of the breeding season, and/or a skewed operational sex ratio. Ultimately, we need more information about bottlenose dolphin social structure at the time of the aggression.     

Habitat and resource partitioning among Indo‐Pacific bottlenose dolphins in Moreton Bay,Australia

Investigating resource partitioning among mobile marine predators such as cetaceans is challenging. Here we integrate multiple methodologies (analyses of habitat use, stable isotopes and trace elements) to assess ecological niche partitioning amongst two genetically divergent sympatric subpopulations (North and South) of Indo‐Pacific bottlenose dolphins (Tursiops aduncus) in Moreton Bay, Australia. Comparisons of the mean locations (latitude, longitude) and environmental variables (distance from sandbanks, distance from shore and water depth) observed at sightings of biopsy‐sampled individuals indicated that the North subpopulation occurred in the northwestern bay in significantly deeper water than the South subpopulation, which was found in southeastern nearshore waters and closer to sandbanks. Ratios of stable carbon and nitrogen isotopes in skin samples suggested that North dolphins foraged on higher trophic level prey in relatively more pelagic, offshore habitats, while South dolphins foraged on lower trophic prey in more nearshore, demersal and/or benthic habitats. Habitat partitioning was also reflected in higher blubber concentrations of most of the 13 measured trace elements, in particular lead, in the coastal South compared to the more pelagic North dolphins. These findings indicate that genetic subpopulations of bottlenose dolphins in Moreton Bay are adapted to different niches.     

Why Do Dolphins Form Mixed‐Species Associations in the Azores?

Mixed‐species associations are temporary associations between individuals of different species that are often observed in birds, primates and cetaceans. They have been interpreted as a strategy to reduce predation risk, enhance foraging success and/or provide a social advantage. In the archipelago of the Azores, four species of dolphins are commonly involved in mixed‐species associations: the common dolphin, Delphinus delphis, the bottlenose dolphin, Tursiops truncatus, the striped dolphin, Stenella coeruleoalba, and the spotted dolphin, Stenella frontalis. In order to understand the reasons why dolphins associate, we analysed field data collected since 1999 by research scientists and trained observers placed onboard fishing vessels. In total, 113 mixed‐species groups were observed out of 5720 sightings. The temporal distribution, habitat (water depth, distance to the coast), behaviour (i.e. feeding, travelling, socializing), size and composition of mixed‐species groups were compared with those of single‐species groups. Results did not support the predation avoidance hypothesis and gave little support to the social advantage hypothesis. The foraging advantage hypothesis was the most convincing. However, the benefits of mixed‐species associations appeared to depend on the species. Associations were likely to be opportunistic in the larger bottlenose dolphin, while there seemed to be some evolutionary constraints favouring associations in the rarer striped dolphin. Comparison with previous studies suggests that the formation of mixed‐species groups depends on several environmental factors, and therefore may constitute an adaptive response.     

The ecological conditions that favor tool use and innovation in wild bottlenose dolphins (Tursiops sp.)

Dolphins are well known for their exquisite echolocation abilities, which enable them to detect and discriminate prey species and even locate buried prey. While these skills are widely used during foraging, some dolphins use tools to locate and extract prey. In the only known case of tool use in free-ranging cetaceans, a subset of bottlenose dolphins (Tursiops sp.) in Shark Bay, Western Australia habitually employs marine basket sponge tools to locate and ferret prey from the seafloor. While it is clear that sponges protect dolphins' rostra while searching for prey, it is still not known why dolphins probe the substrate at all instead of merely echolocating for buried prey as documented at other sites. By 'sponge foraging' ourselves, we show that these dolphins target prey that both lack swimbladders and burrow in a rubble-littered substrate. Delphinid echolocation and vision are critical for hunting but less effective on such prey. Consequently, if dolphins are to access this burrowing, swimbladderless prey, they must probe the seafloor and in turn benefit from using protective sponges. We suggest that these tools have allowed sponge foraging dolphins to exploit an empty niche inaccessible to their non-tool-using counterparts. Our study identifies the underlying ecological basis of dolphin tool use and strengthens our understanding of the conditions that favor tool use and innovation in the wild.     

Synchrony,leadership, and association in male Indo-pacific bottlenose dolphins (Tursiops aduncus)

Male Indo-pacific bottlenose dolphins in Shark Bay, Western Australia, have converged with humans in the formation of nested male alliances and the use of synchrony in alliance behavior. Further, the strength of association among allied male dolphins varies and the stability of alliances correlates with the rate that males consort with estrus females (and is thus a possible indicator of dominance). To examine the possibility that synchrony reflects alliance association strength and dominance relationships, we analyzed videotapes from focal follows of two groups of males that reflect the range of alliance size and the strength of association between individuals in the population. We examined two variables: leadership during synchronous behaviors, based on which animal in a synchronously surfacing pair surfaced first, and the degree of synchrony, based on temporal differences in synchronous surfacing. We predicted that closer associates would exhibit a greater degree of synchrony and that one dolphin in a dyad would consistently lead. Contrary to our predictions, the degree of synchrony was inversely related to strength of association within alliances. This surprising result suggests that individuals with less secure bonds may strive more to achieve synchrony. We found no evidence of leadership during synchronous surfacing or between synchrony and other behavioral variables. Proximate mechanisms for synchronous behavior, such as entrainment and mutual motor imitation (“the mirror game” paradigm), may inhibit leadership in this context. Our results show that synchrony during surfacing is not a useful behavior to examine for dominance relationships in wild dolphins but it may be a useful tool to examine variation in alliance relationships.     

Selection of critical habitats for bottlenose dolphins (Tursiops truncatus) based on behavioral data,in relation to marine traffic in the Istanbul Strait,Turkey

Marine traffic is a significant source of disturbance to the bottlenose dolphin population in the Istanbul Strait, Turkey. To determine the importance of this threat, behavioral data together with sighting data of both dolphins and marine vessels were assessed for 2012. The current study suggests that the Istanbul Strait is used mostly as a foraging ground for bottlenose dolphins. Nonetheless, in the same area there is intense marine traffic as well as increase of industrial fishing activities in autumn. The findings of this study indicated that high‐speed ferries and high‐speed boats were the most significant source of disturbance. Moreover, increased densities of fishing vessels resulted in a drastic decline of dolphin sightings. This study highlights that vessel type, speed, distance, and density have a cumulative negative effect on dolphins. In order to mitigate the impacts of vessels, it is necessary to establish managed areas in the Istanbul Strait. Such proposed areas should limit speed and density of marine traffic and have specific restrictions on vessel routes. We propose three different seasonal managed areas according to their values as critical habitat for bottlenose dolphins in the strait.     

Fear factor: do dugongs (<Emphasis Type="Italic">Dugong dugon</Emphasis>) trade food for safety from tiger sharks (<Emphasis Type="Italic">Galeocerdo cuvier</Emphasis>)?

Predators can influence plants indirectly by altering spatial patterns of herbivory, so studies assessing the relationship between perceived predation risk and habitat use by herbivores may improve our understanding of community organization. In marine systems, the effects of predation danger on space use by large herbivores have received little attention, despite the possibility that predator-mediated alterations in patterns of grazing by these animals influence benthic community structure. We evaluated the relationship between habitat use by foraging dugongs (Dugong dugon) and the threat of tiger shark predation in an Australian embayment (Shark Bay) between 1997 and 2004. Dugong densities were quantified in shallow (putatively dangerous) and deep (putatively safe) habitats (seven survey zones allocated to each habitat), and predation hazard was indexed using catch rates of tiger sharks (Galeocerdo cuvier); seagrass volume provided a measure of food biomass within each zone. Overall, dugongs selected shallow habitats, where their food is concentrated. Foragers used shallow and deep habitats in proportion to food availability (input matching) when large tiger sharks were scarce and overused deep habitats when sharks were common. Furthermore, strong synchrony existed between daily measures of shark abundance and the extent to which deep habitats were overused. Thus, dugongs appear to adaptively manage their risk of death by allocating time to safe but impoverished foraging patches in proportion to the likelihood of encountering predators in profitable but more dangerous areas. This apparent food-safety trade-off has important implications for seagrass community structure in Shark Bay, as it may result in marked temporal variability in grazing pressure. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia

Highly mobile marine species in areas with no obvious geographic barriers are expected to show low levels of genetic differentiation. However, small‐scale variation in habitat may lead to resource polymorphisms and drive local differentiation by adaptive divergence. Using nuclear microsatellite genotyping at 20 loci, and mitochondrial control region sequencing, we investigated fine‐scale population structuring of inshore bottlenose dolphins (Tursiops aduncus) inhabiting a range of habitats in and around Moreton Bay, Australia. Bayesian structure analysis identified two genetic clusters within Moreton Bay, with evidence of admixture between them (F_ST = 0.05, P = 0.001). There was only weak isolation by distance but one cluster of dolphins was more likely to be found in shallow southern areas and the other in the deeper waters of the central northern bay. In further analysis removing admixed individuals, southern dolphins appeared genetically restricted with lower levels of variation (AR = 3.252, π = 0.003) and high mean relatedness (r = 0.239) between individuals. In contrast, northern dolphins were more diverse (AR = 4.850, π = 0.009) and were mixing with a group of dolphins outside the bay (microsatellite‐based STRUCTURE analysis), which appears to have historically been distinct from the bay dolphins (mtDNA Φ_ST = 0.272, P < 0.001). This study demonstrates the ability of genetic techniques to expose fine‐scale patterns of population structure and explore their origins and mechanisms. A complex variety of inter‐related factors including local habitat variation, differential resource use, social behaviour and learning, and anthropogenic disturbances are likely to have played a role in driving fine‐scale population structure among bottlenose dolphins in Moreton Bay.     

Genetic divergence between two phenotypically distinct bottlenose dolphin ecotypes suggests separate evolutionary trajectories

Due to their worldwide distribution and occupancy of different types of environments, bottlenose dolphins display considerable morphological variation. Despite limited understanding about the taxonomic identity of such forms and connectivity among them at global scale, coastal (or inshore) and offshore (or oceanic) ecotypes have been widely recognized in several ocean regions. In the Southwest Atlantic Ocean (SWA), however, there are scarce records of bottlenose dolphins differing in external morphology according to habitat preferences that resemble the coastal‐offshore pattern observed elsewhere. The main aim of this study was to analyze the genetic variability, and test for population structure between coastal (n = 127) and offshore (n = 45) bottlenose dolphins sampled in the SWA to assess whether their external morphological distinction is consistent with genetic differentiation. We used a combination of mtDNA control region sequences and microsatellite genotypes to infer population structure and levels of genetic diversity. Our results from both molecular marker types were congruent and revealed strong levels of structuring (microsatellites F_ST = 0.385, p < .001; mtDNA F_ST =  0.183, p < .001; Φ_ST = 0.385, p < .001) and much lower genetic diversity in the coastal than the offshore ecotype, supporting patterns found in previous studies elsewhere. Despite the opportunity for gene flow in potential “contact zones”, we found minimal current and historical connectivity between ecotypes, suggesting they are following discrete evolutionary trajectories. Based on our molecular findings, which seem to be consistent with morphological differentiations recently described for bottlenose dolphins in our study area, we recommend recognizing the offshore bottlenose dolphin ecotype as an additional Evolutionarily Significant Unit (ESU) in the SWA. Implications of these results for the conservation of bottlenose dolphins in SWA are also discussed.     

High calf mortality in bottlenose dolphins in the Bay of Islands,New Zealand–a local unit in decline

Bottlenose dolphins (Tursiops truncatus) in the Bay of Islands, New Zealand, have been studied for almost two decades. Since 2003, fewer than 150 dolphins visited the bay during each season and the local unit has declined 7.5% annually from 1997 to 2006. The causes of decline are unclear but probably include mortality and emigration. Here, we used a long‐term database to estimate reproductive parameters of female bottlenose dolphins including recruitment rates. A total of 704 surveys were conducted in which 5,577 sightings of 408 individually identified dolphins were collected; of these 53 individuals were identified as reproductive females. The calving rate increased between periods (1997–1999 = 0.13, CL = 0.07–0.21; 2003–2005 = 0.25, CL = 0.16–0.35 calves/reproductive female/year). A 0.25 calving rate suggests that on average, a female gives birth only once every four years, which is consistent with the estimated calving interval (4.3 yr, SD = 1.45) but still is lower than values reported for other populations. Conversely, apparent mortality rates to age 1+ (range: 0.34–0.52) and 2+ (range: 0.15–0.59) were higher than values reported elsewhere. The high apparent calf mortality in conjunction with a decline in local abundance, highlight the vulnerability of bottlenose dolphins in the Bay of Islands. Long‐term studies are required to understand the causes of high calf mortality and the decline in local abundance. Meanwhile, management should focus on minimizing sources of anthropogenic disturbance and enforcing compliance with current legislation.     

Decline in local abundance of bottlenose dolphins (Tursiops truncatus) in the Bay of Islands,New Zealand

Regional populations of bottlenose dolphins (Tursiops truncatus) around New Zealand are genetically isolated from each other and the species was recently classified as nationally endangered based on relatively small population sizes and reports of high calf mortality. Here, we estimate the abundance and trends in one of these regional populations, the Bay of Islands, using a photo‐identification database collected from 1997 to 1999 and from 2003 to 2006, containing a total of 3,841 records of 317 individual dolphins. Estimates of abundance obtained with the robust design fluctuated widely but showed a significant decline in the number of dolphins present in the bay over time (7.5% annual rate of decline). Temporary emigration was random and fluctuated considerably (γ  =  0.18, SE = 0.07 to γ  =  0.84, SE = 0.06). Apparent survival was estimated at 0.928 (CI = 0.911–0.942). Seasonal estimates (26 seasons) obtained in POPAN also showed a significant decline in abundance (5.8% annual rate of decline). Despite the decline observed in local abundance, dolphins continue to be found regularly in the Bay of Islands, suggesting that fewer dolphins use the bay on regular basis. Consequently, it seems that a change in habitat use, mortality and possibly low recruitment could underlie the apparent local decline.