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opencc-zeroMar 2020View details →

Description and classification of echolocation clicks of Indian Ocean humpback (Sousa plumbea) and Indo-Pacific bottlenose (Tursiops aduncus) dolphins from Menai Bay, Zanzibar, East Africa

Passive acoustic monitoring (PAM) is a powerful method to study the occurrence, movement and behavior of echolocating odontocetes (toothed whales) in the wild. However, in areas occupied by more than one species, echolocation clicks need to be classified into species. The present study investigated whether the echolocation clicks produced by small, at-risk, resident sympatric populations of Indian Ocean humpback dolphin (Sousa plumbea) and Indo-Pacific bottlenose dolphin (Tursiops aduncus) in Menai Bay, Zanzibar, East Africa, could be classified to allow species specific monitoring. Underwater sounds of S. plumbea and T. aduncus groups were recorded using a SoundTrap 202HF in January and June-August 2015. Eight acoustic parameters, i.e. -10 dB duration, peak, centroid, lower -3 and lower -10 dB frequencies, and -3 dB, -10 dB and root-mean-squared bandwidth, were used to describe and compare the two species' echolocation clicks. Statistical analyses showed that S. plumbea clicks had significantly higher peak, centroid, lower -3 and lower -10 dB frequencies compared to T. aduncus, whereas duration and bandwidth parameters were similar for the two species. Random Forest (RF) classifiers were applied to determine parameters that could be used to classify the two species from echolocation clicks and achieved 28.6% and 90.2% correct species classification rates for S. plumbea and T. aduncus, respectively. <a name="_Hlk32088545">Both species were classified at a higher rate than expected at random, however the identified classifiers would only be useful for T. aduncus monitoring.</a> <a name="_Hlk32088580">The frequency and bandwidth parameters provided most power for species classification.</a> <a name="_Hlk32088592">Further study is necessary to identify useful classifiers for S. plumbea.</a> This study represents a first step in acoustic <a name="_Hlk32088605">description </a>and classification of S. plumbea and T. aduncus in the western Indian Ocean region, with potential application for future acoustic monitoring of species-specific temporal and spatial occurrence in these sympatric species.

opencc-zeroDec 2013View details →

Data from: Habitat-driven population structure of bottlenose dolphins, Tursiops truncatus, in the North-East Atlantic

Despite no obvious barrier to gene flow, historical environmental processes and ecological specializations can lead to genetic differentiation in highly mobile animals. Ecotypes emerged in several large mammal species as a result of niche specializations and/or social organization. In the North-West Atlantic, two distinct bottlenose dolphin (Tursiops truncatus) ecotypes (i.e. 'coastal' and 'pelagic') have been identified. Here, we investigated the genetic population structure of North-East Atlantic (NEA) bottlenose dolphins on a large scale through the analysis of 381 biopsy-sampled or stranded animals using 25 microsatellites and a 682-bp portion of the mitochondrial control region. We shed light on the likely origin of stranded animals using a carcass drift prediction model. We showed, for the first time, that coastal and pelagic bottlenose dolphins were highly differentiated in the NEA. Finer-scale population structure was found within the two groups. We suggest that distinct founding events followed by parallel adaptation may have occurred independently from a large Atlantic pelagic population in the two sides of the basin. Divergence could be maintained by philopatry possibly as a result of foraging specializations and social organization. As coastal environments are under increasing anthropogenic pressures, small and isolated populations might be at risk and require appropriate conservation policies to preserve their habitats. While genetics can be a powerful first step to delineate ecotypes in protected and difficult to access taxa, ecotype distinction should be further documented through diet studies and the examination of cranial skull features associated with feeding.

opencc-zeroDec 2008View details →

Data from: A worldwide perspective on the population structure and genetic diversity of bottlenose dolphins (Tursiops truncatus) in New Zealand

Bottlenose dolphins (Tursiops truncatus) occupy a wide range of coastal and pelagic habitats throughout tropical and temperate waters worldwide. In some regions, "inshore" and "offshore" forms or ecotypes differ genetically and morphologically, despite no obvious boundaries to interchange. Around New Zealand, bottlenose dolphins inhabit 3 coastal regions: Northland, Marlborough Sounds, and Fiordland. Previous demographic studies showed no interchange of individuals among these populations. Here, we describe the genetic structure and diversity of these populations using skin samples collected with a remote biopsy dart. Analysis of the molecular variance from mitochondrial DNA (mtDNA) control region sequences (n = 193) showed considerable differentiation among populations (Fst = 0.17, Φst = 0.21, P < 0.001) suggesting little or no female gene flow or interchange. All 3 populations showed higher mtDNA diversity than expected given their small population sizes and isolation. To explain the source of this variation, 22 control region haplotypes from New Zealand were compared with 108 haplotypes worldwide representing 586 individuals from 19 populations and including both inshore and offshore ecotypes as described in the Western North Atlantic. All haplotypes found in the Pacific, regardless of population habitat use (i.e., coastal or pelagic), are more divergent from populations described as inshore ecotype in the Western North Atlantic than from populations described as offshore ecotype. Analysis of gene flow indicated long-distance dispersal among coastal and pelagic populations worldwide (except for those haplotypes described as inshore ecotype in the Western North Atlantic), suggesting that these populations are interconnected on an evolutionary timescale. This finding suggests that habitat specialization has occurred independently in different ocean basins, perhaps with Tursiops aduncus filling the ecological niche of the inshore ecotype in some coastal regions of the Indian and Western Pacific Oceans.

opencc-zeroDec 2014View details →

Data from: The importance of delineating networks by activity type in bottlenose dolphins (Tursiops truncatus) in Cedar Key, Florida

Network analysis has proved to be a valuable tool for studying the behavioural patterns of complex social animals. Often such studies either do not distinguish between different behavioural states of the organisms or simply focus attention on a single behavioural state to the exclusion of all others. In either of these approaches it is impossible to ascertain how the behavioural patterns of individuals depend on the type of activity they are engaged in. Here we report on a network-based analysis of the behavioural associations in a population of bottlenose dolphins (Tursiops truncatus) in Cedar Key, Florida. We consider three distinct behavioural states—socializing, travelling and foraging—and analyse the association networks corresponding to each activity. Moreover, in constructing the different activity networks we do not simply record a spatial association between two individuals as being either present or absent, but rather quantify the degree of any association, thus allowing us to construct weighted networks describing each activity. The results of these weighted activity networks indicate that networks can reveal detailed patterns of bottlenose dolphins at the population level; dolphins socialize in large groups with preferential associations; travel in small groups with preferential associates; and spread out to forage in very small, weakly connected groups. There is some overlap in the socialize and travel networks but little overlap between the forage and other networks. This indicates that the social bonds maintained in other activities are less important as they forage on dispersed, solitary prey. The overall network, not sorted by activity, does not accurately represent any of these patterns.

opencc-zeroDec 2015View details →

Data from: Genetic isolation between coastal and fishery-impacted, offshore bottlenose dolphin (Tursiops spp.) populations

The identification of species and population boundaries is important in both evolutionary and conservation biology. In recent years, new population genetic and computational methods for estimating population parameters and testing hypotheses in a quantitative manner have emerged. Using a Bayesian framework and a quantitative model-testing approach, we evaluated the species status and genetic connectedness of bottlenose dolphin (Tursiops spp.) populations off remote northwestern Australia, with a focus on pelagic 'offshore' dolphins subject to incidental capture in a trawl fishery. We analysed 71 dolphin samples from three sites beyond the 50 m depth contour (the inshore boundary of the fishery) and up to 170 km offshore, including incidentally caught and free-ranging individuals associating with trawl vessels, and 273 dolphins sampled at 12 coastal sites inshore of the 50 m depth contour and within 10 km of the coast. Results from 19 nuclear microsatellite markers showed significant population structure between dolphins from within the fishery and coastal sites, but also among dolphins from coastal sites, identifying three coastal populations. Moreover, we found no current or historic gene flow into the offshore population in the region of the fishery, indicating a complete lack of recruitment from coastal sites. Mitochondrial DNA corroborated our findings of genetic isolation between dolphins from the offshore population and coastal sites. Most offshore individuals formed a monophyletic clade with common bottlenose dolphins (T. truncatus), while all 273 individuals sampled coastally formed a well-supported clade of Indo-Pacific bottlenose dolphins (T. aduncus). By including a quantitative modelling approach, our study explicitly took evolutionary processes into account for informing the conservation and management of protected species. As such, it may serve as a template for other, similarly inaccessible study populations.

opencc-by-4.0Sep 2024View details →

Particle trajectories generated by the eDNA fate and transport model for the Atlantic bottlenose dolphin (Tursiops truncatus) -- Part I

<ul> <li>"release" includes particle trajectories generated by the eDNA fate and transport model, which was driven by the hydrodynamics simulated with the realistic wind and tidal forcings.</li> <li>The python codes used to read the particle trajectories and get the particle counts in each model grid cell can be found in https://github.com/Jilian0717/eDNA_fate_transport_model/tree/main/particle_density</li> </ul>

opencc-by-4.0Sep 2024View details →

Particle trajectories generated by the eDNA fate and transport model for the Atlantic bottlenose dolphin (Tursiops truncatus) -- Part II

<ul> <li>"release_no_wind" includes particle trajectories generated by the eDNA fate and transport model, which was driven by the hydrodynamics simulated without wind forcing. The purpose is to diagnose the influence of wind on particle distributions.</li> <li>The python codes used to read the particle trajectories and get the particle counts in each model grid cell can be found in https://github.com/Jilian0717/eDNA_fate_transport_model/tree/main/particle_density</li> </ul>

opencc-zeroDec 2014View details →

Data from: Genome-wide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus)

Harmful algal blooms (HABs), which can be lethal in marine species and cause illness in humans, are increasing worldwide. In the Gulf of Mexico, HABs of Karenia brevis produce neurotoxic brevetoxins that cause large-scale marine mortality events. The long history of such blooms, combined with the potentially severe effects of exposure, may have produced a strong selective pressure for evolved resistance. Advances in next-generation sequencing, in particular genotyping-by-sequencing, greatly enable the genomic study of such adaptation in natural populations. We used restriction site-associated DNA (RAD) sequencing to investigate brevetoxicosis resistance in common bottlenose dolphins (Tursiops truncatus). To improve our understanding of the epidemiology and aetiology of brevetoxicosis and the potential for evolved resistance in an upper trophic level predator, we sequenced pools of genomic DNA from dolphins sampled from both coastal and estuarine populations in Florida and during multiple HAB-associated mortality events. We sequenced 129 594 RAD loci and analysed 7431 single nucleotide polymorphisms (SNPs). The allele frequencies of many of these polymorphic loci differed significantly between live and dead dolphins. Some loci associated with survival showed patterns suggesting a common genetic-based mechanism of resistance to brevetoxins in bottlenose dolphins along the Gulf coast of Florida, but others suggested regionally specific mechanisms of resistance or reflected differences among HABs. We identified candidate genes that may be the evolutionary target for brevetoxin resistance by searching the dolphin genome for genes adjacent to survival-associated SNPs.

Figure 5 in The common bottlenose dolphin (Tursiops truncatus) ecotypes of the western North Atlantic revisited: an integrative taxonomic investigation supports the presence of distinct species

Figure 5. Worldwide morphological analyses of bottlenose dolphins. Scatter plot of the principal component 1 (PC1) and 2 (PC2) scores from the analysis of 18 skull measurements and 316 bottlenose dolphin skulls. Ellipses correspond to the 95% confidence interval. Samples are differentiated by type classification and geographical region. The holotype Tursiops truncatus is represented by an open triangle.

Figure 2 in The common bottlenose dolphin (Tursiops truncatus) ecotypes of the western North Atlantic revisited: an integrative taxonomic investigation supports the presence of distinct species

Figure 2. Traditional morphometric analyses of bottlenose dolphins of the western North Atlantic. A, scatter plot of the principal component 1 (PC1) and 2 (PC2) scores from the analysis of 25 cranial variables and 147 samples. Ellipses correspond to the 95% confidence interval. The shape of the data points represents the ecotype (coastal or offshore) as defined based on random forest (RF) results. The colour of the data points represents the clustering classifications according to density clustering (DC) results: black, samples follow the same classification (coastal or offshore) as RF and the a priori stratification; orange, 'cluster-3' identified only by DC (see main text). B, violin plot of the total external body length (TL) differentiated per sex (F, female; M, male) and ecotype.

Figure 4. A, B in The common bottlenose dolphin (Tursiops truncatus) ecotypes of the western North Atlantic revisited: an integrative taxonomic investigation supports the presence of distinct species

Figure 4. A, B, genetic clustering and relationship of bottlenose dolphins of the western North Atlantic. Membership probabilities of bottlenose dolphins in the western North Atlantic were based on 19 nuclear microsatellite loci and inferred using TESS (A) and STRUCTURE (B). Each column represents one individual, with colours representing the proportional membership to each of the clusters: white, coastal cluster; black, offshore cluster. C, median joining network of mitochondrial DNA haplotypes of bottlenose dolphins of the western North Atlantic. Haplotypes found in samples identified as the coastal ecotype are shown in white and those identified as the offshore ecotype in black. The size of the circles is proportional to the haplotype frequency in each group. Red diamonds indicate either extinct or unsampled haplotypes. Small red numbers on the branches represent the step mutations; branches without numbers represent one step mutation. The unique heteroplasmic haplotypes were not included in this analysis owing to program limitations to deal with ambiguous bases. The haplotype (Ttr2) obtained for the holotype Tursiops erebennus is in red.

Figure 1 in The common bottlenose dolphin (Tursiops truncatus) ecotypes of the western North Atlantic revisited: an integrative taxonomic investigation supports the presence of distinct species

Figure 1. Map of the western North Atlantic study area showing the sampling locations of samples with only morphological data available (brown), with morphological and genetic data available (cyan) or with only genetic data available (gold). The 200 m isobath line is shown in bold black. Thin black lines represent the 2000 and 4000 m isobaths.

Figure 3 in The common bottlenose dolphin (Tursiops truncatus) ecotypes of the western North Atlantic revisited: an integrative taxonomic investigation supports the presence of distinct species

Figure 3. Three-dimensional geometric morphometric (GM) analyses of bottlenose dolphins of the western North Atlantic. A, allometry plot of predicted lines based on fitted values (unique allometries model) to visualize how shape allometry varies by ecotype. The PredLine method calculates fitted values from the procD.lm fit and plots the first principal component of the predicted values against size, i.e. lnCS (see Adams & Nistri, 2010). B, scatter plot of the principal component 1 (PC1) and 2 (PC2) scores based on 23 cranial landmarks and 90 samples. Ellipses correspond to the 95% confidence interval. Samples are differentiated by sex (F, female; M, male; U, unknown) and ecotype. The mean specific shape variation along PC1 (bottom right) and PC2 (top left) is also shown. Grey represents the mean shape, whereas black represents the change in shape from the mean shape. Sample 1, USNM504096; sample 2, USNM572261.

Figure 7 in The common bottlenose dolphin (Tursiops truncatus) ecotypes of the western North Atlantic revisited: an integrative taxonomic investigation supports the presence of distinct species

Figure 7. Assembled portions of the postcranial skeleton of the holotype Tursiops erebennus (Cope, 1865) deposited in the Academy of Natural Sciences of Drexel University (museum number ANSP 3020).

Figure 6 in The common bottlenose dolphin (Tursiops truncatus) ecotypes of the western North Atlantic revisited: an integrative taxonomic investigation supports the presence of distinct species

Figure 6. Compressed phylogenetic tree of bottlenose dolphins based on maximum likelihood. For sample information and the full tree, see the Supporting Information (Table S7; Fig. S11, respectively). The clade formed by seven haplotypes from this study found as the wNA coastal ecotype (and two GenBank haplotypes of the Bahamas and Cuba, respectively) is coloured in white, whereas the clade composed of three coastal haplotypes of the Gulf of Mexico, 15 of the Bahamas and Caribbean Sea, and Ttr2 (wNA coastal haplotype; Tursiops erebennus haplotype; GOMx coastal haplotype) is coloured in red. Most the haplotypes forming the Tursiops truncatus offshore clade (N = 192; including haplotypes from the present study found in the wNA offshore ecotype, in addition to GenBank haplotypes found in T. truncatus worldwide) are coloured in black. Highlighted inside the offshore clade are the haplotypes found in T. t. gephyreus (green) and 'Tursiops australis' (purple). The clade composed of coastal T. truncatus from Ecuador and Peru is coloured in light blue, whereas Tursiops aduncus clades are coloured in orange (one clade composed of haplotypes from Bangladesh/African waters and another of haplotypes from Chinese/Australian waters and one haplotype found in Bangladesh). The haplotype found in the holotype T. aduncus is shown in bold. Bootstrap values (UFBoot) cut-off ≥ 80, because UFBoot achieves more unbiased support values. Shimodaira–Hasegawa-like approximate likelihood ratio test (SH-aLRT; first value) and UFBoot (second value) bootstrap values are represented on the tree branches (see also Supporting Information, Fig. S11). Abbreviations: AFR, western Indian Ocean–African coast; AUS, Australian coast; BGD, Bangladeshi coast; CHN, Chinese coast; eNA, eastern North Atlantic; eSP, eastern South Pacific; MED, Mediterranean Sea; wNA, western North Atlantic; wNP, western North Pacific; wSA, western South Atlantic; wSP, western South Pacific.

opencc-zeroJul 2023View details →

Passive electroreception in bottlenose dolphins Tursiops truncatus: implication for micro- and large-scale orientation

For the two dolphin species Sotalia guianensis and Tursiops truncatus, it was shown that the vibrissal crypts located on the rostrum represent highly innervated, ampullary electroreceptors and that both species are correspondingly sensitive to weak electric fields. For a comparative assessment of the sensitivity of the bottlenose dolphin's electroreceptive system, we determined detection thresholds for DC and AC electric fields with two bottlenose dolphins. In a psychophysical experiment, the animals were trained to respond to electric field stimuli using the go/no-go paradigm. We show that bottlenose dolphins are able to detect DC electric fields as low as 2.4 &[mu]V cm -1 and 5.5 &[mu]V cm -1, respectively, a detection threshold in the same order of magnitude as those in the platypus and the Guiana dolphin. Detection thresholds for AC fields (1, 5, and 25 Hz) were generally higher than those for DC fields, and the sensitivity for AC fields decreased with increasing frequency. Although the electroreceptive sensitivity of dolphins is lower than that of elasmobranchs, it is suggested that it allows orientation at micro and large scales. In dolphins pursuing benthic foraging strategies, electroreception may facilitate short-range prey detection and target-oriented snapping of their prey. Furthermore, we discuss that the ability to detect weak electric fields may enable dolphins to detect the Earth's magnetic field through induction-based magnetoreception, thus allowing large-scale orientation.