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

Genomic Divergence and the Evolution of Ecotypes in Bottlenose Dolphins (Genus Tursiops)

Climatic changes have caused major environmental restructuring throughout the world's oceans. Marine organisms have responded to novel conditions through various biological systems, including genomic adaptation. Growing accessibility of next-generation DNA sequencing methods to study nonmodel species has recently allowed genomic changes underlying environmental adaptations to be investigated. This study used double-digest restriction-site associated DNA (ddRAD) sequence data to investigate the genomic basis of ecotype formation across currently recognized species and subspecies of bottlenose dolphins (genus Tursiops) in the Southern Hemisphere. Subspecies-level genomic divergence was confirmed between the offshore common bottlenose dolphin (T. truncatus truncatus) and the inshore Lahille's bottlenose dolphin (T. t. gephyreus) from the southwestern Atlantic Ocean (SWAO). Similarly, subspecies-level divergence is suggested between inshore (eastern Australia) Indo-Pacific bottlenose dolphin (T. aduncus) and the proposed Burrunan dolphin (T. australis) from southern Australia. Inshore bottlenose dolphin lineages generally had lower genomic diversity than offshore lineages, a pattern particularly evident for T. t. gephyreus, which showed exceptionally low diversity. Genomic regions associated with cardiovascular, musculoskeletal, and energy production systems appear to have undergone repeated adaptive evolution in inshore lineages across the Southern Hemisphere. We hypothesize that comparable selective pressures in the inshore environment drove similar adaptive responses in each lineage, supporting parallel evolution of inshore bottlenose dolphins. With climate change altering marine ecosystems worldwide, it is crucial to gain an understanding of the adaptive capacity of local species and populations. Our study provides insights into key adaptive pathways that may be important for the long-term survival of cetaceans and other organisms in a changing marine environment.

The Seabed Makes the Dolphins: Physiographic Features Shape the Size and Structure of the Bottlenose Dolphin Geographical Units

The common bottlenose dolphin (Tursiops truncatus) is a cosmopolitan delphinid, regularly present in the Mediterranean Sea. According to previous studies, this dolphin tends to form resident geographical units scattered on the continental shelf. We investigated how the physiographic characteristics of the area of residence, with special reference to the size and shape of the continental shelf, affect the home range and the group size of the local units. We analysed and compared data collected between 2004–2016 by 15 research groups operating in different study areas of the Mediterranean Sea: the Alboran Sea, in the South-Western Mediterranean, the Gulf of Lion and the Pelagos Sanctuary for the marine mammals, in the North-Western Mediterranean, and the Gulf of Ambracia, in the North-Central Mediterranean Sea. We have found that in areas characterised by a wide continental platform, dolphins have wider home ranges and aggregate into larger groups. In areas characterized by a narrow continental platform, dolphins show much smaller home ranges and aggregate into smaller groups. The results obtained from this collective research effort highlight the importance of data sharing to improve our scientific knowledge in the field of cetaceans and beyond.

Form, function, and divergence of a generic fin shape in small cetaceans

Tail flukes as well as the dorsal fin are the apomorphic traits of cetaceans which appeared during the evolutionary process of adaptation to the aquatic life. Both appendages present a wing-like shape associated with lift generation and low drag. We hypothesized that the evolution of fins as lifting structures led to a generic wing design, where the dimensionless parameters of the fin cross-sections are invariant with respect to the body length and taxonomy of small cetaceans (Hypothesis I). We also hypothesized that constraints on variability of a generic fin shape are associated with the primary function of the fin as a fixed or flapping hydrofoil (Hypothesis II). To verify these hypotheses, we examined how the variation in the fin’s morphological traits is linked to the primary function, species and body length. Hydrodynamic characteristics of the fin cross-sections were examined with the CFD software and compared with similar engineered airfoils. Generic wing design of both fins was found in a wing-like planform and a streamlined cross-sectional geometry optimized for lift generation. Divergence in a generic fin shape both on the planform and cross-sectional level was found to be related with the fin specialization in fixed or flapping hydrofoil function. Cross-sections of the dorsal fin were found to be optimized for the narrow range of small angles of attack. Cross-sections of tail flukes were found to be more stable for higher angles of attack and had gradual stall characteristics. The obtained results provide an insight into the divergent evolutionary pathways of a generic wing-like shape of the fins of cetaceans under specific demands of thrust production, swimming stability and turning control.

Breeding program in rehabilitated bottlenose dolphins (Tursiops truncatus gephyreus) from the Southwestern Atlantic Ocean

Tursiops truncatus gephyreus is only found in the inshore waters of the Southwestern Atlantic Ocean. They are organized in small socially, structured groups, which lead to low genetic variability and high anthropogenic threats. Currently, the information about their reproductive biology and management is still insufficient. Thus, this study aims to present novel information recorded for 20 years regarding reproductive parameters in a small population of captive T. t. gephyreus. Three of the animals involved were found stranded in La Plata River estuary and, the other two were born at the oceanarium. Thirteen semen evaluations showed high-quality semen with a low percentage of sperm abnormalities. Twelve pregnancies and parturitions were observed. There was a clear calving seasonality during austral spring and summer. The duration of phase-2 of labor was approximately 80 min, being the caudal presentation the most frequent. The average inter-birth interval (IBI) was about 33 months. This is the first report that closely monitored parturition, IBI, and seminal evaluation in this species. Information gathered during this program will allow the development of adequate conservation plans for free-ranging populations.

New genetic diversity for endangered bottlenose dolphin subspecies along the Argentine coast

This study analyzed mtDNA sequences of two bottlenose dolphin subspecies found along the northern Patagonian coast, Argentina: the endangered Tursiops truncatus gephyreus and the data deficient Tursiops truncatus truncatus. Three haplotypes were recovered from nine samples. The most frequent haplotype represented the coastal morph, also two haplotypes showing falcate dorsal fin, a characteristic describing the oceanic morph. This finding suggests that both morphs may exist in sympatry in Argentina. Furthermore, sampling was extended beyond the species’ previously known range, including individuals as far as seven hundred kilometers to the south. Therefore, new genetic data, despite being preliminary, hint at an unexpectedly higher genetic diversity of matrilines than previously anticipated.

Skull morphology of bottlenose dolphins from different ocean populations with emphasis on South America

The bottlenose dolphin, genus Tursiops, is cosmopolitan occurring in tropical and temperate regions, with morphological variation between and within different oceans. Since the genus' taxonomy has been under discussion for a long time, this work aimed at analyzing the cranial variability of T. truncatus from different regions of the world. Geometric Morphometrics analyses were performed in 201 skulls of adult specimens, on dorsal, ventral, and lateral views, from the Eastern North Pacific, Eastern North Atlantic, Eastern South Atlantic, and Western South Atlantic oceans. The results indicate differences between individuals that inhabit the Atlantic and Pacific oceans. Within the Atlantic Ocean, there is an evident longitudinal differentiation of specimens from the eastern and western regions. A latitudinal separation was also observed, considering specimens from the North and South Atlantic Ocean. In the Western South Atlantic statistical differences were found between two morphological groups, identified as T. gephyreus (sensu Lahille, 1908) and T. truncatus, and the cross-validation presented 98% as minimum confidence for correct classification of these two groups. The present study provides strong morphological support to consider these two lineages as separate species.

Ecological divergence and speciation in common bottlenose dolphins in the western South Atlantic

Coastal and offshore ecotypes of common bottlenose dolphins have been recognized in the western South Atlantic, and it is possible that trophic niche divergence associated with social interactions is leading them to genetic and phenotypic differentiation. The significant morphological differentiation observed between these ecotypes suggests they represent two different subspecies. However, there is still a need to investigate whether there is congruence between morphological and genetic data to rule out the possibility of ecophenotypic variation accompanied by gene flow. Mitochondrial DNA (mtDNA) control region sequence data and 10 microsatellite loci collected from stranded and biopsied dolphins sampled in coastal and offshore waters of Brazil as well as 106 skulls for morphological analyses were used to determine whether the morphological differentiation was supported by genetic differentiation. There was congruence among the data sets, reinforcing the presence of two distinct ecotypes. The divergence may be relatively recent, however, given the moderate values of mtDNA nucleotide divergence (dA = 0.008), presence of one shared mtDNA haplotype and possibly low levels of gene flow (around 1% of migrants per generation). Results suggest the ecotypes may be in the process of speciation and reinforce they are best described as two different subspecies until the degree of nuclear genetic divergence is thoroughly evaluated: Tursiops truncatus gephyreus (coastal ecotype) and T. t. truncatus (offshore ecotype). The endemic distribution of T. t. gephyreus in the western South Atlantic and number of anthropogenic threats in the area reinforces the importance of protecting this ecotype and its habitat.

Ontogenetic and ecotypic variation in the coloration and morphology of rainbow trout (Oncorhynchus mykiss) in a stream–lake system

Alternative ecotypes of diverse animal taxa exhibit distinct, habitat-specific phenotypes. Rainbow trout (Oncorhynchus mykiss), a salmonid fish, exhibits stream-resident (fluvial), lake-migrant (adfluvial) and ocean-migrant (anadromous) ecotypes throughout its range. We investigated the coloration, and morphology associated with swimming performance of wild, native non-anadromous rainbow trout in connected stream and lake habitats of a south-west Alaskan watershed to assess if they exhibited phenotypic diversity consistent with the presence of alternative fluvial and adfluvial ecotypes. Colour differences among rainbow trout of different size classes and habitats (stream or lake) indicated ecotype-specific pathways, diverging at the same point in ontogeny and resulting in different terminal coloration patterns. Specifically, lake-caught fish exhibited distinct silvering of the body, whereas stream-caught fish displayed banded coloration when small and bronze colour when larger. The morphology of lake-caught rainbow trout also differed from that of stream-caught fish in features associated with swimming performance, and they exhibited both shared and unique morphological patterns compared to sympatric Salvelinus species in those habitats [Dolly Varden (S. malma) in streams, and Arctic char (S. alpinus) in the lake]. Greater morphological variation within stream- than lake-caught rainbow trout, and their limited overlap in morphology, suggested population-specific partial migration. This study highlights the intraspecific diversity of migratory behaviour and how conservation of particular phenotypes depends on managing both for genotypes and for habitats.

Spatiotemporal use predicts social partitioning of bottlenose dolphins with strong home range overlap

Ranging behaviour and temporal patterns of individuals are known to be fundamental sources of variation in social networks. Spatiotemporal dynamics can both provide and inhibit opportunities for individuals to associate, and should therefore be considered in social analysis. This study investigated the social structure of a Lahille's bottlenose dolphin (Tursiops truncatus gephyreus) population, which shows different spatiotemporal patterns of use and gregariousness between individuals. For this, we constructed an initial social network using association indices corrected for gregariousness and then uncovered affiliations from this social network using generalized affiliation indices. The association-based social network strongly supported that this dolphin population consists of four social units highly correlated to spatiotemporal use patterns. Excluding the effects of gregariousness and spatiotemporal patterns, the affiliation-based social network suggested an additional two social units. Although the affiliation-based social units shared a large part of their core areas, space and/or time use by individuals of the different units were generally distinct. Four of the units were strongly associated with both estuarine and shallow coastal areas, while the other two units were restricted to shallow coastal waters to the south (SC) and north of the estuary (NC), respectively. Interactions between individuals of different social units also occurred, but dolphins from the NC were relatively more isolated and mainly connected to SC dolphins. From a conservation management perspective, it is recommended that information about the dolphin social units should be incorporated in modeling intrapopulation dynamics and viability, as well as for investigating patterns of gene flow among them.

Short-distance barriers affect genetic variability of Rhizophora mangle L. in the Yucatan Peninsula

The environmental variability at local scale results in different physiognomic types of mangrove forest. However, this variability has never been considered in studies of mangrove genetic variability. This study analyzed the genetic and morphological variability and structure of Rhizophora mangle at regional and local scales in the Yucatan Peninsula. Thirteen mangrove populations (eight scrub and five tall), located in seven sites, were sampled, and their morphological variability and relationship with the availability of phosphorus and salinity were analyzed. The diversity and genetic structure were estimated at different hierarchical levels with nine microsatellites, also Bayesian inference and Principal Coordinates Analysis were used. We found a great morphological variability of R. mangle that responded to local environmental variability and not to the precipitation gradient of the peninsula. The genetic diversity found in the peninsula was greater than that reported for other populations in Mexico and was grouped into two regions: the Gulf of Mexico and the Caribbean Sea. At a local scale, tall and scrub mangroves had significant genetic differentiation suggesting that ecological barriers promote genetic differentiation within sites. These results need to be considered in future population genetic studies and for mangrove management and conservation.

Genetic divergence and fine scale population structure of the common bottlenose dolphin (Tursiops truncatus, Montagu) found in the Gulf of Guayaquil, Ecuador

The common bottlenose dolphin, Tursiops truncatus, is widely distributed along the western coast of South America. In Ecuador, a resident population of bottlenose dolphins inhabits the inner estuarine area of the Gulf of Guayaquil located in the southwestern part of the country and is under threat from different human activities in the area. Only one genetic study on South American common bottlenose dolphins has been carried out to date, and understanding genetic variation of wildlife populations, especially species that are identified as threatened, is crucial for defining conservation units and developing appropriate conservation strategies. In order to evaluate the evolutionary link of this population, we assessed the phylogenetic relationships, phylogeographic patterns, and population structure using mitochondrial DNA (mtDNA). The sampling comprised: (i) 31 skin samples collected from free-ranging dolphins at three locations in the Gulf of Guayaquil inner estuary, (ii) 38 samples from stranded dolphins available at the collection of the “Museo de Ballenas de Salinas,” (iii) 549 mtDNA control region (mtDNA CR) sequences from GenBank, and (iv) 66 concatenated sequences from 7-mtDNA regions (12S rRNA, 16S rRNA, NADH dehydrogenase subunit I–II, cytochrome oxidase I and II, cytochrome b, and CR) obtained from mitogenomes available in GenBank. Our analyses indicated population structure between both inner and outer estuary dolphin populations as well as with distinct populations of T. truncatus using mtDNA CR. Moreover, the inner estuary bottlenose dolphin (estuarine bottlenose dolphin) population exhibited lower levels of genetic diversity than the outer estuary dolphin population according to the mtDNA CR. Finally, the estuarine bottlenose dolphin population was genetically distinct from other T. truncatus populations based on mtDNA CR and 7-mtDNA regions. From these results, we suggest that the estuarine bottlenose dolphin population should be considered a distinct lineage. This dolphin population faces a variety of anthropogenic threats in this area; thus, we highlight its fragility and urge authorities to issue prompt management and conservation measures.

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 FST = 0.385, p < .001; mtDNA FST =  0.183, p < .001; ΦST = 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.