Atypical panmixia in a European dolphin species (Delphinus delphis): implications for the evolution of diversity across oceanic boundaries

Despite the scarcity of geographical barriers in the ocean environment, delphinid cetaceans often exhibit marked patterns of population structure on a regional scale. The European coastline is a prime example, with species exhibiting population structure across well‐defined environmental boundaries. Here we undertake a comprehensive population genetic study on the European common dolphin (Delphinus delphis, based on 492 samples and 15 loci) and establish that this species shows exceptional panmixia across most of the study range. We found differentiation only between the eastern and western Mediterranean, consistent with earlier studies, and here use approximate Bayesian computations to explore different scenarios to explain the observed pattern. Our results suggest that a recent population bottleneck likely contributed significantly to the differentiation of the Eastern Mediterranean population (in Greek waters). This interpretation is consistent with independent census data that suggest a sharp population decline in the recent past. The implication is that an unperturbed population may currently show panmixia across the full study range. This exception to the more typical pattern of population structure seen for other regional dolphin species (and for common dolphin populations elsewhere in the world) suggests particular ecological or life‐history traits distinct to this species in European waters.     

Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic

Highly mobile species in the marine environment may be expected to show little differentiation at the population level, but this is often not the case. Instead cryptic population structure is common, and effective conservation will require an understanding of how these patterns evolve. Here we present an assessment from both sides of the North Atlantic of differentiation among populations of a dolphin species that inhabits mainly pelagic waters, the Atlantic white-sided dolphin. We compare eleven putative populations in the western and eastern North Atlantic at mtDNA and microsatellite DNA loci and find reduced nucleotide diversity and signals for historical bottlenecks and post-bottleneck expansions in all regions. We calculate expansion times to have occurred during the early Holocene, following the last glacial maximum (LGM). We find evidence for connectivity among populations from either side of the North Atlantic, and differentiation between putative populations in the far northeast compared with all other areas sampled. Some data suggest the possibility of separate refugia during the LGM explaining this pattern, although ongoing ecological processes may also be a factor. We discuss the implications for developing effective programs of conservation and management in the context of ongoing anthropogenic impact.     

Eco-Evolutionary Processes Generating Diversity Among Bottlenose Dolphin, <Emphasis Type="Italic">Tursiops truncatus</Emphasis>, Populations off Baja California,Mexico

For highly mobile species that nevertheless show fine-scale patterns of population genetic structure, the relevant evolutionary mechanisms determining structure remain poorly understood. The bottlenose dolphin (Tursiops truncatus) is one such species, exhibiting complex patterns of genetic structure associated with local habitat dependence in various geographic regions. Here we studied bottlenose dolphin populations in the Gulf of California and Pacific Ocean off Baja California where habitat is highly structured to test associations between ecology, habitat dependence and genetic differentiation. We investigated population structure at a fine geographic scale using both stable isotope analysis (to assess feeding ecology) and molecular genetic markers (to assess population structure). Our results show that there are at least two factors affecting population structure for both genetics and feeding ecology (as indicated by stable isotope profiles). On the one hand there is a signal for the differentiation of individuals by ecotype, one foraging more offshore than the other. At the same time, there is differentiation between the Gulf of California and the west coast of Baja California, meaning that for example, nearshore ecotypes were both genetically and isotopically differentiated either side of the peninsula. We discuss these data in the context of similar studies showing fine-scale population structure for delphinid species in coastal waters, and consider possible evolutionary mechanisms.     

Hierarchical population structure and habitat differences in a highly mobile marine species: the Atlantic spotted dolphin

Recent molecular studies have shown that highly mobile species with continuous distributions can exhibit fine‐scale population structure. In this context, we assessed genetic structure within a marine species with high dispersal potential, the Atlantic spotted dolphin (Stenella frontalis). Using 19 microsatellite loci and mitochondrial control region sequences, population structure was investigated in the western North Atlantic, the Gulf of Mexico and the Azores Islands. Analyses of the microsatellite data identified four distinct genetic clusters, which were supported by the control region sequences. The highest level of divergence was seen between two clusters corresponding to previously described morphotypes that inhabit oceanic and shelf waters. The combined morphological and genetic evidence suggests these two lineages are on distinct evolutionary trajectories and could be considered distinct subspecies despite their parapatry. Further analysis of the continental shelf cluster resulted in three groups: animals inhabiting shelf waters in the western North Atlantic, the eastern Gulf of Mexico and the western Gulf of Mexico. Analyses of environmental data indicate the four genetic clusters inhabit distinct habitats in terms of depth and sea surface temperature. Contemporary dispersal rate estimates suggest all of these populations should be considered as distinct management units. Conversely, no significant genetic differentiation was observed between S. frontalis from offshore waters of the western North Atlantic and the Azores, which are separated by approximately 4500 km. Overall, the hierarchical structure observed within the Atlantic spotted dolphin shows that the biogeography of the species is complex because it is not shaped solely by geographic distance.     

Whistle characteristics of a newly recorded Indo-Pacific humpback dolphin (Sousa chinensis) population in waters southwest of Hainan Island,China, differ from other humpback dolphin populations

Indo-Pacific humpback dolphins (Sousa chinensis) use whistles to communicate with their conspecifics. Little is known about the acoustic repertoire of Indo-Pacific humpback dolphins in waters southwest of Hainan Island, a newly recorded population in 2014. In this study, whistles of Hainan humpback dolphin population were collected by using autonomous acoustic recorders. The fundamental frequencies and durations of whistles were in ranges of 0.71–21.35 kHz and 0.06–2.22 s, respectively. Significant intraspecific differences in duration and frequency of whistles were found between the Hainan population and the other geographically neighboring populations (in Chinese waters) or the population in Malaysia waters. Compared with other Sousa species, significant interspecific differences were also observed. Based on clustering analysis, the whistle parameters of neighboring populations were likely similar to each other. Significant differences were found between humpback dolphins in waters southwest of Hainan Island and those dolphins in the neighboring areas, supporting the hypothesis that this population may be independent. Ambient noise measurements in waters of Hainan Island, Zhanjiang, and Sanniang Bay showed that humpback dolphin populations may use whistles with longer duration, lower frequency, and fewer inflection points for more effective communication to adapt to a noisier environment.     

Genetic evidence on the demography of speciation in allopatric dolphin species

Under a neutral model, the stochastic lineage sorting that leads to gene monophyly proceeds slowly in large populations. Therefore, in many recent species with large population size, the genome will have mixed support for monophyly unless historical bottlenecks have accelerated coalescence. We use genealogical patterns in mitochondrial DNA and in introns of four nuclear loci to test for historical bottlenecks during the speciation and divergence of two temperate Lagenorhynchus dolphin species isolated by tropical Pacific waters (an antitropical distribution). Despite distinct morphologies, foraging behaviors, and mitochondrial DNAs, these dolphin species are polyphyletic at all four nuclear loci. The abundance of shared polymorphisms between these sister taxa is most consistent with the maintenance of large effective population sizes (5.09 x 10(4) to 10.9 x 10(4)) during 0.74-1.05 million years of divergence. A variety of population size histories are possible, however. We used gene tree coalescent probabilities to explore the rejection region for historical bottlenecks of different intensity given best estimates of effective population size under a strict isolation model of divergence. In L. obliquidens the data are incompatible with a colonization propagule of an effective size of 10 or fewer individuals. Although the ability to reject less extreme historical bottlenecks will require data from additional loci, the intermixed genealogical patterns observed between these dolphin sister species are highly probable only under an extended history of large population size. If similar demographic histories are inferred for other marine antitropical taxa, a parsimonious model for the Pleistocene origin of these distributions would not involve rare breaches of a constant dispersal barrier by small colonization propagules. Instead, a history of large population size in L. obliquidens and L. obscurus contributes to growing biological and environmental evidence that the equatorial barrier became permeable during glacial/interglacial cycles, leading to vicariant isolation of antitropical populations.     

Risso’s dolphins (<Emphasis Type="Italic">Grampus griseus</Emphasis>) in UK waters are differentiated from a population in the Mediterranean Sea and genetically less diverse

The Risso’s dolphin (Grampus griseus) has a worldwide distribution, but little is known about their population genetic structure. Local coastal populations are never known to be abundant, and are sometimes under anthropogenic impact. Therefore the question of regional differentiation by genetic drift and overall diversity levels is of conservation interest. Here we present preliminary data that clearly indicate genetic differentiation and lower genetic diversity of a population sampled in UK waters (primarily from the Western Isles, Scotland) compared to a Mediterranean sample. Significant differentiation was found in comparison with a sample from the Mediterranean for both microsatellite DNA markers (F _ST = 0.0296) and mtDNA sequence data (F _ST = 0.260; ϕ _ST = 0.542). Allelic diversity was lower in the UK for nearly all loci.     

Restricted dispersal in a continuously distributed marine species: common bottlenose dolphins Tursiops truncatus in coastal waters of the western North Atlantic

The marine environment provides an opportunity to examine population structure in species with high dispersal capabilities and often no obvious barriers to genetic exchange. In coastal waters of the western North Atlantic, common bottlenose dolphins, Tursiops truncatus, are a highly mobile species with a continuous distribution from New York to Florida. We examine if the highly mobile nature coupled with no obvious geographic barriers to movement in this region result in a large panmictic population. Mitochondrial control region sequences and 18 microsatellite loci indicate dolphins are partitioning the habitat both latitudinally and longitudinally. A minimum of five genetically differentiated populations were identified among 404 samples collected in the range of New Jersey to northern Florida using both genetic marker types, some inhabiting nearshore coastal waters and others utilizing inshore estuarine waters. The genetic results reject the hypothesis of a single stock of coastal bottlenose dolphins put forth after the 1987–1988 epizootic that caused a large‐scale die‐off of dolphins and suggest instead the disease vector was transferred from one population to the next as a result of seasonal migratory movements of some populations. These coastal Atlantic populations also differ significantly from bottlenose dolphin samples collected in coastal waters of the northern Gulf of Mexico, implying a long‐term barrier to movement between the two basins.     

Evidence for Distinct Coastal and Offshore Communities of Bottlenose Dolphins in the North East Atlantic

Bottlenose dolphin stock structure in the northeast Atlantic remains poorly understood. However, fine scale photo-id data have shown that populations can comprise multiple overlapping social communities. These social communities form structural elements of bottlenose dolphin (Tursiops truncatus) populations, reflecting specific ecological and behavioural adaptations to local habitats. We investigated the social structure of bottlenose dolphins in the waters of northwest Ireland and present evidence for distinct inshore and offshore social communities. Individuals of the inshore community had a coastal distribution restricted to waters within 3 km from shore. These animals exhibited a cohesive, fission-fusion social organisation, with repeated resightings within the research area, within a larger coastal home range. The offshore community comprised one or more distinct groups, found significantly further offshore (>4 km) than the inshore animals. In addition, dorsal fin scarring patterns differed significantly between inshore and offshore communities with individuals of the offshore community having more distinctly marked dorsal fins. Specifically, almost half of the individuals in the offshore community (48%) had characteristic stereotyped damage to the tip of the dorsal fin, rarely recorded in the inshore community (7%). We propose that this characteristic is likely due to interactions with pelagic fisheries. Social segregation and scarring differences found here indicate that the distinct communities are likely to be spatially and behaviourally segregated. Together with recent genetic evidence of distinct offshore and coastal population structures, this provides evidence for bottlenose dolphin inshore/offshore community differentiation in the northeast Atlantic. We recommend that social communities should be considered as fundamental units for the management and conservation of bottlenose dolphins and their habitat specialisations.     

TAXONOMIC STATUS AND GEOGRAPHICAL CRANIAL VARIATION OF COMMON DOLPHINS (DELPHINUS) IN THE EASTERN NORTH ATLANTIC

The common dolphin has a widespread distribution and is relatively abundant in the temperate to subtropical waters of the eastern North Atlantic. However, it is not known whether different species, subspecies, or populations occur in this region. We examined 393 common dolphin skulls obtained from both stranded and bycaught individuals collected between 1901 and 2005. The series included skulls of 152 females and 199 males, from animals ranging in body length from 93 to 230 cm and 105 to 244 cm, respectively. The ranges of total body length, skull size, RL/ZGW ratio and maximum upper alveolar (tooth) count of common dolphins in the eastern North Atlantic overlapped with those of both short- ( D. delphis ) and long-beaked ( D. capensis ) species found off the Californian coast. However, in the absence of additional data, the common dolphin in the eastern North Atlantic is regarded here as a large form of Delphinus delphis . Sexual dimorphism and possible sex-linked characters were identified within the sample. Results of the current study indicate some population differentiation within the eastern North Atlantic, with common dolphins off Portugal showing segregation in morphometric characteristics from common dolphins in other areas.     

厦门水域中华白海豚出现于围头湾

厦门海域的中华白海豚是一个受威胁的种群。以往有关该种群的调查范围主要集中在厦门以及邻近的南部漳州海域。为了获得厦门岛东部海域（包括晋江围头湾、小嶝岛以及大嶝岛部分水域）白海豚的分布和数量等信息,本文于2013年6—8月对该水域进行了船基样线法调查和照相识别研究。调查期间共目击到白海豚26群,照相识别白海豚个体27头。所有照相识别的白海豚个体均与厦门中华白海豚个体识别数据库中的个体匹配,表明厦门中华白海豚的分布区至少向东延伸至围头湾。本文白海豚遇见率为5.8群/100km和24.8头/100km,均要高于以往在厦门水域的调查结果,表明大嶝岛—围头湾水域是厦门中华白海豚的重要栖息地之一,值得优先保护和管理。     

Origin and radiation of Southern Hemisphere coastal dolphins (genus Cephalorhynchus)

The genus Cephalorhynchus (Gray 1846) consists of four species of small coastal dolphins distributed in cool temperate waters around the Southern Hemisphere. Each species is sympatric with other members of the subfamily Lissodelphininae but widely separated from other congeners. To describe the origin and radiation of these species, we examined 442 bp of mitochondrial DNA control region sequences of 307 individuals from the genus Cephalorhynchus and compared these to sequences from other members of the subfamily Lissodelphininae. We investigate the hypotheses that Cephalorhynchus is a monophyletic genus or, alternatively, that the four species have arisen separately from pelagic Lissodelphine species and have converged morphologically. Our results support the monophyly of Cephalorhynchus within the Lissodelphininae and a pattern of radiation by colonization. We confirm a pattern of shallow but diagnosable species clades with Heaviside's dolphin as the basal branch. We further examine the monophyly of maternal haplotypes represented by our large population sample for each species. Based on this phylogeographic pattern, we propose that Cephalorhynchus originated in the waters of South Africa and, following the West Wind Drift, colonized New Zealand and then South America. The Chilean and Commerson's dolphins then speciated along the two coasts of South America, during the glaciation of Tierra del Fuego. Secondary radiations resulted in genetically isolated populations for both the Kerguelen Island Commerson's dolphin and the North Island Hector's dolphin. Our results suggest that coastal, depth-limited odontocetes are prone to population fragmentation, isolation and occasionally long-distance movements, perhaps following periods of climatic change.     

Evidence for male dispersal along the coasts but no migration in pelagic waters in dusky dolphins (Lagenorhynchus obscurus)

Using nine nuclear species-specific microsatellite loci and two mitochondrial gene fragments (cytochrome b and control region), we investigated the processes that have shaped the geographical distribution of genetic diversity exhibited by contemporary dusky dolphin (Lagenorhynchus obscurus) populations. A total of 221 individuals from four locations (Peru, Argentina, southern Africa, and New Zealand) were assayed, covering most of the species’ distribution range. Although our analyses identify a general demographic decline in the Peruvian dusky dolphin stock (recently affected by high natural and human-induced mortality levels), comparison between the different molecular markers hint at an ancient bottleneck that predates recent El Niño oscillations and human exploitation. Moreover, we find evidence of a difference in dispersal behaviour of dusky dolphins along the South American coast and across the Atlantic. While data in Peruvian and Argentine waters are best explained by male-specific gene flow between these two populations, our analyses suggest that dusky dolphins from Argentina and southern Africa recently separated from an ancestral Atlantic population and, since then, diverged without considerable gene flow. The inclusion of a few New Zealand samples further confirms the low levels of genetic differentiation among most dusky dolphin populations. Only the Peruvian dusky dolphin stock is highly differentiated, especially at mitochondrial loci, suggesting that major fluctuations in its population size have led to an increased rate of genetic drift.     

Distribution and abundance of Indo‐Pacific humpback dolphins in Leizhou Bay,China

Abstract

The Indo‐Pacific humpback dolphin (Sousa chinensis) is under severe threat in Chinese waters. Only four small populations of this dolphin are known to survive in the East China Sea and South China Sea. We conducted exploratory surveys from June to September 2005, and found a population of humpback dolphins in Leizhou Bay. Thirty‐eight individuals were identified and catalogued, of which 26 were photographed and re‐identified on more than one occasion, and nine were sighted on five or more occasions each. Our preliminary estimate of the size of the Leizhou population is about 237 individuals, second only to the Pearl River estuary population. We suggest that Leizhou Bay has the potential to serve as a “humpback dolphin sanctuary” in Chinese waters.     

An analysis of sightings of Cetacea in British waters

An analysis is carried out of all documented sightings of cetaceans in British waters between 1950–1975, received by the Cetacean Group. Two major problems which must be taken into account in such an analysis are difficulties of specific identification and bias from uneven coverage.
The results show that porpoises are present in coastal waters for much of the year. The pattern of movements for this species is rather confused. Most dolphin species show peak numbers in summer, earliest in the north of Britain and later further south. Risso's dolphins may enter British waters rather earlier in spring than other species. Killer whales occur off the west coast of Britain and Ireland mainly between June-September. Pilot whales are seen in North Britain at most times of the year but otherwise enter British waters along the west coast in spring. Bottle-nosed whales and the larger whale species, including the Rorquals, are found only on the north and west coasts in summer and early autumn. For all species, herd size increases at the same time as increase in the numbers of sightings reported. Different species have different herd sizes with the largest occurring amongst porpoise and all dolphin species except Risso's dolphin, and the smallest amongst the large whale species. Herds may be accompanied by young individuals in spring-late summer, depending on the species.     

Spatio-temporal analysis of cetacean strandings and bycatch in a UK fisheries hotspot

Marine vertebrate strandings data can provide insights into the long-term dynamics of cetacean populations, and the threats they face. We investigate whether the spatio-temporal patterns of cetacean strandings around Cornwall, SW Britain, have changed in the past century. Analysis of strandings from 1911 to 2006 (n = 2,257) show that, since the mid-1970s, the relative frequency of strandings of common dolphins (Delphinus delphis), harbour porpoises (Phocoena phocoena) and pilot whales (Globicephala melas) has increased significantly. Seasonal peaks in strandings frequencies are apparent, between December and March for harbour porpoises and common dolphins, and between November and January for pilot whales. There were significant positive trends in the number of common dolphin and harbour porpoise strandings, as a proportion of total strandings, over time. Strandings of common dolphins, porpoises and all other species occur more frequently on the south coast of Cornwall. A total of 415 cetaceans were subject to full veterinary necropsy to determine cause of death, between 1990 and 2006, and 253 (61%) of these individuals were determined to have died due to bycatch in fishing gear. Analyses of industrialised fishing pressure in UK waters show the seas around Cornwall to be one of the most heavily fished areas of the UK. We suggest a number of factors that could be responsible for the recent increases in cetacean strandings in southwest UK waters in recent years, including survey effort, as well as abundance and range shifts that are potentially linked with climate change. Although detectable levels of bycatch rate have not increased over time, fisheries interactions are in significant part responsible for mortality patterns and are worthy of more detailed investigation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Demography and genetics suggest reversal of dolphin source‐sink dynamics,with implications for conservation

The forecast for the viability of populations depends upon metapopulation dynamics: the combination of reproduction and mortality within populations, as well as dispersal between populations. This study focuses on an Indo‐Pacific bottlenose dolphin (Tursiops aduncus) population in coastal waters near Bunbury, Western Australia. Demographic modeling of this population suggested that recent reproductive output was not sufficient to offset mortality. Migrants from adjacent populations might make up this deficit, so that Bunbury would act as a “sink,” or net recipient population. We investigated historical dispersal in and out of Bunbury, using microsatellites and mitochondrial DNA of 193 dolphins across five study locations along the southwestern Australian coastline. Our results indicated limited gene flow between Bunbury and adjacent populations. The data also revealed a net‐dispersal from Bunbury to neighboring populations, with microsatellites showing that more than twice as many individuals per generation dispersed out of Bunbury than into Bunbury. Therefore, in historic times, Bunbury appears to have acted as a source population, supporting nearby populations. In combination with the prior finding that Bunbury is currently not producing surplus offspring to support adjacent populations, this potential reversal of source‐sink dynamics may have serious conservation implications for Bunbury and other populations nearby.     

Population structure of nuclear and mitochondrial DNA variation among South American Burmeister’s porpoises (<Emphasis Type="Italic">Phocoena spinipinnis</Emphasis>)

Little is known about the biology of Burmeister’s porpoises (Phocoena spinipinnis), a small cetacean species endemic to South American waters. Information on stock structure, however, is urgently needed, as the species suffers from considerable mortality due to local fishery activities throughout its distribution range. Using mitochondrial control region sequences and 11 species-specific microsatellite loci, we assessed the genetic differentiation among 118 stranded, incidentally or directly-caught Burmeister’s porpoises from different localities in Peruvian, Chilean, and Argentine waters. F-statistics and Bayesian clustering analyses indicate a major population differentiation along the South American Pacific coast, separating Peruvian from both Chilean and Argentine individuals. Interestingly, this population boundary is consistent with the population structure found in another sympatrically-occurring cetacean species: the dusky dolphin (Lagenorhynchus obscurus). Given that vulnerability to local depletion for South American coastal porpoises and dolphins is probably highest in the Peruvian population (due to high exploitation levels and recurrent El Niño events), the genetic data reported here considerably strengthen the need for conservation efforts focused on regulation of catches in local waters. Moreover, we discuss possible genetic differentiation among Burmeister’s porpoises (i) from the Atlantic and Pacific Ocean and (ii) from different Peruvian harbors. Finally, cross-species amplifications suggest that our newly-developed microsatellite markers will be useful in population genetic studies in the five other extant porpoise species.     

Factors affecting the persistence of endangered Ganges River dolphins (Platanista gangetica gangetica)

The Ganges–Brahmaputra–Meghna and Karnaphuli (GBMK) River Basin in Nepal, India, and Bangladesh is among the world's most biodiverse river basins. However, human‐induced habitat modification processes threaten the ecological structure of this river basin. Among the GBMK’s diverse flora and fauna of this freshwater ecosystem, the endemic Ganges River dolphin (Platanista gangetica gangetica; GRD) is one of the most charismatic species in this freshwater ecosystem. Though a >50% population size reduction has occurred since 1957, researchers and decision‐makers often overlook the persistence (or evolutionary potential) of this species in the highly fragmented GBMK. We define the evolutionary potential as the ability of species/populations to adapt in a changing environment by maintaining their genetic diversity. Here, we review how evolutionary trap mechanisms affect the dynamics and viability of the GRD (hereafter Ganges dolphin) populations after rapid declines in their population size and distribution. We detected six potential trap mechanisms that might affect the Ganges dolphin populations discretely or in combination: (a) habitat modification; (b) occurrence of finite and geographically restricted local populations; (c) ratio of effective to estimate population size; (d) increasing risk of inbreeding depression in genetically isolated groups; (e) at‐risk behavioral attributes; and (f) direct fisheries–dolphin interactions. Because evolutionary traps appear most significant during low water season, they adversely affect demographic parameters, which reduce evolutionary potential. These traps have already caused local extirpation events; therefore, we recommend translocation among populations, including restoring and preserving essential habitats as immediate conservation strategies. Integrative evolutionary potential information based on demographic, genetic, and environmental data is still lacking. Thus, we identify gaps in the knowledge and suggest integrative approaches to understand the future of Ganges dolphins in South Asian waterways.     

Isolation by environmental distance in mobile marine species: molecular ecology of franciscana dolphins at their southern range

The assessment of population structure is a valuable tool for studying the ecology of endangered species and drafting conservation strategies. As we enhance our understanding about the structuring of natural populations, it becomes important that we also understand the processes behind these patterns. However, there are few rigorous assessments of the influence of environmental factors on genetic patterns in mobile marine species. Given their dispersal capabilities and localized habitat preferences, coastal cetaceans are adequate study species for evaluating environmental effects on marine population structure. The franciscana dolphin, a rare coastal cetacean endemic to the Western South Atlantic, was studied to examine these issues. We analysed genetic data from the mitochondrial DNA and 12 microsatellite markers for 275 franciscana samples utilizing frequency‐based, maximum‐likelihood and Bayesian algorithms to assess population structure and migration patterns. This information was combined with 10 years of remote sensing environmental data (chlorophyll concentration, water turbidity and surface temperature). Our analyses show the occurrence of genetically isolated populations within Argentina, in areas that are environmentally distinct. Combined evidence of genetic and environmental structure suggests that isolation by distance and a process here termed isolation by environmental distance can explain the observed correlations. Our approach elucidated important ecological and conservation aspects of franciscana dolphins, and has the potential to increase our understanding of ecological processes influencing genetic patterns in other marine species.