The main conclusions of this work are that the separation of Delphinus species based on the rostral index alone is not justified, and that D. capensis is not a valid species. Short and long-beaked common dolphins in the Atlantic and in some areas of the Pacific, therefore, all belong to a single species, Delphinus delphis. This conclusion supports accumulating evidence from genetic, morphological, ecological and stable isotope data [14–22,36]. We have also found evidence for the existence of an endemic common dolphin species in the NE Pacific, previously proposed by Heyning & Perrin [1] and Rosel et al. [11], possibly Delphinus bairdii (see discussion below).

Molecular taxonomy

Our results have several taxonomic implications. The most obvious one is the existence of a single Delphinus species in the Atlantic, as individuals morphologically assigned to D. capensis based on rostral length/zygomatic width (RL/ZW) ratios do not differ genetically from short-beaked individuals from several localities in the South and North Atlantic. That conclusion is reinforced by the fact that samples from the type locality of D. capensis (South Africa, SE Atl) were included in the analyses. Thus, according to genetic data, D. capensis is not a valid species. Common dolphins in the Atlantic belong to a single species, Delphinus delphis Linnaeus, 1758 (type locality “Oceano Europaeo”, or NE Atlantic). Throughout the Discussion, unless otherwise stated, the terms “short” and “long-beaked” common dolphins refer to morphotypes, not species.

We believe that the main confusion in the taxonomy of Delphinus was the strong weight given to rostral length, after the very thorough work of Heyning & Perrin [6]. The existence of two Californian common dolphin species with different rostral index ranges had been previously proposed by Banks & Brownell [37], after analyses of 64 skulls. Heyning & Perrin [6] analysed 26 cranial and 38 body measurements, as well as 19 post-cranial meristics and coloration patterns of a very large number of specimens from California. They did not find significant differences for any of the characters measured, other than coloration patterns and RL/ZW. Since coloration is too variable and not always available for museum specimens, RL/ZW became the rule of thumb for diagnosing the two species in California. Heyning & Perrin [6] correctly concluded that the long-beaked and short-beaked forms belonged to different species, commenting that their conclusion was also supported by genetic data, then in press, by Rosel et al. [11], and assigned the long-beaked individuals to D. capensis, because it had priority over D. bairdii Dall, 1873, a species with the long-beaked morphotype whose type locality was California, but which had been synonymised with D. capensis (by van Bree & Purves [12]). Our results completely agree with those of Heyning & Perrin [6] and also with Rosel et al. [11] and Kingston & Rosel [38] in that two Delphinus species occur in the NE Pacific, off the Californian coast. However, our data do not support Heyning & Perrin’s conclusion that the long-beaked species from California was the same as the long-beaked Delphinus capensis from the SE Atlantic. It is clear that even though RL/ZW is significantly different between the two Californian species, it cannot be treated as a diagnostic character between Delphinus species worldwide. The large weight put upon the RL/ZW ratio was understandable considering that it was the only significant difference found between the two Californian species, but our results show that extrapolating it to other parts of the world was a mistake. Remarkably, Heyning & Perrin [6] noticed not only that modal RL/ZW ratios were higher in South Africa, but also that vertebrae counts differed between long-beaked common dolphins from California (77–80 vertebrae) and South Africa (72–76 vertebrae), but chose to ignore that difference and focus, instead, on the RL/ZW ratio. Once the distinction of the two species in California was established both by good morphometric and genetic works, and the synonymy of D. bairdii and D. capensis had been wrongly proposed by van Bree & Purves [12], D. delphis and D. capensis became the two accepted species in the genus, with the RL/ZW ratio as the sole diagnostic character between them. This was used by researchers to identify common dolphins worldwide, even when genetic data consistently indicated that short-beaked and long-beaked common dolphins from the Atlantic did not form reciprocally monophyletic groups [21,22]. Interestingly, even though the latter authors did not draw any taxonomic conclusions on their work, which was based on both nuclear and mitochondrial markers, they hint at the possible non validity of D. capensis, stating that “the presently recognized long-beaked common dolphin species (Delphinus capensis) may prove to be invalid”, but at the same time that “it seems unlikely, despite their close genetic relationship, that all ecologically and morphologically distinct Delphinus populations belong to the same species”. One of the reasons for their reluctance to reject the validity of D. capensis may have been their limited sampling of SW Atlantic dolphins (N = 7). When we used a larger sample size (N = 37 new samples), including an area where long-beaked and short-beaked dolphins live in sympatry, it became clear that the two morphotypes did not correspond to genetically distinct groups (Fig 3) and are, probably, the result of phenotypic plasticity.

The difference in rostral length that distinguishes the two morphotypes seems to be related to niche partitioning, rather than speciation. Recently, Pinela et al. [36] found that short and long-beaked common dolphins from Mauritania had different isotopic signatures, which seem to reflect different feeding habits. The morphology of the rostrum is highly correlated with feeding specialisation, and some authors have suggested that as an explanation for convergence on the long-beaked morphotype [18,21]. According to Pinela et al. [36], in Mauritania longer beaks would correspond to feeding either in a higher trophic level or in more offshore habitats, in comparison to shorter beaks. Correlation between rostrum length and distance to the coast has been observed in many localities where the two morphotypes occur sympatrically, although usually the opposite pattern has been reported (longer beaks associated with shallower waters) [6,14,16].

Because mitochondrial DNA is inherited as a single locus, it is more susceptible to the confounding effects of stochastic lineage sorting and introgression, and may not depict the true evolutionary history, especially in the case of recent radiations [39–41]. Thus, the cytochrome b tree may not correspond to the species tree. The paraphyly observed in our trees could result from ancestral shared polymorphisms between very recently diverged species, or to historical and/or recurrent hybridisation between them. Studies have been able to detect shallow divergence of delphinid species using cytochrome b data [42–45], but this gene could simply be uninformative for Delphinus. However, the differentiation of long-beaked common dolphins from NE Pac shown in the cytochrome b tree seems to contradict this hypothesis. In any case, treatment of the Delphinus issue will probably benefit from including other mitochondrial genes (e.g. [46]), if not the complete mitogenome.

In addition, caution should be taken when considering mitochondrial data alone, especially a single locus. But with Delphinus, other genetic markers also do not support the existence of two cosmopolitan species. The studies by Natoli et al. [21] and Amaral et al. [22] used different genetic markers and slightly different geographic sampling, with similar results, which are also similar to ours. Nevertheless, our main conclusions are quite dissimilar, owing to different interpretation of data, especially in the case of Amaral et al. [22]. It is interesting that, even though these latter authors could not recover a statistically supported phylogeny of Delphinus species through Bayesian coalescence reconstruction based on a reasonable set of gene loci (one mitochondrial and five nuclear ones), they preferred to argue for the existence of several speciation events that might have taken place around the world. The reason for the lack of reciprocal monophyly would be incomplete lineage sorting (shared ancestral polymorphisms) and possibly extensive introgression, both resulting from a recent radiation of Delphinus (although the analytical method they used is theoretically adequate to solve genealogical relationships in such scenarios, [47]). We agree that incomplete lineage sorting and hybridisation may be important phenomena in the recent evolution of Delphinus. However, we consider that if they are so pervasive as to obliterate any phylogenetic signal, D. delphis and D. capensis should still be considered a single species.

Considering the worldwide distribution of common dolphins, the only genetic differentiation possibly strong enough to imply specific status would be that of long-beaked common dolphins from the NE Pacific. They have been considered recently as a highly differentiated population of Delphinus capensis [21,22], but since that species is not valid, they may in fact correspond to the Delphinus bairdii of Dall [48]. Two studies before Heyning & Perrin [6] argued in favour of two common dolphin species in the NE Pacific [37,49]. Van Bree & Purves [12] recognised the two morphotypes in California, but believed that intermediate types found in other parts of the world indicated they all belonged to D. delphis. Taking into consideration that long-beaked common dolphins from the NE Pacific are genetically differentiated from all other common dolphins ([11,21,22,38] and this study), the revalidation of Delphinus bairdii may be justified.

Our analyses also affect the currently accepted subspecies of D. capensis. Despite the very few sequences available to date, genetic data do not support the validity of the subspecies Delphinus capensis tropicalis van Bree, 1971 [5,50] (which, in any case, would be a subspecies of D. delphis, considering that D. capensis is invalid). The tropicalis-form is genetically divergent from other common dolphin populations (Table S1 of [22], but the paraphyly observed in phylogenetic trees ([22] and this study) argues against considering it a taxonomically valid entity. However, subspecific differentiation is not necessarily expected to result in monophyly, due to the very shallow divergence, which leads to incomplete lineage sorting and facilitates hybridisation. Another possibility would be slow lineage sorting due to very large effective population sizes–a likely scenario for pelagic schooling dolphins such as Delphinus in the Indian Ocean. In this setting, genetic drift would not have been severe enough to result in monophyly. The morphological evidence provided by Amaha [15] may suffice to support the subspecies D. delphis tropicalis. In the case of common dolphins from the Black Sea (Delphinus delphis ponticus Barabash-Nikiforov, 1935 [51]), preliminary genetic data suggest that they differ from those from the Eastern Mediterranean (D. delphis delphis) [52], but more samples need to be analysed to clarify this issue. The subspecific status of the tropicalis-form and of Black Sea common dolphins should be further investigated with the inclusion of more samples, genetic markers with higher resolution and phylogeographic analyses.

The issue about Delphinus species and subspecies should continue to receive attention in the coming years. Future studies using genetic data with increased resolution, including mitogenomes and a larger coverage of nuclear genomes from several specimens, should provide further clarity for the taxonomy of this genus. For example, recent mitogenomic data from 139 killer whales (Orcinus orca) provided unprecedented support for the genetic differentiation of ecotypes [53], which was corroborated by nuclear phylogenomic analyses using RAD-sequencing data [54]. Those results may lead to revision of the currently monotypic genus Orcinus. Analyses such as these are becoming more accessible due to next-generation sequencing technologies, and will likely be a promising avenue for future research on the Delphinus issue.