MOLECULAR SYSTEMATICS OF RIVER DOLPHINS INFERRED FROM COMPLETE MITOCHONDRIAL CYTOCHROME-B GENE SEQUENCES

1,140 bp of the complete mitochondrial cytochrome- b gene sequences of baiji ( Lipotes vexillifer ), franciscana ( Pontoporia blainvillei ), and Ganges river dolphin ( Platanista gangetica gangetica ) were determined to address the systematic position and phylogeny of extant river dolphins with combination of homologous sequences of other cetaceans. The neighbor-joining (NJ), maximum parsimony (MP), and maximum likelihood (ML) phylogenetic analyses all identified the river dolphins into three lineages, i. e., Platanista, Lipotes , and Inia + Pontoporia . The Lipotes did not have sister relationship with either Platanista or Inia + Pontoporia , which strongly supported the referral of Lipotes to a separate family, i. e. , Lipotidae. There were very high sequence divergences between all river dolphin genera, suggesting a relatively longer period of separation time than those among other odontocete families.     

淡水豚类线粒体DNA 12S rRNA基因的序列变异及其分子系统学研究

淡水豚类４个代表属「白暨豚（Ｌｉｐｏｔｅｓ）、恒河豚（Ｐｌａｔａｎｉｓｔａ）、弗西豚（Ｐｏｎｔｏｐｏｒｉａ）和亚河豚（Ｉｎｉａ）」ｍｔＤＮＡ １２Ｓ ｒＲＮＡ基因的序列差异水平,高于其他齿鲸类科间的差异,特别是远远高于海豚总科内的科间差异。研究结果支持它们应归属于不同的科,即白暨豚科（Ｌｉｐｏｔｉｉｄａｅ）、恒河豚科（Ｐｌａｔａｎｉｓｔｉｄａｅ）、弗西豚科（Ｐｏｎｔｏｐｏｒｉｄａｅ）和亚河豚科（Ｉ     

淡水豚类分子系统发生的研究

测定了白暨豚和恒河豚细胞色素ｂ基因３０７ｂｐ的ＤＮＡ序列,并与其它鲸类的相应序列合并,分析了淡水豚类（恒河豚、印河豚、白暨豚、亚河豚和弗西豚）的系统学位置和系统发生。淡水豚类不同属间的序列差异已达到或超过了其它齿鲸类科间的差异水平,因此它们分别归属于不同的科,即恒河豚科、白暨豚科、亚河豚科和弗西豚科。系统发生分析支持淡水豚类和海豚类之间具有下述的关系：（恒河豚科（（白暨豚科（亚河豚科,弗西豚科））海豚总科））。即淡水豚的４个科中,恒河豚科是最早分化的一支,其次是白暨豚科,然后是亚河豚科和弗西豚科的分化。白暨豚科和亚河豚科＋弗西豚科组成海豚总科的姊妹群,并与海豚总科一同组成海豚下目。恒河豚与其它淡水豚类间无直接的亲缘关系。淡水豚类是并系的。把恒河豚类独立为恒河豚总科是合理的。初步认为有理由把白暨豚类也作为一个总科级的支系。恒河豚和印河豚间的序列差异极小,两者可能只是同一个种的２个亚种。     

Hearing loss in stranded odontocete dolphins and whales

The causes of dolphin and whale stranding can often be difficult to determine. Because toothed whales rely on echolocation for orientation and feeding, hearing deficits could lead to stranding. We report on the results of auditory evoked potential measurements from eight species of odontocete cetaceans that were found stranded or severely entangled in fishing gear during the period 2004 through 2009. Approximately 57% of the bottlenose dolphins and 36% of the rough-toothed dolphins had significant hearing deficits with a reduction in sensitivity equivalent to severe (70-90 dB) or profound (>90 dB) hearing loss in humans. The only stranded short-finned pilot whale examined had profound hearing loss. No impairments were detected in seven Risso's dolphins from three different stranding events, two pygmy killer whales, one Atlantic spotted dolphin, one spinner dolphin, or a juvenile Gervais' beaked whale. Hearing impairment could play a significant role in some cetacean stranding events, and the hearing of all cetaceans in rehabilitation should be tested.     

Phylogenetic Relationships Between the Orders Artiodactyla and Cetacea: A Combined Assessment of Morphological and Molecular Evidence

A character analysis of selected conservative morphological traits from extant and fossil artiodactyls and cetaceans was combined with a similar analysis of conservative nucleotide positions from the complete mitochondrial cytochrome b sequences of available extant artiodactyls, cetaceans, sirenians, perissodactyls, and other mammals. This combined analysis focuses on the evidence that supports conflicting hypotheses of artiodactyl monophyly, including the affinities of hippopotamids and the monophyly or paraphyly of odontocete cetaceans. Highly conserved morphological traits of the astragalus and deciduous dentition provide strong corroboration of artiodactyl monophyly, including extant and fossil hippopotamids. In contrast, cytochrome b gene sequences are incapable of confirming this monophyly, due to excessive homoplasy of nucleotide and amino acid traits within extant Eutheria. In like manner, highly conserved and uniquely derived morphological features of the skull and auditory regions provide robust corroboration of Odontoceti monophyly, including extant and fossil physeteroids. Several nucleotide similarities do exist between physeteroids and mysticetes; however, most are either silent third-position transversions or occur also in two or more odontocete families. We suggest that increased taxon sampling, combined with functional considerations of amino acids and their secondary structure in protein-coding genes, are essential requirements for the phylogenetic interpretations of molecules at higher taxonomic levels, especially when they conflict with well-supported hypotheses of mammalian phylogeny, corroborated by uniquely derived morphological traits from extant and fossil taxa.     

Head morphology in perinatal dolphins: a window into phylogeny and ontogeny

In this paper on the ontogenesis and evolutionary biology of odontocete cetaceans (toothed whales), we investigate the head morphology of three perinatal pantropical spotted dolphins (Stenella attenuata) with the following methods: computer-assisted tomography, magnetic resonance imaging, conventional X-ray imaging, cryo-sectioning as well as gross dissection. Comparison of these anatomical methods reveals that for a complete structural analysis, a combination of modern imaging techniques and conventional morphological methods is needed. In addition to the perinatal dolphins, we include series of microslides of fetal odontocetes (S. attenuata, common dolphin Delphinus delphis, narwhal Monodon monoceros). In contrast to other mammals, newborn cetaceans represent an extremely precocial state of development correlated to the fact that they have to swim and surface immediately after birth. Accordingly, the morphology of the perinatal dolphin head is very similar to that of the adult. Comparison with early fetal stages of dolphins shows that the ontogenetic change from the general mammalian bauplan to cetacean organization was characterized by profound morphological transformations of the relevant organ systems and roughly seems to parallel the phylogenetic transition from terrestrial ancestors to modern odontocetes.     

Reconstructing Body Size in Extinct Crown Cetacea (Neoceti) Using Allometry,Phylogenetic Methods and Tests from the Fossil Record

Living cetaceans exhibit interspecific size ranging across several orders of magnitude, and rank among the largest vertebrates ever. Details of how cetaceans evolved different body sizes, however, remain obscure, because they lack basic morphological proxies that have been traditionally used in other fossil vertebrates. Here, we reconstruct the body size of extinct crown group cetaceans (Neoceti) using different regression methods on extant skull and length data, in a phylogenetic context. Because most fossil cetaceans are fragmentary, we developed regression equations to predict total length based on cranial metrics that are preserved on most fossil crania. The resultant regression equations are based on a database of skull and length data from most extant lineages of cetaceans (n = 45 species; 272 specimens), sampling all living mysticete genera and all major clades of odontocetes. In generating predictive equations, we compared both conventional species data regression and independent contrast regression methods, as well as single trait predictors and a new approach that combines the advantages of a partial least squares (PLS) multivariate regression with independent contrasts. This last approach leverages the predictive power of using multiple correlated proxies. Lastly, we used the rare occurrences of fossil cetaceans with preserved total lengths to test the performance of our predictive equations for reconstructing body size from skull measurements alone. Our results demonstrate that incorporating information about phylogenetic relationships and multiple cranial measures in PLS scaling studies increases the accuracy of reconstructed body size, most notably by reducing prediction intervals by more than 70%. With this empirical foundation, we highlight the outline of major features in the evolution of body size for Neoceti and future opportunities to use these metrics for paleobiological questions.     

Phylogenetic position of Platanista gangetica: insights from the mitochondrial cytochrome b and nuclear interphotoreceptor retinoid-binding protein gene sequences

The evolutionary relationship of peculiar and poorly known Ganges River dolphin with extinct and extant cetaceans has been in the state of confusion for more than a century. The close resemblance of platanistidae with some of the extinct taxon viz., Dalpiaziniidae and Waipatiidae and their sister group relationship with many of the extant lineages of cetaceans has been reported but none of the alternative hypotheses provide an unambiguous placement for this species. The present study provides insights into the molecular relationships of Platanista with other cetaceans based on comprehensive analyses of the mitochondrial cytochrome b and nuclear interphotoreceptor retinoid-binding protein gene sequences, obtained from 15 specimens of Ganges dolphin from India and Bangladesh. The mean substitution distance analysis of phylogenetically informative characters in the cytochrome b sequences suggested that Platanista gangetica is significantly closer (P<0.001) to Mysticeti than to any other group of toothed whales. However, the conventional methods of phylogenetic reconstruction supported this finding with low to moderate (41-69%) bootstrap values.     

Molecular phylogenetics of 'river dolphins' and the baiji mitochondrial genome

It is well known that the classical river dolphins are not a natural group, but up to now the phylogenetic relationships among them are not very clear because different views have been referred from different studies. In the present study, we determined the complete nucleotide sequence of the mitochondrial (mt) genome of the baiji (Lipotes vexillifer), the most endangered cetacean species, and conducted phylogenetic analyses for the classical river dolphins based on data from cetacean mitochondrial genomes available. In our analyses, the classical river dolphins split into two separate lineages, Platanista and Lipotes+(Inia+Pontoporia), having no sister relationship with each other, and the Platanista lineage is always within the odontocete clade instead of having a closer affinity to Mysticeti. The position of the Platanista is more basal, suggesting separate divergence of this lineage well before the other one. The Lipotes has a sister relationship with Inia+pontoporia, and they together formed the sister group to the Delphinoidea. This result strongly supports paraphyly of the classical river dolphins, and the nonplatanistoid river dolphins do represent a monophyletic grouping, with the Lipotidae as the sister taxa to (Iniidae+Pontoporiidae), and is well congruent with the studies based on short interspersed repetitive elements (SINEs).     

First report of major histocompatibility complex class II loci from the Amazon pink river dolphin (genus Inia)

We report the first major histocompatibility complex (MHC) DQB1 sequences for the two species of pink river dolphins (Inia geoffrensis and Inia boliviensis) inhabiting the Amazon and Orinoco River basins. These sequences were found to be polymorphic within the Inia genus and showed shared homology with cetacean DQB-1 sequences, especially, those of the Monodontidae and Phocoenidae. On the other hand, these sequences were shown to be divergent from those described for other riverine dolphin species, such as Lipotes vexillifer, the Chinese river dolphin. Two main conclusions can be drawn from our results: 1) the Mhc DQB1 sequences seem to evolve more rapidly than other nuclear sequences in cetaceans, and 2) differential positive selective pressures acting on these genes cause concomitant divergent evolutionary histories that derive phylogenetic reconstructions that could be inconsistent with widely accepted intertaxa evolutionary relationships elucidated with other molecular markers subjected to a neutral dynamics.     

Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes

The order Cetartiodactyla includes cetaceans (whales, dolphins and porpoises) that are found in all oceans and seas, as well as in some rivers, and artiodactyls (ruminants, pigs, peccaries, hippos, camels and llamas) that are present on all continents, except Antarctica and until recent invasions, Australia. There are currently 332 recognized cetartiodactyl species, which are classified into 132 genera and 22 families. Most phylogenetic studies have focused on deep relationships, and no comprehensive time-calibrated tree for the group has been published yet. In this study, 128 new complete mitochondrial genomes of Cetartiodactyla were sequenced and aligned with those extracted from nucleotide databases. Our alignment includes 14,902 unambiguously aligned nucleotide characters for 210 taxa, representing 183 species, 107 genera, and all cetartiodactyl families. Our mtDNA data produced a statistically robust tree, which is largely consistent with previous classifications. However, a few taxa were found to be para- or polyphyletic, including the family Balaenopteridae, as well as several genera and species. Accordingly, we propose several taxonomic changes in order to render the classification compatible with our molecular phylogeny. In some cases, the results can be interpreted as possible taxonomic misidentification or evidence for mtDNA introgression. The existence of three new cryptic species of Ruminantia should therefore be confirmed by further analyses using nuclear data. We estimate divergence times using Bayesian relaxed molecular clock models. The deepest nodes appeared very sensitive to prior assumptions leading to unreliable estimates, primarily because of the misleading effects of rate heterogeneity, saturation and divergent outgroups. In addition, we detected that Whippomorpha contains slow-evolving taxa, such as large whales and hippos, as well as fast-evolving taxa, such as river dolphins. Our results nevertheless indicate that the evolutionary history of cetartiodactyls was punctuated by four main phases of rapid radiation during the Cenozoic era: the sudden occurrence of the three extant lineages within Cetartiodactyla (Cetruminantia, Suina and Tylopoda); the basal diversification of Cetacea during the Early Oligocene; and two radiations that involve Cetacea and Pecora, one at the Oligocene/Miocene boundary and the other in the Middle Miocene. In addition, we show that the high species diversity now observed in the families Bovidae and Cervidae accumulated mainly during the Late Miocene and Plio-Pleistocene.     

Molecular systematics of South American dolphins Sotalia: sister taxa determination and phylogenetic relationships, with insights into a multi-locus phylogeny of the Delphinidae

The evolutionary relationships among members of the cetacean family Delphinidae, the dolphins, pilot whales and killer whales, are still not well understood. The genus Sotalia (coastal and riverine South American dolphins) is currently considered a member of the Stenoninae subfamily, along with the genera Steno (rough toothed dolphin) and Sousa (humpbacked dolphin). In recent years, a revision of this classification was proposed based on phylogenetic analysis of the mitochondrial gene cytochrome b, wherein Sousa was included in the Delphininae subfamily, keeping only Steno and Sotalia as members of the Stenoninae subfamily. Here we investigate the phylogenetic placement of Sotalia using two mitochondrial genes, six autosomal introns and four Y chromosome introns, providing a total of 5,196 base pairs (bp) for each taxon in the combined dataset. Sequences from these genomic regions were obtained for 17 delphinid species, including at least one species from each of five or six currently recognized subfamilies plus five odontocete outgroup species. Maximum Parsimony, Maximum Likelihood and Bayesian phylogenetic analysis of independent (each fragment) and combined datasets (mtDNA, nuDNA or mtDNA+nuDNA) showed that Sotalia and Sousa fall within a clade containing other members of Delphininae, exclusive of Steno. Sousa was resolved as the sister taxon to Sotalia according to analysis of the nuDNA dataset but not analysis of the mtDNA or combined mtDNA+nuDNA datasets. Based on the results from our multi-locus analysis, we offer several novel changes to the classification of Delphinidae, some of which are supported by previous morphological and molecular studies.     

Fossil Dolphin Otekaikea marplesi (Latest Oligocene,New Zealand) Expands the Morphological and Taxonomic Diversity of Oligocene Cetaceans

The Oligocene Epoch was a time of major radiation of the Odontoceti (echolocating toothed whales, dolphins). Fossils reveal many odontocete lineages and considerable structural diversity, but whether the clades include some crown taxa or only archaic groups is contentious. The New Zealand fossil dolphin “Prosqualodon” marplesi (latest Oligocene, ≥23.9 Ma) is here identified as a crown odontocete that represents a new genus, Otekaikea, and adds to the generic diversity of Oligocene odontocetes. Otekaikea marplesi is known only from the holotype, which comprises a partial skeleton from the marine Otekaike Limestone of the Waitaki Valley. Otekaikea marplesi was about 2.5 m long; it had procumbent anterior teeth, and a broad dished face for the nasofacial muscles implicated in production of echolocation sounds. The prominent condyles and unfused cervical vertebrae suggest a flexible neck. A phylogenetic analysis based on morphological features places Otekaikea marplesi in the extinct group Waipatiidae, within the clade Platanistoidea. The phylogeny implies an Oligocene origin for the lineage now represented by the endangered Ganges River dolphin (Platanista gangetica), supporting an Oligocene history for the crown Odontoceti.     

Mitochondrial phylogenetics and evolution of mysticete whales

The phylogenetic relationships among baleen whales (Order: Cetacea) remain uncertain despite extensive research in cetacean molecular phylogenetics and a potential morphological sample size of over 2 million animals harvested. Questions remain regarding the number of species and the monophyly of genera, as well as higher order relationships. Here, we approach mysticete phylogeny with complete mitochondrial genome sequence analysis. We determined complete mtDNA sequences of 10 extant Mysticeti species, inferred their phylogenetic relationships, and estimated node divergence times. The mtDNA sequence analysis concurs with previous molecular studies in the ordering of the principal branches, with Balaenidae (right whales) as sister to all other mysticetes base, followed by Neobalaenidae (pygmy right whale), Eschrichtiidae (gray whale), and finally Balaenopteridae (rorquals + humpback whale). The mtDNA analysis further suggests that four lineages exist within the clade of Eschrichtiidae + Balaenopteridae, including a sister relationship between the humpback and fin whales, and a monophyletic group formed by the blue, sei, and Bryde's whales, each of which represents a newly recognized phylogenetic relationship in Mysticeti. We also estimated the divergence times of all extant mysticete species, accounting for evolutionary rate heterogeneity among lineages. When the mtDNA divergence estimates are compared with the mysticete fossil record, several lineages have molecular divergence estimates strikingly older than indicated by paleontological data. We suggest this discrepancy reflects both a large amount of ancestral polymorphism and long generation times of ancestral baleen whale populations.     

Evolution and function of anterior cervical vertebral fusion in tetrapods

The evolution of vertebral fusion is a poorly understood phenomenon that results in the loss of mobility between sequential vertebrae. Non‐pathological fusion of the anterior cervical vertebrae has evolved independently in numerous extant and extinct mammals and reptiles, suggesting that the formation of a ‘syncervical’ is an adaptation that arose to confer biomechanical advantage(s) in these lineages. We review syncervical anatomy and evolution in a broad phylogenetic context for the first time and provide a comprehensive summary of proposed adaptive hypotheses. The syncervical generally consists of two vertebrae (e.g. hornbills, porcupines, dolphins) but can include fusion of seven cervical vertebrae in some cetaceans. Based on the ecologies of taxa with this trait, cervical fusion most often occurs in fossorial and pelagic taxa. In fossorial taxa, the syncervical likely increases the out‐lever force during head‐lift digging. In cetaceans and ricochetal rodents, the syncervical may stabilize the head and neck during locomotion, although considerable variation exists in its composition without apparent variability in locomotion. Alternatively, the highly reduced cervical vertebral centra may require fusion to prevent mechanical failure of the vertebrae. In birds, the syncervical of hornbills may have evolved in response to their unique casque‐butting behaviour, or due to increased head mass. The general correlation between ecological traits and the presence of a syncervical in extant taxa allows more accurate interpretation of extinct animals that also exhibit this unique trait. For example, syncervicals evolved independently in several groups of marine reptiles and may have functioned to stabilize the head at the craniocervical joint during pelagic locomotion, as in cetaceans. Overall, the origin and function of fused cervical vertebrae is poorly understood, emphasizing the need for future comparative biomechanical studies interpreted in an evolutionary context.     

Phylogenomic analyses and improved resolution of Cetartiodactyla

The remarkable antiquity, diversity, and significance in the ecology and evolution of Cetartiodactyla have inspired numerous attempts to resolve their phylogenetic relationships. However, previous analyses based on limited samples of nuclear genes or mitochondrial DNA sequences have generated results that were either inconsistent with one another, weakly supported, or highly sensitive to analytical conditions. Here, we present strongly supported results based upon over 1.4 Mb of an aligned DNA sequence matrix from 110 single-copy nuclear protein-coding genes of 21 Cetartiodactyla species, which represent major Cetartiodactyla lineages, and three species of Perissodactyla and Carnivora as outgroups. Phylogenetic analysis of this newly developed genomic sequence data using a codon-based model and recently developed models of the rate autocorrelation resolved the phylogenetic relationships of the major cetartiodactylan lineages and of those lineages with a high degree of confidence. Cetacea was found to nest within Artiodactyla as the sister group of Hippopotamidae, and Tylopoda was corroborated as the sole base clade of Cetartiodactyla. Within Cetacea, the monophyletic status of Odontoceti relative to Mysticeti, the basal position of Physeteroidea in Odontoceti, the non-monophyly of the river dolphins, and the sister relationship between Delphinidae and Monodontidae + Phocoenidae were strongly supported. In particular, the groups of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins) were validated as unnatural groups. Additionally, a very narrow time frame of ∼3 My (million years) was found for the rapid diversification of delphinids in the late Miocene, which made it difficult to resolve the phylogenetic relationships within the Delphinidae, especially for previous studies with limited data sets. The present study provides a statistically well-supported phylogenetic framework of Cetartiodactyla, which represents an important step toward ending some of the often-heated, century-long debate on their evolution.     

Rapid Laurasian diversification of a pantropical bird family during the Oligocene–Miocene transition

Disjunct, pantropical distributions are a common pattern among avian lineages, but disentangling multiple scenarios that can produce them requires accurate estimates of historical relationships and timescales. Here, we clarify the biogeographical history of the pantropical avian family of trogons (Trogonidae) by re-examining their phylogenetic relationships and divergence times with genome-scale data. We estimated trogon phylogeny by analysing thousands of ultraconserved element (UCE) loci from all extant trogon genera with concatenation and coalescent approaches. We then estimated a time frame for trogon diversification using MCMCTree and fossil calibrations, after which we performed ancestral area estimation using BioGeoBEARS. We recovered the first well-resolved hypothesis of relationships among trogon genera. Trogons comprise three clades, each confined to one of three biogeographical regions: Africa, Asia and the Neotropics, with the African clade sister to the others. These clades diverged rapidly during the Oligocene-Miocene transition. Our biogeographical analyses identify a Eurasian origin for stem trogons and a crown clade arising from ancestors broadly distributed across Laurasia and Africa. The pantropical ranges of trogons are relicts of a broader Afro-Laurasian distribution that was fragmented across Africa, Asia and the New World in near coincident fashion during the Oligocene-Miocene transition by global cooling and changing habitats along the Beringian land bridge and North Africa.     

The emergence of cetaceans: phylogenetic analysis of male social behaviour supports the Cetartiodactyla clade

The phylogeny of cetaceans is still unresolved. Two hypotheses prevail for the position of cetaceans among ungulates. The first hypothesis shows that Artiodactyla is monophyletic and is sister taxon to a clade composed of cetaceans and mesonychians. The second one shows that Artiodactyla is paraphyletic and contains Cetacea that is sister taxon of Hippopotamida. These hypotheses are based on fossil records and molecular studies. The behaviour of extant species can provide as much phylogenetic information as other classical parameters. I considered the behaviour observed during male agonistic interactions in placental mammals in order to determine which of these hypotheses was supported by the behaviour of extant species. Headbutting was only observed in ruminants, hippopotamids and cetaceans, supporting the paraphyletic nature of Artiodactyla. Primitive ruminants (tragulids) and two genera of ruminants (Moschus and Oreamnos) were not observed headbutting. These secondary losses were only present in 6.25% of the 48 surveyed ruminant genera. Head-to-head attacks emerged in pigs, which have developed dermal protusions. Yet, these confrontations are not based on mutual blow delivery. The behavioural evidence supports the inclusion of cetaceans in Artiodactyla.     

Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins

Recently diverged taxa are often characterized by high rates of hybridization, which can complicate phylogenetic reconstruction. For this reason, the phylogenetic relationships and evolutionary history of dolphins are still not very well resolved; the question of whether the genera Tursiops and Stenella are monophyletic is especially controversial. Here, we performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hypothesis of Tursiops and Stenella. Phylogenetic reconstruction with the maximum likelihood and Bayesian methods of concatenated loci, as well as with coalescence analyses of sliding window trees, produced a concordant and well-supported tree. Our studies support the non-monophyletic status of Tursiops and Stenella because the species referred these genera do not form exclusive monophyletic clades. This suggests that the current taxonomy of both genera might not reflect their evolutionary history and may underestimate their diversity. A four-taxon D-statistic (ABBA-BABA) test, five-taxon D_FOIL test, and tree-based PhyloNet analyses all showed extensive gene flow across dolphin species, which could explain the instability in resolving phylogenetic relationship of oceanic dolphins with different and limited markers. This study could be a good case to demonstrate how genomic data can reveal complex speciation and phylogeny in rapidly radiating animal groups.

     

New insights into the phylogenetic relationships among the oceanic dolphins (Cetacea: Delphinidae)

The phylogenetic relationships of oceanic dolphins (family Delphinidae) remain unclear. Several works using mitochondrial and/or nuclear DNA on different genera and species have been published, though no consensus exists regarding even the subfamilies that conform the family. Here, a new phylogeny for the family Delphinidae, including 36 different complete mitochondrial genomes (plus two outgroups), was constructed under Bayesian and maximum likelihood approaches. Results indicate identical tree topology in both cases, with almost all nodes fully supported independently of the reconstruction approach. This topology is different from those previously published and proposes new phylogenetic relationships among subfamilies, genera and species of the family. These findings are critically important for the study of oceanic dolphin taxonomy, ecology, evolution and conservation, and highlight the importance of revisiting and resolving uncertain phylogenies.