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Small coastal dolphins endemic to south-eastern Australia have variously been assigned to described species Tursiops truncatus, T. aduncus or T. maugeanus; however the specific affinities of these animals is controversial and have recently been questioned. Historically 'the southern Australian Tursiops' was identified as unique and was formally named Tursiops maugeanus but was later synonymised with T. truncatus. Morphologically, these coastal dolphins share some characters with both aforementioned recognised Tursiops species, but they also possess unique characters not found in either. Recent mtDNA and microsatellite genetic evidence indicates deep evolutionary divergence between this dolphin and the two currently recognised Tursiops species. However, in accordance with the recommendations of the Workshop on Cetacean Systematics, and the Unified Species Concept the use of molecular evidence alone is inadequate for describing new species. Here we describe the macro-morphological, colouration and cranial characters of these animals, assess the available and new genetic data, and conclude that multiple lines of evidence clearly indicate a new species of dolphin. We demonstrate that the syntype material of T. maugeanus comprises two different species, one of which is the historical 'southern form of Tursiops' most similar to T. truncatus, and the other is representative of the new species and requires formal classification. These dolphins are here described as Tursiops australis sp. nov., with the common name of 'Burrunan Dolphin' following Australian aboriginal narrative. The recognition of T. australis sp. nov. is particularly significant given the endemism of this new species to a small geographic region of southern and south-eastern Australia, where only two small resident populations in close proximity to a major urban and agricultural centre are known, giving them a high conservation value and making them susceptible to numerous anthropogenic threats.

Advances in molecular techniques have enabled the study of genetic diversity and population structure in many different contexts. Studies that assess the genetic structure of cetacean populations often use biopsy samples from free-ranging individuals and tissue samples from stranded animals or individuals that became entangled in fishery or aquaculture equipment. This leads to the question of how representative the location of a stranded or entangled animal is with respect to its natural range, and whether similar results would be obtained when comparing carcass samples with samples from free-ranging individuals in studies of population structure. Here we use tissue samples from carcasses of dolphins that stranded or died as a result of bycatch in South Australia to investigate spatial population structure in two species: coastal bottlenose (Tursiops sp.) and short-beaked common dolphins (Delphinus delphis). We compare these results with those previously obtained from biopsy sampled free-ranging dolphins in the same area to test whether carcass samples yield similar patterns of genetic variability and population structure. Data from dolphin carcasses were gathered using seven microsatellite markers and a fragment of the mitochondrial DNA control region. Analyses based on carcass samples alone failed to detect genetic structure in Tursiops sp., a species previously shown to exhibit restricted dispersal and moderate genetic differentiation across a small spatial scale in this region. However, genetic structure was correctly inferred in D. delphis, a species previously shown to have reduced genetic structure over a similar geographic area. We propose that in the absence of corroborating data, and when population structure is assessed over relatively small spatial scales, the sole use of carcasses may lead to an underestimate of genetic differentiation. This can lead to a failure in identifying management units for conservation. Therefore, this risk should be carefully assessed when planning population genetic studies of cetaceans.

By analysing genomic sequences in echolocating mammals it is shown that convergence is not a rare process restricted to a handful of loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus; analyses involved sequence comparisons across 22 mammals, including 4 new bat genomes, and found signatures consistent with convergence in genes linked to hearing or deafness, but surprisingly also to vision. Widespread convergent evolution at genetic level Convergent evolution, through which similar traits evolve in unrelated lineages, is a familiar demonstration of the power of natural selection. These traits are usually viewed as representing alternate evolutionary solutions involving different sets of genes, but that view is challenged by a study of echolocating mammals. Analysis of the genomic sequences in 22 echolocating species, including four new bat genomes, reveals that convergence is not a rare process restricted to a handful of loci but is widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Convergence is particularly strong in genes linked to hearing or deafness, but surprisingly, also to vision. Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes 1 , 2 , 3 . However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures 4 , 5 . Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level 6 , 7 , 8 , 9 . Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution 9 , 10 , although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.

True river dolphins are some of the rarest and most endangered of all vertebrates. They comprise relict evolutionary lineages of high taxonomic distinctness and conservation value, but are afforded little protection. We report the discovery of a new species of a river dolphin from the Araguaia River basin of Brazil, the first such discovery in nearly 100 years. The species is diagnosable by a series of molecular and morphological characters and diverged from its Amazonian sister taxon 2.08 million years ago. The estimated time of divergence corresponds to the separation of the Araguaia-Tocantins basin from the Amazon basin. This discovery highlights the immensity of the deficit in our knowledge of Neotropical biodiversity, as well as vulnerability of biodiversity to anthropogenic actions in an increasingly threatened landscape. We anticipate that this study will provide an impetus for the taxonomic and conservation reanalysis of other taxa shared between the Araguaia and Amazon aquatic ecosystems, as well as stimulate historical biogeographical analyses of the two basins.

Environmental DNA (eDNA) serves as a non-invasive tool for monitoring the presence of specific organisms in challenging or hard-to-access areas. We attempted non-invasive monitoring of Korean cetacean species by extracting eDNA from the western and southern seas of the Republic of Korea, as well as around Jeju Island. In the present study, we focused on two representative cetaceans of the Korean Sea: the narrow-ridged finless porpoise ( Neophocaena asiaeorientalis sunameri ) and oceanic dolphins (Family Delphinidae). When selecting polymerase chain reaction primers, mitochondrial DNA (mtDNA) of N. asiaeorientalis and microsatellite Slo4 of oceanic dolphins were identified as the most effective gene sequences in high abundance in low concentration eDNA samples, using tissue samples for eDNA detection of the target species. A total of 139 samples were collected, and eDNA was detected from finless porpoises ( Neophocaena sp.) in 94 samples (68%) and from oceanic dolphins in 50 samples (36%). Significantly, eDNA revealed the considerable presence of finless porpoise around Jeju Island, despite a lack of visual confirmation. In the Yellow Sea, eDNA primarily detected the presence of common dolphin ( Delphinus delphis ), orca ( Orcinus orca ), and Indo-Pacific bottlenose dolphin ( Tursiops aduncus ). Indo-Pacific bottlenose dolphins were identified along the coast of Jeju Island. The value of this research lies in being the first attempt to explore cetacean eDNA across various species in Korea. Further cetacean eDNA research should focus on developing metabarcoding primers capable of detecting a greater variety of cetacean species and primers for detecting specific porpoise species. This study will serve as a valuable reference for future studies.

The taxonomy of common dolphins (Delphinus sp.) has always been controversial, with over twenty described species since the original description of the type species of the genus (Delphinus delphis Linnaeus, 1758). Two species and four subspecies are currently accepted, but recent molecular data have challenged this view. In this study we investigated the molecular taxonomy of common dolphins through analyses of cytochrome b sequences of 297 individuals from most of their distribution. We included 37 novel sequences from the Southwestern Atlantic Ocean, a region where the short- and long-beaked morphotypes occur in sympatry, but which had not been well sampled before. Skulls of individuals from the Southwestern Atlantic were measured to test the validity of the rostral index as a diagnostic character and confirmed the presence of the two morphotypes in our genetic sample. Our genetic results show that all common dolphins in the Atlantic Ocean belong to a single species, Delphinus delphis. According to genetic data, the species Delphinus capensis is invalid. Long-beaked common dolphins from the Northeastern Pacific Ocean may constitute a different species. Our conclusions prompt the need for revision of currently accepted common dolphin species and subspecies and of Delphinus delphis distribution.

Understanding the evolution of diversity and the resulting systematics in marine systems is confounded by the lack of clear boundaries in oceanic habitats, especially for highly mobile species like marine mammals. Dolphin populations and sibling species often show differentiation between coastal and offshore habitats, similar to the pelagic/littoral or benthic differentiation seen for some species of fish. Here we test the hypothesis that lineages within the polytypic genus Tursiops track past changes in the environment reflecting ecological drivers of evolution facilitated by habitat release. We used a known recent time point for calibration (the opening of the Bosphorus) and whole mitochondrial genome (mitogenome) sequences for high phylogenetic resolution. The pattern of lineage formation suggested an origin in Australasia and several early divisions involving forms currently inhabiting coastal habitats. Radiation in pelagic environments was relatively recent, and was likely followed by a return to coastal habitat in some regions. The timing of some nodes defining different ecotypes within the genus clustered near the two most recent interglacial transitions. A signal for an increase in diversification was also seen for dates after the last glacial maximum. Together these data suggest the tracking of habitat preference during geographic expansions, followed by transition points reflecting habitat shifts, which were likely associated with periods of environmental change.

Background Echolocation was a key development in toothed whale evolution, enabling their adaptation and diversification across various environments. Previous bioacoustic and morphological studies suggest that environmental pressures have influenced the evolution of echolocation in toothed whales. This hypothesis demands further investigation, especially regarding the molecular mechanisms involved in the adaptive radiation of toothed whales across multiple habitats. Here we show that the coding sequences of four hearing genes involved in echolocation ( CDH23 , prestin , TMC1 , and CLDN14 ) have different signatures of molecular evolution among riverine, coastal, and oceanic dolphins, suggesting that the evolutionary constraints of these habitats shaped the underlying genetic diversity of the toothed whale sonar. Results Our comparative analysis across 37 odontocete species revealed patterns of accelerated evolution within coastal and riverine lineages, supporting the hypothesis that shallow habitats pose specific selective pressures to sonar propagation, which are not found in the deep ocean. All toothed whales with genes evolving under positive selection are shallow coastal species, including three species that have recently diverged from freshwater lineages ( Cephalorhynchus commersonii , Sotalia guianensi s, and Orcaella heinsohni - CDH23 ), and three species that operate specialized Narrow Band High Frequency (NBHF) Sonars ( Phocoena sinus - prestin , Neophocaena phocaenoides - TMC1 and Cephalorhynchus commersonii - CDH23 ). For river dolphins and deep-diving toothed whales, we found signatures of positive selection and molecular convergence affecting specific sites on CDH23 , TMC1 , and prestin . Positively selected sites (PSS) were different in number, identity, and substitution rates ( dN / dS ) across riverine, coastal, and oceanic toothed whales. Conclusion Here we shed light on potential molecular mechanisms underlying the diversification of toothed whale echolocation. Our results suggest that toothed whale hearing genes changed under different selective pressures in coastal, riverine, and oceanic environments.

Toothed whales (Odontoceti) are adapted for catching prey underwater and possess some of the most derived feeding specializations of all mammals, including the loss of milk teeth (monophyodonty), high tooth count (polydonty), and the loss of discrete tooth classes (homodonty). Many extant odontocetes possess some combination of short, broad rostra, reduced tooth counts, fleshy lips, and enlarged hyoid bones—all adaptations for suction feeding upon fishes and squid. We report a new fossil odontocete from the Oligocene (approx. 30 Ma) of South Carolina (Inermorostrum xenops, gen. et sp. nov.) that possesses adaptations for suction feeding: toothlessness and a shortened rostrum (brevirostry). Enlarged foramina on the rostrum suggest the presence of enlarged lips or perhaps vibrissae. Phylogenetic analysis firmly places Inermorostrum within the Xenorophidae, an early diverging odontocete clade typified by long-snouted, heterodont dolphins. Inermorostrum is the earliest obligate suction feeder within the Odontoceti, a feeding mode that independently evolved several times within the clade. Analysis of macroevolutionary trends in rostral shape indicate stabilizing selection around an optimum rostral shape over the course of odontocete evolution, and a post-Eocene explosion in feeding morphology, heralding the diversity of feeding behaviour among modern Odontoceti.

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.