Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages

Biology and Cultural Importance of the Narwhal

Though narwhal have survived multiple ice ages, including 2.5 Ma and the last interglacial period with warming temperatures, Arctic climate change during the Anthropocene introduces new challenges. Despite their evolutionary connection to Arctic Pleistocene fossils, narwhal archeocete ancestors from the Pliocene (Bohaskaia monodontoides) and Miocene (Denebola and Odobenocetopsidae) inhabited warm waters. Narwhal Arctic adaptation holds valuable insights into unique traits, including thin skin; extreme diving capacity; and a unique straight, spiraled, and sensory tooth organ system. Inaccessible weather, ice conditions, and darkness limit scientific studies, though Inuit knowledge adds valuable observations of narwhal ecology, biology, and behavior. Existing and future studies in myriad fields of physical, chemical, biological, and genetic science, combined and integrated with remote sensing and imaging technologies, will help elucidate narwhal evolution, biology, and adaptation. When integrated with Qaujimajatuqangit, "the Inuit way of knowing," these studies help describe interesting biologic expressions of the narwhal.

Reevaluation of Rhipidomys emiliae (J.A. Allen 1916) and description of a new Rhipidomys (Rodentia: Cricetidae) species from Amazonia and Cerrado

We present the revalidation of the sigmodontinae rodent species R. emiliae, as well as the description of a new species for the genus Rhipidomys. The maximum likelihood analysis recovers R. emiliae as sister species of the clade with Rhipidomys sp. nov. and R. ipukensis, with high bootstrap values. Comparisons between these species based on the external, cranial, and dental morphology identified several unique characters in Rhipidomys sp. nov., including more grayish brown color of the dorsal coat, subsquamosal fenestra wide and long, angular process ends in the same position of the end of condyloid process, conspicuous protostyle and enterostyle. We describe a new karyotype (2n = 44 and FN = 64) for the genus and, based on an integrative analysis together with morphology and molecular phylogeny, assign it to R. emiliae, and assign the karyotype with 2n = 44 and FN = 52 to Rhipidomys sp. nov.. The analysis integrating data indicated that R. emiliae has a geographic distribution restricted to the lowlands of eastern Amazonia, whereas Rhipidomys sp. nov. occurs in the central Amazonia and Cerrado. The data showed that some Rhipidomys species have its distribution currently limited by rivers, as Rhipidomys sp. nov. occurring west of the Araguaia-Tocantins interfluve, R. emiliae east of the Tocantins River, and R. ipukensis between the Tocantins and Araguaia rivers. This work, in addition to revealing a still unknown biodiversity describing a species, brings a new understanding to the genus, and shows how integrating different markers helps in the correct association between the nominal form and the karyotype.

Integrative taxonomy suggests that South American freshwater nematodes Echinocephalus and their host stingrays co-originated in late Oligocene to early Miocene

Nematoda of the genus Echinocephalus Molin, 1858 include species from the Gnathostomatidae family, the adult stages of which parasitize the stomach and spiral intestine of elasmobranchs as their final hosts. In the present study, we describe Echinocephalus spinosus n. sp. found parasitizing the spiral valve of the freshwater stingray Potamotrygon motoro from the Tapajós River, in the Amazon Basin, in the state of Pará, Brazil. In the study we performed morphological (light and scanning electron microscopy) and molecular (small subunit ribosomal ribonucleic acid (SSU rDNA) and mitochondrial cytochrome c oxidase I sequencing) analyses. E. spinosus n. sp. is only the second species of the Echinocephalus genus described from a strictly freshwater environment. The SSU rDNA based phylogenetic analyses showed Echinocephalus clade as a sister lineage of Gnathostoma, and that the new species arises as a sister to Echinocephalus cf. pseudouncinatus. Time-calibrated phylogenetic analysis revealed that the origin of the freshwater Echinocephalus coincides with the recently proposed origin of the freshwater host potamotrygonin stingray, namely the late Oligocene to early Miocene, when the western Amazon was dominated by the Pebas wetlands, an epicontinental marine/freshwater system.

Evolutionary drivers of morphological differentiation among three bottlenose dolphin lineages, Tursiops spp. (Delphinidae), in the northwest Indian Ocean utilizing linear and geometric morphometric techniques

Local adaptation and adaptive radiations are typically associated with phenotypic variation suited to alternative environments. In the marine environment, the nature of relevant ecological or environmental transitions is poorly understood, especially for highly mobile species. Here we compare three genetic lineages in the genus Tursiops (bottlenose dolphins), using linear measurements and geometric morphometric techniques, in the context of environmental variation in the northwest Indian Ocean. Cranial morphology was clearly differentiated comparing Tursiops truncatus and Tursiops aduncus, while a recently discovered genetic lineage, found in the Arabian Sea, was morphologically most similar to T. aduncus from the same region, but distinct for various measures, particularly metrics associated with the lateral dimension of the skull. The extent of divergence between T. truncatus and T. aduncus compared to differences between the T. aduncus lineages is consistent with the recent phylogeny for these species. Therefore, with the corroboration of genetic and morphological inference, we propose two conservation units of T. aduncus be recognized in the region at a sub-specific level so that their conservation can be managed effectively. We consider possible evolutionary mechanisms associated with regional habitat characteristics and the exploitation of distinct prey resources.

Highly divergent herpesviruses in threatened river dolphins from Brazil

River dolphins are a highly threatened polyphyletic group comprised of four odontocete families: Iniidae, Pontoporiidae, Lipotidae, and Platanistidae, the first two endemic to South America. To address the knowledge gap regarding infectious agents in this cetacean group, we surveyed the presence of herpesviruses by PCR in skin and/or blood samples of live-captured Amazon (Inia geoffrensis, n = 25) and Bolivian (Inia boliviensis, n = 22) river dolphins of the Amazon basin and in selected tissue samples of franciscanas (Pontoporia blainvillei, n = 27) stranded or bycaught in southeastern Brazil. Additionally, available franciscana tissue samples were examined by histopathology. Herpesvirus DNA was amplified in 13 Bolivian river dolphins (59.1%, 95% CI 38.5–79.6%) and 14 franciscanas (51.9%, 95% CI 33.0–70.7%). All Amazon river dolphins were herpesvirus-negative. Two different herpesviruses were found in Bolivian river dolphins: a previously known gammaherpesvirus detected in blood and/or skin samples of all positive individuals and a novel alphaherpesvirus in the skin of one animal. A new gammaherpesvirus was found in several franciscana samples—the first herpesvirus recorded in Pontoporiidae. Intranuclear inclusion bodies consistent with herpesvirus were observed in the lymph node of one franciscana. The high divergence among the obtained herpesviruses and those previously described can be explained by viral-host coevolution, and by the fact that these populations are fairly isolated.

Phylogenetic relationships, population demography, and species delimitation of the Alouatta belzebul species complex (Atelidae: Alouattinae)

Howler monkeys (genus Alouatta) exhibit the most extensive distribution among platyrrhines, comprising Mesoamerican and South American species groups, with the South American group including the Brazilian endemic A. belzebul species complex encompassing A. belzebul, A. discolor, and A. ululata. We herein analyzed their phylogenetic relationship, nucleotide and haplotype diversity, and population demography based on the mitochondrial gene cytochrome b. The phylogenetic and median-joining network analyses distinguished A. discolor, distributed in the west bank of the Xingu River, from A. belzebul on the east bank. This river is a zoogeographic barrier for these species. We did not find evidence of phylogenetic structure between the A. belzebul populations of opposite banks of the Tocantins River, likely related to the changes in the position of this river to the northeast in the late Pleistocene. The A. belzebul along this river showed great morphologic and haplotype diversity, and A. belzebul from the Amazon have kept a larger population size than A. discolor. We herein describe the karyotype of A. discolor, which was similar to those described for A. ululata and A. belzebul. Our results showed two well-defined and supported clades for A. discolor and A. belzebul. However, a new assessment of A. ululata across a large distribution of sampling is required due to the lack of a clear phylogenetic structure.

Cranial anatomy of Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 (Reptilia: Ichthyosauria) from the Middle Triassic Besano Formation of Monte San Giorgio, Italy/Switzerland: taxonomic and palaeobiological implications

Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 was described on the basis of a single fossil excavated near Besano (Italy) nearly three decades ago. Here, we re-examine its cranial osteology and assign five additional specimens to B. leptorhynchus, four of which were so far undescribed. All of the referred specimens were collected from the Middle Triassic outcrops of the Monte San Giorgio area (Italy/Switzerland) and are housed in various museum collections in Europe. The revised diagnosis of the taxon includes the following combination of cranial characters: extreme longirostry; an elongate frontal not participating in the supratemporal fenestra; a prominent 'triangular process' of the quadrate; a caudoventral exposure of the postorbital on the skull roof; a prominent coronoid (preglenoid) process of the surangular; tiny conical teeth with coarsely-striated crown surfaces and deeply-grooved roots; mesial maxillary teeth set in sockets; distal maxillary teeth set in a short groove. All these characters are shared with the holotype of Mikadocephalus gracilirostris Maisch & Matzke, 1997, which we consider as a junior synonym of B. leptorhynchus. An updated phylogenetic analysis, which includes revised scores for B. leptorhynchus and several other shastasaurids, recovers B. leptorhynchus as a basal merriamosaurian, but it is unclear if Shastasauridae form a clade, or represent a paraphyletic group. The inferred body length of the examined specimens ranges from 1 m to about 8 m. The extreme longirostry suggests that B. leptorhynchus primarily fed on small and elusive prey, feeding lower in the food web than an apex predator: a novel ecological specialisation never reported before the Anisian in a large diapsid. This specialization might have triggered an increase of body size and helped to maintain low competition among the diverse ichthyosaur fauna of the Besano Formation.

A new elasmosaurid (Sauropterygia: Plesiosauria) from the non-marine to paralic Dinosaur Park Formation of southern Alberta, Canada

Elasmosaurid plesiosaurian remains have been documented from non-marine to paralic (fluvial to estuarine) sediments of the upper Campanian Dinosaur Park Formation (DPF) of southern Alberta since 1898. Despite this long collection history, this material has received relatively little research attention, largely due to the highly fragmentary nature of most recovered specimens. However, this assemblage is significant, as it constitutes a rare occurrence of plesiosaurian remains in a non-marine depositional environment. This study reports on a recently collected and prepared specimen, which represents the most complete elasmosaurid yet collected from the DPF. This specimen preserves the trunk region, the base of the neck and tail, a partial fore and hind limb, and tooth, and is sufficiently complete to be assigned as the holotype of a new genus and species. This new taxon is diagnosed by a distinctive character state combination including a boomerang-shaped clavicular arch with acute anterior process, convex anterolateral margin, deeply embayed posterior margin, and pronounced ventral keel, together with the presence of 22 dorsal vertebrae, and the anterior dorsal centra bearing a ventral notch. The DPF plesiosaurian fossils were recovered from both estuarine/bay and fluvial palaeochannel sediments. The holotype skeleton represents an osteologically mature individual with an estimated body length of around 5 m, although the largest referred DPF elasmosaurid might have been closer to 7 m, which is considerably larger than other plesiosaurians reported from non-marine deposits. This suggests small-body lengths relative to typical elasmosaurids from marine settings, but is consistent with other plesiosaurians recovered from non-marine sediments. The identification of a distinct elasmosaurid taxon in the DPF might be evidence of niche-partitioning among the predominantly oceanic members of the ubiquitous plesiosaurian clade.

Complete mitogenome of Ganges river dolphin, Platanista gangetica gangetica and its phylogenetic relationship with other cetaceans

The Ganges river dolphin, Platanista gangetica gangetica is one of the endangered cetaceans. Due to increasing anthropogenic activities, it has faced a significant reduction in distribution range since the late 1800s and has even gone extinct from most of the early localities. The investigation of complete mitogenome holds significant relevance for identifying evolutionary relationships and monitoring the endangered species. Herein, we report and characterize for the first time the 16,319 bp complete mitochondrial genome of P. g. gangetica. It comprises 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and one control region (CR). The genome composition was A + T biased (59.6%) and exhibited a positive AT-skew (0.104) and negative GC-skew (- 0.384). All the genes were encoded on the heavy strand, except eight tRNAs and the ND6 gene. In the CR, an 18 bp tandem repeat sequence was observed. Our Bayesian Inference (BI) and Maximum Likelihood (ML) based phylogenetic analysis indicated that studied river dolphins were polyphyletic and the placement of Platanista was to be more basal than other river dolphins (Lipotes, Inia and Pontoporia). The pairwise genetic distance of Platanista with other cetaceans was varied, with an overall close affinity with whales. The model-based BI and ML phylogenetic analysis indicated that Platanista clustering with Ziphiidae with high to moderate supportive values (PP/BP = 98/68). The results of this study provide insights important for the conservation genetics and further evolutionary studies of the freshwater river dolphins.

Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\sim $\end{document}3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$>$\end{document}38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]

Extensive Diversity and Disparity of the Early Miocene Platanistoids (Cetacea, Odontoceti) in the Southeastern Pacific (Chilcatay Formation, Peru)

Several aspects of the fascinating evolutionary history of toothed and baleen whales (Cetacea) are still to be clarified due to the fragmentation and discontinuity (in space and time) of the fossil record. Here we open a window on the past, describing a part of the extraordinary cetacean fossil assemblage deposited in a restricted interval of time (19–18 Ma) in the Chilcatay Formation (Peru). All the fossils here examined belong to the Platanistoidea clade as here redefined, a toothed whale group nowadays represented only by the Asian river dolphin Platanista gangetica. Two new genera and species, the hyper-longirostrine Ensidelphis riveroi and the squalodelphinid Furcacetus flexirostrum, are described together with new material referred to the squalodelphinid Notocetus vanbenedeni and fragmentary remains showing affinities with the platanistid Araeodelphis. Our cladistic analysis defines the new clade Platanidelphidi, sister-group to Allodelphinidae and including E. riveroi and the clade Squalodelphinidae + Platanistidae. The fossils here examined further confirm the high diversity and disparity of platanistoids during the early Miocene. Finally, morphofunctional considerations on the entire platanistoid assemblage of the Chilcatay Formation suggest a high trophic partitioning of this peculiar cetacean paleocommunity.

The newly described Araguaian river dolphins, Inia araguaiaensis (Cetartiodactyla, Iniidae), produce a diverse repertoire of acoustic signals

The recent discovery of the Araguaian river dolphin (Inia araguaiaensis) highlights how little we know about the diversity and biology of river dolphins. In this study, we described the acoustic repertoire of this newly discovered species in concert with their behaviour. We analysed frequency contours of 727 signals (sampled at 10 ms temporal resolution). These contours were analyzed using an adaptive resonance theory neural network combined with dynamic time-warping (ARTwarp). Using a critical similarity value of 96%, frequency contours were categorized into 237 sound-types. The most common types were emitted when calves were present suggesting a key role in mother-calf communication. Our findings show that the acoustic repertoire of river dolphins is far from simple. Furthermore, the calls described here are similar in acoustic structure to those produced by social delphinids, such as orcas and pilot whales. Uncovering the context in which these signals are produced may help understand the social structure of this species and contribute to our understanding of the evolution of acoustic communication in whales.

Novel herpesviruses in riverine and marine cetaceans from South America

Herpesvirus (HV) infections in cetaceans are frequently associated with skin and mucosal lesions. Although HV infections have been reported worldwide, their occurrence in southern Atlantic marine mammals is still poorly understood. We tested skin, oral and genital mucosal beta-actin PCR-positive samples from 109 free-ranging Brazilian cetaceans using a universal herpesvirus DNA polymerase PCR. Herpesvirus-positive skin samples from a Guiana dolphin (Sotalia guianensis), a dwarf sperm whale (Kogia sima), a Bolivian river dolphin (Inia boliviensis), and a lingual sample from an Atlantic spotted dolphin (Stenella frontalis) were histologically evaluated. Additional tissue samples from these animals were also PCR-positive for HV, including a novel sequence obtained from the dwarf sperm whale's stomach and mesenteric lymph node. Four novel HV species were detected in the Guiana dolphin (one), the dwarf sperm whale (two) and the Bolivian river dolphin (one). The cutaneous lesions (marked, focally extensive, chronic proliferative dermatitis) of the Guiana dolphin and the Bolivian river dolphin were similar to previous HV reports in cetaceans, despite the absence of intranuclear inclusion bodies. This is the largest HV survey in South American cetaceans and the first detection of HV infection in riverine dolphins worldwide.

Convergent evolution misled taxonomy in schizothoracine fishes (Cypriniformes: Cyprinidae)

Highly specialized grade (HSG; genera Gymnocypris, Oxygymnocypris, Schizopygopsis, Platypharodon and Chuanchia) of the Schizothoracinae (Cypriniformes: Cyprinidae) are endemic to the Qinghai-Tibet Plateau (QTP). Previously, two distinct ecomorphs were recognized according to trophic traits. One was a limnetic omnivore with normal lower jaw morphology, terminal mouth, and moderate or dense gill rakers, mostly inhabiting in open water of lakes, including Gymnocypris and Oxygymnocypris. Another was a benthic feeder with inferior mouth, sparse gill rakers and sharp horny sheath on the lower jaw for scraping of attached prey off hard substrates, including Schizopygopsis, Platypharodon and Chuanchia. However, traditional taxonomy of HSG based on these trophic traits presented extensive conflicts with the molecular studies in recent years. The possible cause could be convergent evolution in morphology, retention of ancestral polymorphisms or mitochondrial introgression, but these hypotheses could not be assessed due to incomplete taxon sampling and only mitochondrial data employed in previous works. Here, we conducted the most comprehensive molecular analysis on HSG fishes to date, using four mitochondrial loci and 152,464 genome-wide SNPs, and including 21 of 24 putative species and one undescribed Schizopygopsis species. Both SNP and mtDNA trees confirmed extensive paraphyly of genera Gymnocypris and Schizopygopsis, where species often were clustered together by watershed instead of by genus. Basal split into the north clade B and the south clade C (ca. 3.03 Ma) approximately by the Tanggula-Tanitawen Mountains in SLAF tree coincided with a violent uplift of the QTP during the phase A of 'Qingzang movement' (ca. 3.6 Ma). Ancestral state reconstruction of the trophic ecomorph showed that the limnetic omnivore ecomorph had evolved repeatedly in clade B and C. Furthermore, we presented a striking case of convergent evolution between two 'subspecies' Gymnocypris chui chui and G. chui longimandibularis, which had diverged as early as two million years ago (ca. 2.42 Ma). Ecological analyses revealed that similar food utilization, particularly in zooplankton, was the main underlying driving force. This work showed an example of taxonomy with the most extensive errors at the genus/species levels due to convergent evolution and suggested that trophic traits could be misleading in fish taxonomy. Therefore, we propose a major generic revision for HSG species.

Tracing whale myoglobin evolution by resurrecting ancient proteins

Extant cetaceans, such as sperm whale, acquired the great ability to dive into the ocean depths during the evolution from their terrestrial ancestor that lived about 50 million years ago. Myoglobin (Mb) is highly concentrated in the myocytes of diving animals, in comparison with those of land animals, and is thought to play a crucial role in their adaptation as the molecular aqualung. Here, we resurrected ancestral whale Mbs, which are from the common ancestor between toothed and baleen whales (Basilosaurus), and from a further common quadrupedal ancestor between whale and hippopotamus (Pakicetus). The experimental and theoretical analyses demonstrated that whale Mb adopted two distinguished strategies to increase the protein concentration in vivo along the evolutionary history of deep sea adaptation; gaining precipitant tolerance in the early phase of the evolution, and increase of folding stability in the late phase.

A close relative of the Amazon river dolphin in marine deposits: a new Iniidae from the late Miocene of Angola

Background

A few odontocetes (echolocating toothed cetaceans) have been able to independently colonize freshwater ecosystems. Although some extant species of delphinids (true dolphins) and phocoenids (porpoises) at least occasionally migrate upstream of large river systems, they have close relatives in fully marine regions. This contrasts with the three odontocete families only containing extant species with a strictly freshwater habitat (Iniidae in South America, the recently extinct Lipotidae in China, and Platanistidae in southeast Asia). Among those, the fossil record of Iniidae includes taxa from freshwater deposits of South America, partly overlapping geographically with the extant Amazon river dolphin Inia geoffrensis, whereas a few marine species from the Americas were only tentatively referred to the family, leaving the transition from a marine to freshwater environment poorly understood.

Methods

Based on a partial odontocete skeleton including the cranium, discovered in late Miocene (Tortonian-Messinian) marine deposits near the estuary of the Cuanza River, Angola, we describe a new large iniid genus and species. The new taxon is compared to other extinct and extant iniids, and its phylogenetic relationships with the latter are investigated through cladistic analysis.

Results and Discussion

The new genus and species Kwanzacetus khoisani shares a series of morphological features with Inia geoffrensis, including the combination of a frontal boss with nasals being lower on the anterior wall of the vertex, the laterally directed postorbital process of the frontal, the anteroposterior thickening of the nuchal crest, and robust teeth with wrinkled enamel. As confirmed (although with a low support) with the phylogenetic analysis, this makes the new taxon the closest relative of I. geoffrensis found in marine deposits. The geographic provenance of K. khoisani, on the eastern coast of South Atlantic, suggests that the transition from the marine environment to a freshwater, Amazonian habitat may have occurred on the Atlantic side of South America. This new record further increases the inioid diversity during the late Miocene, a time interval confirmed here as the heyday for this superfamily. Finally, this first description of a Neogene cetacean from inland deposits of western sub-Saharan Africa reveals the potential of this large coastal area for deciphering key steps of the evolutionary history of modern cetaceans in the South Atlantic.

A new large squalodelphinid (Cetacea, Odontoceti) from Peru sheds light on the Early Miocene platanistoid disparity and ecology

The South Asian river dolphin (Platanista gangetica) is the only extant survivor of the large clade Platanistoidea, having a well-diversified fossil record from the Late Oligocene to the Middle Miocene. Based on a partial skeleton collected from the Chilcatay Formation (Chilcatay Fm; southern coast of Peru), we report here a new squalodelphinid genus and species, Macrosqualodelphis ukupachai. A volcanic ash layer, sampled near the fossil, yielded the ⁴⁰Ar/³⁹Ar age of 18.78 ± 0.08 Ma (Burdigalian, Early Miocene). The phylogenetic analysis places Macrosqualodelphis as the earliest branching squalodelphinid. Combined with several cranial and dental features, the large body size (estimated body length of 3.5 m) of this odontocete suggests that it consumed larger prey than the other members of its family. Together with Huaridelphis raimondii and Notocetus vanbenedeni, both also found in the Chilcatay Fm, this new squalodelphinid further demonstrates the peculiar local diversity of the family along the southeastern Pacific coast, possibly related to their partition into different dietary niches. At a wider geographical scale, the morphological and ecological diversity of squalodelphinids confirms the major role played by platanistoids during the Early Miocene radiation of crown odontocetes.

The remarkable convergence of skull shape in crocodilians and toothed whales

The striking resemblance of long-snouted aquatic mammals and reptiles has long been considered an example of morphological convergence, yet the true cause of this similarity remains untested. We addressed this deficit through three-dimensional morphometric analysis of the full diversity of crocodilian and toothed whale (Odontoceti) skull shapes. Our focus on biomechanically important aspects of shape allowed us to overcome difficulties involved in comparing mammals and reptiles, which have fundamental differences in the number and position of skull bones. We examined whether diet, habitat and prey size correlated with skull shape using phylogenetically informed statistical procedures. Crocodilians and toothed whales have a similar range of skull shapes, varying from extremely short and broad to extremely elongate. This spectrum of shapes represented more of the total variation in our dataset than between phylogenetic groups. The most elongate species (river dolphins and gharials) are extremely convergent in skull shape, clustering outside of the range of the other taxa. Our results suggest the remarkable convergence between long-snouted river dolphins and gharials is driven by diet rather than physical factors intrinsic to riverine environments. Despite diverging approximately 288 million years ago, crocodilians and odontocetes have evolved a remarkably similar morphological solution to feeding on similar prey.

Molecular Epidemiology of Anisakis and Anisakiasis: An Ecological and Evolutionary Road Map

This review addresses the biodiversity, biology, distribution, ecology, epidemiology, and consumer health significance of the so far known species of Anisakis, both in their natural hosts and in human accidental host populations, worldwide. These key aspects of the Anisakis species' biology are highlighted, since we consider them as main driving forces behind which most of the research in this field has been carried out over the past decade. From a public health perspective, the human disease caused by Anisakis species (anisakiasis) appears to be considerably underreported and underestimated in many countries or regions around the globe. Indeed, when considering the importance of marine fish species as part of the everyday diet in many coastal communities around the globe, there still exist significant knowledge gaps as to local epidemiological and ecological drivers of the transmission of Anisakis spp. to humans. We further identify some key knowledge gaps related to Anisakis species epidemiology in both natural and accidental hosts, to be filled in light of new 'omic' technologies yet to be fully developed. Moreover, we suggest that future Anisakis research takes a 'holistic' approach by integrating genetic, ecological, immunobiological, and environmental factors, thus allowing proper assessment of the epidemiology of Anisakis spp. in their natural hosts, in human populations, and in the marine ecosystem, in both space and time.

Morphological convergence in 'river dolphin' skulls

Convergent evolution can provide insights into the predictability of, and constraints on, the evolution of biodiversity. One striking example of convergence is seen in the ‘river dolphins’. The four dolphin genera that make up the ‘river dolphins’ (Inia geoffrensis, Pontoporia blainvillei, Platanista gangetica and Lipotes vexillifer) do not represent a single monophyletic group, despite being very similar in morphology. This has led many to using the ‘river dolphins’ as an example of convergent evolution. We investigate whether the skulls of the four ‘river dolphin’ genera are convergent when compared to other toothed dolphin taxa in addition to identifying convergent cranial and mandibular features. We use geometric morphometrics to uncover shape variation in the skulls of the ‘river dolphins’ and then apply a number of phylogenetic techniques to test for convergence. We find significant convergence in the skull morphology of the ‘river dolphins’. The four genera seem to have evolved similar skull shapes, leading to a convergent morphotype characterised by elongation of skull features. The cause of this morphological convergence remains unclear. However, the features we uncover as convergent, in particular elongation of the rostrum, support hypotheses of shared feeding mode or diet and thus provide the foundation for future work into convergence within the Odontoceti.

Morphological and genetic diversity in Callithrix hybrids in an anthropogenic area in southeastern Brazil (Primates: Cebidae: Callitrichinae)

Two species of Callithrix, C. jacchus (Linnaeus, 1758) and C. penicillata (É. Geoffroy, 1812), are considered invasive in Rio de Janeiro. This study determined the genetic and morphological diversity and verified the species involved in the hybridization of 10 individuals from the municipalities of Silva Jardim (N = 9) and Rio das Ostras (N = 1). We compared the external morphology and skull of C. jacchus (N = 15) and C. penicillata (N = 14) specimens deposited in the collection of the National Museum of Rio de Janeiro (MN- UFRJ). Phylogenetic (maximum likelihood and Bayesian inference) and phylogeographical analyses (network analysis) were performed based on cytochrome b sequences. These analyses included hybrids from the metropolitan region of Rio de Janeiro (N = 3), C. penicillata (N = 2), C. jacchus (N = 2), C. geoffroyi (N = 2), C. kuhlii (N = 2), C. aurita (N = 1), and as outgroups, Mico emiliae (N = 1) and Saguinus mystax (N = 1). The pelage and skull characters of most hybrids were more closely related to C. jacchus. Skull morphometric analysis revealed an intermediate state for the hybrids. Phylogenetic analyses revealed a high similarity between the hybrids and C. penicillata. Six haplotypes of hybrids were identified. Network analysis including them and C. penicillata recovered the topology generated by phylogenetic analysis. The results corroborate that C. jacchus and C. penicillata participate in the hybridization process. There was no geographic structure between hybrids from the coastal lowlands and from the metropolitan region of Rio de Janeiro.

Social sounds produced by franciscana dolphins, Pontoporia blainvillei (Cetartiodactyla, Pontoporiidae)

Franciscana dolphin (Pontoporia blainvillei) whistles were documented for the first time during 2003-2013 in Babitonga Bay estuary, South Brazil, together with burst pulses. Recordings were made from small boats under good sea conditions, and recording equipment that allowed analysis of sounds up to 96 kHz. The recordings were made in the presence of 2-31 franciscana dolphins. During 23 h and 53 min, 90 whistles and 51 burst pulse series were recorded. Although Guiana dolphins (Sotalia guianensis) inhabit nearby waters, none were observed in the area during the recordings. The authors recorded ten types of whistles. The initial frequency varied between 1.6 and 94.6 kHz, and the final frequency varied between 0.7 and 94.5 kHz; the authors were not able to determine if dolphin whistles exceeded the 96 kHz recording limit of the authors' equipment, although that is likely, especially because some whistles showed harmonics. Whistle duration varied between 0.008 and 0.361 s. Burst pulses had initial frequencies between 69 and 82.1 kHz (77 ± 3.81). These results showed that P. blainvillei produces whistles and burst pulses, although they seem to be produced infrequently.

The karyotype of Trinomys paratus (Rodentia: Echimyidae) with comments about its phylogenetic relationship

The spiny rat Trinomys, with ten endemic species in eastern Brazil, has a complex taxonomy. We carried out a revision of the karyotypes of Trinomys, described for the first time the karyotype of Trinomys paratus and performed the first phylogenetic analysis including all Trinomys species based on the mitochondrial cytochrome b gene. The T. paratus karyotype showed diploid number of 58 and fundamental autosomal number of 112. Diploid and fundamental autosomal numbers (FNa), and chromosomes’ morphology, are similar to those described for Trinomys eliasi. T. paratus appears as sister taxa of T. eliasi; in turn, this clade was recovered as the sister group of Trinomys setosus, as previously reported, confirming that sister species of Trinomys has conserved karyotypes, and suggesting that karyological evolution in this genus could be slower than species differentiation.

Resolved phylogeny and biogeography of the root pathogen Armillaria and its gasteroid relative, Guyanagaster

Background

Armillaria is a globally distributed mushroom-forming genus composed primarily of plant pathogens. Species in this genus are prolific producers of rhizomorphs, or vegetative structures, which, when found, are often associated with infection. Because of their importance as plant pathogens, understanding the evolutionary origins of this genus and how it gained a worldwide distribution is of interest. The first gasteroid fungus with close affinities to Armillaria—Guyanagaster necrorhizus—was described from the Neotropical rainforests of Guyana. In this study, we conducted phylogenetic analyses to fully resolve the relationship of G. necrorhizus with Armillaria. Data sets containing Guyanagaster from two collecting localities, along with a global sampling of 21 Armillaria species—including newly collected specimens from Guyana and Africa—at six loci (28S, EF1α, RPB2, TUB, actin-1 and gpd) were used. Three loci—28S, EF1α and RPB2—were analyzed in a partitioned nucleotide data set to infer divergence dates and ancestral range estimations for well-supported, monophyletic lineages.

Results

The six-locus phylogenetic analysis resolves Guyanagaster as the earliest diverging lineage in the armillarioid clade. The next lineage to diverge is that composed of species in Armillaria subgenus Desarmillaria. This subgenus is elevated to genus level to accommodate the exannulate mushroom-forming armillarioid species. The final lineage to diverge is that composed of annulate mushroom-forming armillarioid species, in what is now Armillaria sensu stricto. The molecular clock analysis and ancestral range estimation suggest the most recent common ancestor to the armillarioid lineage arose 51 million years ago in Eurasia. A new species, Guyanagaster lucianii sp. nov. from Guyana, is described.

Conclusions

The armillarioid lineage evolved in Eurasia during the height of tropical rainforest expansion about 51 million years ago, a time marked by a warm and wet global climate. Species of Guyanagaster and Desarmillaria represent extant taxa of these early diverging lineages. Desarmillaria represents an armillarioid lineage that was likely much more widespread in the past. Guyanagaster likely evolved from a gilled mushroom ancestor and could represent a highly specialized endemic in the Guiana Shield. Armillaria species represent those that evolved after the shift in climate from warm and tropical to cool and arid during the late Eocene. No species in either Desarmillaria or Guyanagaster are known to produce melanized rhizomorphs in nature, whereas almost all Armillaria species are known to produce them. The production of rhizomorphs is an adaptation to harsh environments, and could be a driver of diversification in Armillaria by conferring a competitive advantage to the species that produce them.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0877-3) contains supplementary material, which is available to authorized users.

Isthminia panamensis, a new fossil inioid (Mammalia, Cetacea) from the Chagres Formation of Panama and the evolution of 'river dolphins' in the Americas

In contrast to dominant mode of ecological transition in the evolution of marine mammals, different lineages of toothed whales (Odontoceti) have repeatedly invaded freshwater ecosystems during the Cenozoic era. The so-called 'river dolphins' are now recognized as independent lineages that converged on similar morphological specializations (e.g., longirostry). In South America, the two endemic 'river dolphin' lineages form a clade (Inioidea), with closely related fossil inioids from marine rock units in the South Pacific and North Atlantic oceans. Here we describe a new genus and species of fossil inioid, Isthminia panamensis, gen. et sp. nov. from the late Miocene of Panama. The type and only known specimen consists of a partial skull, mandibles, isolated teeth, a right scapula, and carpal elements recovered from the Piña Facies of the Chagres Formation, along the Caribbean coast of Panama. Sedimentological and associated fauna from the Piña Facies point to fully marine conditions with high planktonic productivity about 6.1-5.8 million years ago (Messinian), pre-dating the final closure of the Isthmus of Panama. Along with ecomorphological data, we propose that Isthminia was primarily a marine inhabitant, similar to modern oceanic delphinoids. Phylogenetic analysis of fossil and living inioids, including new codings for Ischyrorhynchus, an enigmatic taxon from the late Miocene of Argentina, places Isthminia as the sister taxon to Inia, in a broader clade that includes Ischyrorhynchus and Meherrinia, a North American fossil inioid. This phylogenetic hypothesis complicates the possible scenarios for the freshwater invasion of the Amazon River system by stem relatives of Inia, but it remains consistent with a broader marine ancestry for Inioidea. Based on the fossil record of this group, along with Isthminia, we propose that a marine ancestor of Inia invaded Amazonia during late Miocene eustatic sea-level highs.

Evidence of Positive Selection of Aquaporins Genes from Pontoporia blainvillei during the Evolutionary Process of Cetaceans

BACKGROUND

Marine mammals are well adapted to their hyperosmotic environment. Several morphological and physiological adaptations for water conservation and salt excretion are known to be present in cetaceans, being responsible for regulating salt balance. However, most previous studies have focused on the unique renal physiology of marine mammals, but the molecular bases of these mechanisms remain poorly explored. Many genes have been identified to be involved in osmotic regulation, including the aquaporins. Considering that aquaporin genes were potentially subject to strong selective pressure, the aim of this study was to analyze the molecular evolution of seven aquaporin genes (AQP1, AQP2, AQP3, AQP4, AQP6, AQP7, and AQP9) comparing the lineages of cetaceans and terrestrial mammals.

RESULTS

Our results demonstrated strong positive selection in cetacean-specific lineages acting only in the gene for AQP2 (amino acids 23, 83, 107,179, 180, 181, 182), whereas no selection was observed in terrestrial mammalian lineages. We also analyzed the changes in the 3D structure of the aquaporin 2 protein. Signs of strong positive selection in AQP2 sites 179, 180, 181, and 182 were unexpectedly identified only in the baiji lineage, which was the only river dolphin examined in this study. Positive selection in aquaporins AQP1 (45), AQP4 (74), AQP7 (342, 343, 356) was detected in cetaceans and artiodactyls, suggesting that these events are not related to maintaining water and electrolyte homeostasis in seawater.

CONCLUSIONS

Our results suggest that the AQP2 gene might reflect different selective pressures in maintaining water balance in cetaceans, contributing to the passage from the terrestrial environment to the aquatic. Further studies are necessary, especially those including other freshwater dolphins, who exhibit osmoregulatory mechanisms different from those of marine cetaceans for the same essential task of maintaining serum electrolyte balance.

Initial Evidence for Adaptive Selection on the NADH Subunit Two of Freshwater Dolphins by Analyses of Mitochondrial Genomes

A small number of cetaceans have adapted to an entirely freshwater environment, having colonized rivers in Asia and South America from an ancestral origin in the marine environment. This includes the ‘river dolphins’, early divergence from the odontocete lineage, and two species of true dolphins (Family Delphinidae). Successful adaptation to the freshwater environment may have required increased demands in energy involved in processes such as the mitochondrial osmotic balance. For this reason, riverine odontocetes provide a compelling natural experiment in adaptation of mammals from marine to freshwater habitats. Here we present initial evidence of positive selection in the NADH dehydrogenase subunit 2 of riverine odontocetes by analyses of full mitochondrial genomes, using tests of selection and protein structure modeling. The codon model with highest statistical support corresponds to three discrete categories for amino acid sites, those under positive, neutral, and purifying selection. With this model we found positive selection at site 297 of the NADH dehydrogenase subunit 2 (d_N/d_S>1.0,) leading to a substitution of an Ala or Val from the ancestral state of Thr. A phylogenetic reconstruction of 27 cetacean mitogenomes showed that an Ala substitution has evolved at least four times in cetaceans, once or more in the three ‘river dolphins’ (Families Pontoporidae, Lipotidae and Inidae), once in the riverine Sotalia fluviatilis (but not in its marine sister taxa), once in the riverine Orcaella brevirostris from the Mekong River (but not in its marine sister taxa) and once in two other related marine dolphins. We located the position of this amino acid substitution in an alpha-helix channel in the trans-membrane domain in both the E. coli structure and Sotalia fluviatilis model. In E. coli this position is located in a helix implicated in a proton translocation channel of respiratory complex 1 and may have a similar role in the NADH dehydrogenases of cetaceans.

Physicochemical evolution and molecular adaptation of the cetacean osmoregulation-related gene UT-A2 and implications for functional studies

Cetaceans have an enigmatic evolutionary history of re-invading aquatic habitats. One of their essential adaptabilities that has enabled this process is their homeostatic strategy adjustment. Here, we investigated the physicochemical evolution and molecular adaptation of the cetacean urea transporter UT-A2, which plays an important role in urine concentration and water homeostasis. First, we cloned UT-A2 from the freshwater Yangtze finless porpoise, after which bioinformatics analyses were conducted based on available datasets (including freshwater baiji and marine toothed and baleen whales) using MEGA, PAML, DataMonkey, TreeSAAP and Consurf. Our findings suggest that the UT-A2 protein shows folding similar to that of dvUT and UT-B, whereas some variations occurred in the functional So and Si regions of the selectivity filter. Additionally, several regions of the cetacean UT-A2 protein have experienced molecular adaptations. We suggest that positive-destabilizing selection could contribute to adaptations by influencing its biochemical and conformational character. The conservation of amino acid residues within the selectivity filter of the urea conduction pore is likely to be necessary for urea conduction, whereas the non-conserved amino acid replacements around the entrance and exit of the conduction pore could potentially affect the activity, which could be interesting target sites for future mutagenesis studies.

Population structure of the endangered franciscana dolphin (Pontoporia blainvillei): reassessing management units

Franciscanas are the most endangered dolphins in the Southwestern Atlantic. Due to their coastal and estuarine habits, franciscanas suffer from extensive fisheries bycatch, as well as from habitat loss and degradation. Four Franciscana Management Areas (FMA), proposed based on biology, demography, morphology and genetic data, were incorporated into management planning and in the delineation of research efforts. We re-evaluated that proposal through the analysis of control region sequences from franciscanas throughout their distribution range (N = 162), including novel sequences from the northern limit of the species and two other previously unsampled localities in Brazil. A deep evolutionary break was observed between franciscanas from the northern and southern portions of the species distribution, indicating that they must be managed as two Evolutionarily Significant Units (ESU). Furthermore, additional FMAs should be recognised to accommodate the genetic differentiation found in each ESU. These results have immediate consequences for the conservation and management of this endangered species.

A new species of river dolphin from Brazil or: how little do we know our biodiversity

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.

The first freshwater mosasauroid (Upper Cretaceous, Hungary) and a new clade of basal mosasauroids

Mosasauroids are conventionally conceived of as gigantic, obligatorily aquatic marine lizards (1000s of specimens from marine deposited rocks) with a cosmopolitan distribution in the Late Cretaceous (90-65 million years ago [mya]) oceans and seas of the world. Here we report on the fossilized remains of numerous individuals (small juveniles to large adults) of a new taxon, Pannoniasaurus inexpectatus gen. et sp. nov. from the Csehbánya Formation, Hungary (Santonian, Upper Cretaceous, 85.3-83.5 mya) that represent the first known mosasauroid that lived in freshwater environments. Previous to this find, only one specimen of a marine mosasauroid, cf. Plioplatecarpus sp., is known from non-marine rocks in Western Canada. Pannoniasaurus inexpectatus gen. et sp. nov. uniquely possesses a plesiomorphic pelvic anatomy, a non-mosasauroid but pontosaur-like tail osteology, possibly limbs like a terrestrial lizard, and a flattened, crocodile-like skull. Cladistic analysis reconstructs P. inexpectatus in a new clade of mosasauroids: (Pannoniasaurus (Tethysaurus (Yaguarasaurus, Russellosaurus))). P. inexpectatus is part of a mixed terrestrial and freshwater faunal assemblage that includes fishes, amphibians turtles, terrestrial lizards, crocodiles, pterosaurs, dinosaurs and birds.