Pakicetus inachus and the origin of whales and dolphins (Mammalia: Cetacea)

The present paper is concerned with the comparative morphology of the archeocete and odontocete skull. Among the archeocetes, the recently described lower Eocene Pakicetus inachus obviously represents an early stage of adaptation to aquatic life. The morphology of the incomplete cranial remains, however, gives no evidence that Pakicetus was an amphibious intermediate stage. The evolution of advanced archeocetes and odontocetes is characterized by the successive acquirement of new morphological devices related to the emission and perception of ultrasound under water. The formation of a sonar system in odontocetes obviously not only helped to compensate for the loss of the peripheral olfactory system but moreover was a substantial factor in the evolution of the exceptional dolphin brain.     

Enamel Ultrastructure in Fossil Cetaceans (Cetacea: Archaeoceti and Odontoceti)

The transition from terrestrial ancestry to a fully pelagic life profoundly altered the body systems of cetaceans, with extreme morphological changes in the skull and feeding apparatus. The Oligocene Epoch was a crucial time in the evolution of cetaceans when the ancestors of modern whales and dolphins (Neoceti) underwent major diversification, but details of dental structure and evolution are poorly known for the archaeocete-neocete transition. We report the morphology of teeth and ultrastructure of enamel in archaeocetes, and fossil platanistoids and delphinoids, ranging from late Oligocene (Waitaki Valley, New Zealand) to Pliocene (Caldera, Chile). Teeth were embedded in epoxy resin, sectioned in cross and longitudinal planes, polished, etched, and coated with gold palladium for scanning electron microscopy (SEM) observation. SEM images showed that in archaeocetes, squalodontids and Prosqualodon (taxa with heterodont and nonpolydont/limited polydont teeth), the inner enamel was organized in Hunter-Schreger bands (HSB) with an outer layer of radial enamel. This is a common pattern in most large-bodied mammals and it is regarded as a biomechanical adaptation related to food processing and crack resistance. Fossil Otekaikea sp. and delphinoids, which were polydont and homodont, showed a simpler structure, with inner radial and outer prismless enamel. Radial enamel is regarded as more wear-resistant and has been retained in several mammalian taxa in which opposing tooth surfaces slide over each other. These observations suggest that the transition from a heterodont and nonpolydont/limited polydont dentition in archaeocetes and early odontocetes, to homodont and polydont teeth in crownward odontocetes, was also linked to a marked simplification in the enamel Schmelzmuster. These patterns probably reflect functional shifts in food processing from shear-and-mastication in archaeocetes and early odontocetes, to pierce-and-grasp occlusion in crownward odontocetes, with the implication of less demanding feeding biomechanics as seen in most extant odontocetes.     

Comparative anatomy of the bony labyrinth of extant and extinct porpoises (Cetacea: Phocoenidae)

The inner ear anatomy of cetaceans, now more readily accessible by means of nondestructive high‐resolution X‐ray computed tomographic (CT) scanning, provides a window into their acoustic abilities and ecological preferences. Inner ear labyrinths also may be a source for additional morphological characters for phylogenetic analyses. In this study, we explore digital endocasts of the inner ear labyrinths of representative species of extinct and extant porpoises (Mammalia: Cetacea: Phocoenidae), a clade of some of the smallest odontocete cetaceans, which produce some of the highest‐frequency clicks for biosonar and communication. Metrics used to infer hearing ranges based on cochlear morphology indicate that all taxa considered could hear high‐frequency sounds, thus the group had already acquired high‐frequency hearing capabilities by the Miocene (9–11 Mya) at the latest. Vestibular morphology indicates that extant species with pelagic preferences have similarly low semicircular canal deviations from 90°, values indicating more sensitivity to head rotations. Species with near‐shore preferences have higher canal deviation values, indicating less sensitivity to head rotations. Extending these analyses to the extinct species, we demonstrate a good match between those predicted to have coastal (such as Semirostrum cerutti) preferences and high canal deviation values. We establish new body length relationships based on correlations with inner ear labyrinth volume, which can be further explored among other aquatic mammals to infer body size of specimens consisting of fragmentary material.     

Morphological variation among the inner ears of extinct and extant baleen whales (Cetacea: Mysticeti)

Living mysticetes (baleen whales) and odontocetes (toothed whales) differ significantly in auditory function in that toothed whales are sensitive to high‐frequency and ultrasonic sound vibrations and mysticetes to low‐frequency and infrasonic noises. Our knowledge of the evolution and phylogeny of cetaceans, and mysticetes in particular, is at a point at which we can explore morphological and physiological changes within the baleen whale inner ear. Traditional comparative anatomy and landmark‐based 3D‐geometric morphometric analyses were performed to investigate the anatomical diversity of the inner ears of extinct and extant mysticetes in comparison with other cetaceans. Principal component analyses (PCAs) show that the cochlear morphospace of odontocetes is tangential to that of mysticetes, but odontocetes are completely separated from mysticetes when semicircular canal landmarks are combined with the cochlear data. The cochlea of the archaeocete Zygorhiza kochii and early diverging extinct mysticetes plot within the morphospace of crown mysticetes, suggesting that mysticetes possess ancestral cochlear morphology and physiology. The PCA results indicate variation among mysticete species, although no major patterns are recovered to suggest separate hearing or locomotor regimes. Phylogenetic signal was detected for several clades, including crown Cetacea and crown Mysticeti, with the most clades expressing phylogenetic signal in the semicircular canal dataset. Brownian motion could not be excluded as an explanation for the signal, except for analyses combining cochlea and semicircular canal datasets for Balaenopteridae. J. Morphol. 277:1599–1615, 2016. © 2016 Wiley Periodicals, Inc.     

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.     

Conflicts with fisheries and intentional killing of freshwater dolphins (Cetacea: Odontoceti) in the Western Brazilian Amazon

We report three cases of conflicts with fishing activities of freshwater dolphins Inia geoffrensis and Sotalia fluviatilis in the Western Brazilian Amazon. The animals presented several cuts produced by perforating and cutting objects, especially on the dorsum, sides and flukes. The wounds were probably caused by harpoons and machetes, gear commonly used by local inhabitants for fishing and agricultural practices in the Amazon. The carcasses had not been subsequently used in any way, which suggests that the animals were not killed for consumption. Conflicts with fishermen and persistent cultural taboos may have led to the deaths. These records are an indication of a growing situation of conflict with fishing activities that should be taken into consideration in the conservation policy planning of aquatic mammals in the Amazon.     

Mandible allometry in extant and fossil Balaenopteridae (Cetacea: Mammalia): the largest vertebrate skeletal element and its role in rorqual lunge feeding

Rorqual whales (crown Balaenopteridae) are unique among aquatic vertebrates in their ability to lunge feed. During a single lunge, rorquals rapidly engulf a large volume of prey‐laden water at high speed, which they then filter to capture suspended prey. Engulfment biomechanics are mostly governed by the coordinated opening and closing of the mandibles at large gape angles, which differentially exposes the floor of the oral cavity to oncoming flow. The mouth area in rorquals is delimited by unfused bony mandibles that form kinetic linkages to each other and with the skull. The relative scale and morphology of these skeletal elements have profound consequences for the energetic efficiency of foraging in these gigantic predators. Here, we performed a morphometric study of rorqual mandibles using a data set derived from a survey of museum specimens. Across adult specimens of extant balaenopterids, mandibles range in size from ～1–6 m in length, and at their upper limit they represent the single largest osteological element of any vertebrate, living or extinct. Our analyses determined that rorqual mandibles exhibit positive allometry, whereby the relative size of these mandibles becomes greater with increasing body size. These robust scaling relationships allowed us to predict mandible length for fragmentary remains (e.g. incomplete and/or fossil specimens), as we demonstrated for two partial mandibles from the latest Miocene of California, USA, and for mandibles from previously described fossil balaenopterids. Furthermore, we showed the allometry of mandible length to body size in extant mysticetes, which hints at fundamental developmental constraints in mysticetes despite their ecomorphological differences in feeding styles. Lastly, we outlined how our findings can be used to test hypotheses about the antiquity and evolution of lunge feeding. © 2012 The Linnean Society of London     

Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea)

Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between descendant lineages and are thus predicted to perform better in the presence of lineage-specific rate heterogeneity. However, it is uncertain how these models perform in the presence of punctuated shifts in substitution rate, especially between closely related clades. Using cetaceans (whales and dolphins) as a case study, we test the performance of these two substitution models in estimating both molecular rates and divergence times in the presence of substantial lineage-specific rate heterogeneity. Our RLC analyses of whole mitochondrial genome alignments find evidence for up to ten clade-specific nucleotide substitution rate shifts in cetaceans. We provide evidence that in the uncorrelated relaxed clock framework, a punctuated shift in the rate of molecular evolution within a subclade results in posterior rate estimates that are either misled or intermediate between the disparate rate classes present in baleen and toothed whales. Using simulations, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated. We further demonstrate how increasing prior age uncertainty can bias rate and age estimates, even while the 95% highest posterior density around age estimates decreases; in other words, increased precision for an inaccurate estimate. We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages.     

Molar enamel thickness in European Miocene and extant hominoidea

Based on a roentgenographic analysis, the molar enamel of certain European Miocene dryopithecines is absolutely thick (r=1.03–1.30 mm in thickness); the molar enamel of certain European pliopithecines is thin (r=0.32–0.82 mm thick). The rank order for enamel thickness in extant hominoids (from thickest to thinnest) is confirmed to beHomo, Pongo, Gorilla, Pan, andHylobates. There is a great deal of enamel thickness variability within the great ape sample. Extant analogues suggest that dryopithecines were probably adapted to a frugivorous/gramnivorous dietary regimen, while pliopithecines were probably better suited to folivory.     

The position of Cetacea within mammalia: phylogenetic analysis of morphological data from extinct and extant taxa

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.     

Intraspecific variation in the dolphins Lagenorhynchus albirostris and L. acutus (Mammalia: Cetacea) in metrical and non-metrical skull characters, with remarks on occurrence

Intraspecific multivariate data analyses of 27 metrical and 20 non-metrical characters were performed on skulls of L. albirostris (Gray, 1846) and L. acutus (Gray, 1826) to distinguish between possible populations from the eastern and the western North Atlantic.
The results from principal component (PC) analysis and partial least square (PLS) analysis suggest that the skulls of L. albirostris were taken from separate populations, whereas those of L. acutus were not.
A difference in the occurrence-patterns of the two species was found, indicating that the degree of intraspecific variation may be linked to the water-depth related distribution.     

The ovaries and reproduction in Pontoporia blainvillei (Cetacea: Platanistidae)

The ovaries of 113 Pontoporia blainvillei (Franciscana dolphin) were examined and their characteristics related to season, body length of the animals and, in some individuals, foetal length. The following conclusions were drawn from the results: most females attain sexual maturity when they reach 136–146 cm body length; most conceptions occur in the period December to February, with a peak in the first half of January; usually only one ovulation occurs, and no animal ovulated more than twice, in a season; postpartum ovulation may occur, and evidence is presented that this is probably followed by conception and that animals may breed once a year but most females breed every other year; body length at birth is greater than 70 cm and less than 85 cm, and probably nearer the smaller figure; the gestation period is 10.5–12 months (depending on what is the actual figure for length at birth, but probably less than 11 months); lactation lasts at least nine months; the corpus luteum contains two morphologically distinct, but apparently functional cell types; there is no apparent morphological difference between corpora lutea which are not associated with pregnancy, and corpora lutea of pregnancy; corpora albicantia may persist for a maximum of four years before being reabsorbed completely.     

Molar enamel thickness and dentine horn height in Gigantopithecus blacki

Absolutely thick molar enamel is consistent with large body size estimates and dietary inferences about Gigantopithecus blacki, which focus on tough or fibrous vegetation. In this study, 10 G. blacki molars demonstrating various stages of attrition were imaged using high-resolution microtomography. Three-dimensional average enamel thickness and relative enamel thickness measurements were recorded on the least worn molars within the sample (n = 2). Seven molars were also virtually sectioned through the mesial cusps and two-dimensional enamel thickness and dentine horn height measurements were recorded. Gigantopithecus has the thickest enamel of any fossil or extant primate in terms of absolute thickness. Relative (size-scaled) measures of enamel thickness, however, support a thick characterization (i.e., not "hyper-thick"); G. blacki relative enamel thickness overlaps slightly with Pongo and completely with Homo. Gigantopithecus blacki dentine horns are relatively short, similar to (but shorter than) those of Pongo, which in turn are shorter than those of humans and African apes. Gigantopithecus blacki molar enamel (and to a lesser extent, that of Pongo pygmaeus) is distributed relatively evenly across the occlusal surface compared with the more complex distribution of enamel thickness in Homo sapiens. The combination of evenly distributed occlusal enamel and relatively short dentine horns in G. blacki results in a flat and low-cusped occlusal surface suitable to grinding tough or fibrous food objects. This suite of molar morphologies is also found to varying degrees in Pongo and Sivapithecus, but not in African apes and humans, and may be diagnostic of subfamily Ponginae.