New genicular joint angle criteria for flexor muscle (Musculus Semimembranosus) during the terrestrial mammals walking.

Background: The genicular or knee joint angles of terrestrial mammals remain constant during the stance phase of walking; however, the angles differ among taxa. The knee joint angle is known to correlate with taxa and body mass among extant mammals, yet several extinct mammals, such as desmostylians, do not have closely related descendants. Furthermore, fossils lose their soft tissues by the time they are unearthed, making body mass estimates difficult. These factors cause significant problems when reconstructing the proper postures of extinct mammals. Terrestrial mammals use potential and kinetic energy for locomotion; particularly, an inverted pendulum mechanism is used for walking. This mechanism requires maintaining the rod length constant, therefore, terrestrial mammals maintain their joint angle in a small range. A muscle reaction referred to as co-contraction is known to increase joint stiffness; both the agonist and antagonist muscles work simultaneously on the same joint at the same time. The musculus semimembranosus flexes the knee joint and acts as an antagonist to muscles that extend it. Methods: Twenty-one species of terrestrial mammals were examined to identify the elements that constitute the angle between the m. semimembranosus and the tibia based on the period between the hindlimb touching down and taking off from the ground. Measurements were captured from videos in high-speed mode (420 fps), selecting 13 pictures from the first 75% of each video while the animals were walking. The angles between the main force line of the m. semimembranosus and the tibia, which were defined as θsm-t, were measured. Results: The maximum and minimum angles between the m. semimembranosus and the tibia (θsm-t) of the stance instance (SI) were successfully determined for more than 80% of the target animals (17 out of 21 species) during SI-1 to SI-13 within ±10° from the mean. The difference between each successive SI was small and, therefore, the θsm-t transition was smooth. According to the results of the total stance differences among the target animals, θsm-t was relatively constant during a stance and, therefore, average θsm-t (θave) can represent each animal. Only Carnivora had a significant difference in the correlation between body mass and θave. In addition, there were significant differences in θave between plantigrade and unguligrade locomotion. Conclusion: Our measurements show that θave was 100 ± 10° regardless taxon, body mass, and locomotor mode. Thus, only three points on skeletons need to be measured to determine θave. This offers a new approximation approach for understanding hindlimb posture that could be applied to the study of the hindlimbs of extinct mammals with no closely related extant descendants.

An Early Miocene kentriodontoid (Cetacea: Odontoceti) from the western North Pacific, and its implications for their phylogeny and paleobiogeography.

So-called 'kentriodontids' are extinct dolphin-like odontocetes known from the Early to Late Miocene worldwide. Although recent studies have proposed that they were monophyletic, their taxonomic relationships still remain controversial. Such a controversy exists partly because of the predominance of primitive morphologies in this taxon, but the fact is that quite a few 'kentriodontids' are known only from fragmentary skulls and/or isolated periotics. A new 'kentriodontid' Platysvercus ugonis gen. et sp. nov. is described based on a nearly complete skull from the upper Lower Miocene Sugota Formation, Akita Prefecture, northern Japan. Based on the phylogenetic analysis of P. ugonis described here, the monophyly of the 'kentriodontids' is confirmed, and it is recognized as the superfamily Kentriodontoidea. This new superfamily is subdivided into two families as new ranks: Kentriodontidae and Lophocetidae. Based on the paleobiogeographic analysis of the Kentriodontoidea, their common ancestor emerged in the North Pacific Ocean and spread over the Northern Hemisphere. Initial diversification of the Kentriodontidae in the North Pacific Ocean and the Lophocetidae in the North Atlantic Ocean was recognized as a vicariance event. The diversification and extinction of the Kentriodontoidea could have been synchronously influenced by climate events during the Middle Miocene.

Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan.

Little is known about the spatiotemporal dynamics of gray wolves in the Pleistocene across low-latitude regions of Eurasia. In Japan, a small-bodied endemic subspecies of Japanese wolves existed and went extinct in the early 1900s. The fossil record indicates that a giant wolf, which reached 70 cm in body height, inhabited Japan during the Pleistocene, but its evolutionary relationship, if any, with the Japanese wolf remains uncertain. Here, to reveal the genetic origin of the Japanese wolf, we analyzed ancient DNA from remains (recovered in Japan) of one Pleistocene wolf that lived 35,000 years ago and one Holocene wolf from 5,000 years ago. The analysis of the mitochondrial DNA revealed that the Pleistocene wolf was not part of the Japanese wolf clade but rather an earlier-diverging lineage. The analysis of the nuclear DNA of the Holocene Japanese wolf revealed that it was an admixture of the Japanese Pleistocene wolf and continental wolf lineages. These findings suggest that the Japanese wolf originated via waves of colonization of multiple Pleistocene wolf populations at 57-35 and 37-14 ka, respectively, followed by interpopulation hybridization.

Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages.

Little is known about how mammalian biogeography on islands was affected by sea-level fluctuations. In the Japanese Archipelago, brown bears (Ursus arctos) currently inhabit only Hokkaido, the northern island, but Pleistocene fossils indicate a past distribution throughout Honshu, Japan's largest island. However, the difficulty of recovering ancient DNA from fossils in temperate East Asia has limited our understanding of their evolutionary history. Here, we analysed mitochondrial DNA from a 32 500-year-old brown bear fossil from Honshu. Our results show that this individual belonged to a previously unknown lineage that split approximately 160 Ka from its sister lineage, the southern Hokkaido clade. This divergence time and fossil record suggest that brown bears migrated from the Eurasian continent to Honshu at least twice; the first population was an early-diverging lineage (greater than 340 Ka), and the second migrated via Hokkaido after approximately 160 Ka, during the ice age. Thus, glacial-age sea-level falls might have facilitated migrations of large mammals more frequently than previously thought, which may have had a substantial impact on ecosystem dynamics in these isolated islands.

The oldest fossil record of the extant genus Berardius (Odontoceti, Ziphiidae) from the Middle to Late Miocene boundary of the western North Pacific.

A new species of a beaked whale that belongs to the extant genus Berardius is described from the Middle to Late Miocene boundary age Tsurushi Formation (ca 12.3-11.5 Ma) on the Sado Island, Niigata Prefecture, Japan. The new species, Berardius kobayashii sp. nov. represents the oldest record of this genus and provides a minimum age for the emergence of this extant genus. Berardius kobayashii sp. nov. has the following generic characters: the ratio between the width of the premaxillary crests and the width of the premaxillary sac fossae is 1.0-1.25, nodular frontals make isolated protuberance on the posterior part of the vertex. Among the species within the genus, B. kobayashii sp. nov. shares a unique character with B. minimus: the apices of the left and right hamular processes of the pterygoids contact medially, forming together a posteriorly directed medial point. In addition, B. kobayashii sp. nov. displays a unique combination of the following characters: it is extremely small in size, and the nasals are short, the ratio between the length of the medial suture of nasals on the vertex and the maximum width of nasals is less than 0.4. Berardius kobayashii sp. nov. fills the gap between the origin of the genus and later diversifications of the extant species. This discovery is also key to elucidate the process of the emergence and dispersal of the genus during the Middle to Late Miocene. Based on the distributional patterns of the fossil and extant species of the genus, the western North Pacific including the Sea of Japan may have been one of the areas for the evolution and radiation of this genus at the time before 11 Ma.

A new kentriodontid (Cetacea: Odontoceti) from the early to middle Miocene of the western North Pacific and a revision of kentriodontid phylogeny.

A new species of an extinct dolphin belonging to the kentriodontids, i.e., Kentriodon sugawarai sp. nov., is described from the upper lower to lowest middle Miocene Kadonosawa Formation in Ninohe City, Iwate Prefecture, northern Japan. The holotype of Kentriodon sugawarai sp. nov., consists of a partial skull with ear bones, mandibular fragments, and some postcranial bones. This new species shares five unique characters with other species of Kentriodon. In addition, the new species differs from other species of the genus in displaying a narrow width of the squamosal lateral to the exoccipital in posterior view, the dorsolateral edge of the opening of the ventral infraorbital foramen that is formed by the maxilla and the lacrimal or the jugal, and at least three anterior dorsal infraorbital foramina. Our phylogenetic analysis based on 393 characters for 103 Odontoceti taxa yielded a consensus tree showing all previously identified kentriodontids as a monophyletic group that comprises the sister group of the crown Dephinoidea, which in turn include Delphinidae, Phocoenidae and Monodontidae. Our analysis also indicates that the distinct innovation of the acoustic apparatus (i.e., 13 out of 29 derived characters are from tympanoperiotic) would have occurred in the ancestral lineage of the Delphinoidea (sensu lato) including the monophyletic Kentriodontidae during their initial evolution and diversification.

The oldest record of the Steller sea lion Eumetopias jubatus (Schreber, 1776) from the early Pleistocene of the North Pacific.

The extant genera of fur seals and sea lions of the family Otariidae (Carnivora: Pinnipedia) are thought to have emerged in the Pliocene or the early Pleistocene in the North Pacific. Among them, the Steller sea lion (Eumetopias jubatus) is the largest and distributed both in the western and eastern North Pacific. In contrast to the limited distribution of the current population around the Japanese Islands that is now only along the coast of Hokkaido, their fossil records have been known from the middle and late Pleistocene of Honshu Island. One such important fossil specimen has been recorded from the upper lower Pleistocene Omma Formation (ca. 1.36-0.83 Ma) in Kanazawa, Ishikawa Prefecture, Japan, which now bears the institutional number GKZ-N 00001. Because GKZ-N 00001 is the earliest fossil having been identified as a species of the sea lion genus Eumetopias, it is of importance to elucidate the evolutionary history of that genus. The morphometric comparisons were made among 51 mandibles of fur seals and sea lions with GKZ-N 00001. As results of bivariate analyses and PCA based on 39 measurements for external morphologies with internal structures by CT scan data, there is almost no difference between GKZ-N 00001 and extant male individuals of E. jubatus. In this regard, GKZ-N 00001 is identified specifically as the Steller sea lion E. jubatus. Consequently, it is recognized as the oldest Steller sea lion in the North Pacific. About 0.8 Ma, the distribution of the Steller sea lion had been already established at least in the Japan Sea side of the western North Pacific.

Three-dimensional tooth surface texture analysis on stall-fed and wild boars (Sus scrofa).

Categorizing the archaeological remains of Sus scrofa as domesticated "pigs" or wild "boars" is often difficult because of their morphological and genetic similarities. For this purpose, we tested whether feeding ecological change of S. scrofa that accompanied their domestication can be detected based on the three-dimensional texture created on the tooth enamel surface by mastication. We scanned the lower tooth surface of one wild and one stall-fed populations of modern S. s. leucomystax and one wild population of S. s. riukiuanus by using a confocal laser microscope. The average body weight of S. s. leucomystax is twice as heavier as that of S. s. riukiuanus. The textures were quantified using the industrial "roughness" standard, ISO 25178, to prevent inter-observer errors and to distinguish small differences that were difficult to detect by two dimensional image observation. The values of parameters related to height and volume were significantly larger in the stall-fed population. Twenty parameters differed significantly between the stall-fed and wild population of S. s. leucomystax, which indicated that the feeding ecological difference affected the ISO parameters of the two boar populations. Six parameters also differed between the wild populations of S. s. leucomystax and S. s. riukiuanus. Surprisingly, no parameter differed between the populations of stall-fed S. s. leucomystax and wild S. s. riukiuanus. Consumption of hard nuts and/or agricultural fruits and crops by the wild population of S. s. riukiuanus may have produced a tooth surface texture similar to that of the stall-fed population of S. s. leucomystax. Further analysis of S. s. riukiuanus with a known diet is necessary to conclude whether ISO parameters reflect the dietary transition accompanying the domestication of Sus (e.g., wild, semi-domestic, and domestic). Until then, caution is needed in discriminating domesticated populations from wild populations that mainly feed on hard objects.

Neuroanatomy and inner ear labyrinths of the narwhal, Monodon monoceros, and beluga, Delphinapterus leucas (Cetacea: Monodontidae).

Narwhals (Monodon monoceros) and belugas (Delphinapterus leucas) are the only extant members of the Monodontidae, and are charismatic Arctic-endemic cetaceans that are at risk from global change. Investigating the anatomy and sensory apparatuses of these animals is essential to understanding their ecology and evolution, and informs efforts for their conservation. Here, we use X-ray CT scans to compare aspects of the endocranial and inner ear labyrinth anatomy of extant monodontids and use the overall morphology to draw larger inferences about the relationship between morphology and ecology. We show that differences in the shape of the brain, vasculature, and neural canals of both species may relate to differences in diving and other behaviors. The cochleae are similar in morphology in the two species, signifying similar hearing ranges and a close evolutionary relationship. Lastly, we compare two different methods for calculating 90var - a calculation independent of body size that is increasingly being used as a proxy for habitat preference. We show that a 'direct' angular measurement method shows significant differences between Arctic and other habitat preferences, but angle measurements based on planes through the semicircular canals do not, emphasizing the need for more detailed study and standardization of this measurement. This work represents the first comparative internal anatomical study of the endocranium and inner ear labyrinths of this small clade of toothed whales.

A new Miocene pinniped Allodesmus (Mammalia: Carnivora) from Hokkaido, northern Japan.

A nearly complete pinniped skeleton from the middle Miocene Okoppezawa Formation (ca 16.3-13.9 Ma), Hokkaido, northern Japan, is described as the holotype of Allodesmus uraiporensis sp. nov. The new species is distinguishable from other species of the genus by having the palatine fissure (incisive foramen) that is located anterior to the canine, an anteriorly located supraorbital process of the frontal, and by having the calcaneum with a developed peroneal tubercle. Our phylogenetic analysis suggests that the subfamily Allodesminae are represented by two genera, Atopotarus and Allodesmus, and the latter genus is represented by at least six species; Al. kernensis, Al. sinanoensis, Al. naorai, Al. packardi, Al. demerei and Al. uraiporensis sp. nov. Allodesmus uraiporensis sp. nov. is one of the oldest and the northernmost record of the genus in the western North Pacific, and it suggests that the diversification of the genus in the western North Pacific was synchronous to the time of their diversification in the eastern North Pacific.

Northern pygmy right whales highlight Quaternary marine mammal interchange.

The pygmy right whale, Caperea marginata, is the most enigmatic living whale. Little is known about its ecology and behaviour, but unusual specialisations of visual pigments [1], mitochondrial tRNAs [2], and postcranial anatomy [3] suggest a lifestyle different from that of other extant whales. Geographically, Caperea represents the only major baleen whale lineage entirely restricted to the Southern Ocean. Caperea-like fossils, the oldest of which date to the Late Miocene, are exceedingly rare and likewise limited to the Southern Hemisphere [4], despite a more substantial history of fossil sampling north of the equator. Two new Pleistocene fossils now provide unexpected evidence of a brief and relatively recent period in geological history when Caperea occurred in the Northern Hemisphere (Figure 1A,B).

Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites.

The Palaeognathae comprise the flightless ratites and the volant tinamous, and together with the Neognathae constitute the extant members of class Aves. It is commonly believed that Palaeognathae originated in Gondwana since most of the living species are found in the Southern Hemisphere [1-3]. However, this hypothesis has been questioned because the fossil paleognaths are mostly from the Northern Hemisphere in their earliest time (Paleocene) and possessed many putative ancestral characters [4]. Uncertainties regarding the origin and evolution of Palaeognathae stem from the difficulty in estimating their divergence times [1, 2] and their remarkable morphological convergence. Here, we recovered nuclear genome fragments from extinct elephant birds, which enabled us to reconstruct a reliable phylogenomic time tree for the Palaeognathae. Based on the tree, we identified homoplasies in morphological traits of paleognaths and reconstructed their morphology-based phylogeny including fossil species without molecular data. In contrast to the prevailing theories, the fossil paleognaths from the Northern Hemisphere were placed as the basal lineages. Combined with our stable divergence time estimates that enabled a valid argument regarding the correlation with geological events, we propose a new evolutionary scenario that contradicts the traditional view. The ancestral Palaeognathae were volant, as estimated from their molecular evolutionary rates, and originated during the Late Cretaceous in the Northern Hemisphere. They migrated to the Southern Hemisphere and speciated explosively around the Cretaceous-Paleogene boundary. They then extended their distribution to the Gondwana-derived landmasses, such as New Zealand and Madagascar, by overseas dispersal. Gigantism subsequently occurred independently on each landmass.

A new Miocene baleen whale from the Peruvian desert.

The Pisco-Ica and Sacaco basins of southern Peru are renowned for their abundance of exceptionally preserved fossil cetaceans, several of which retain traces of soft tissue and occasionally even stomach contents. Previous work has mostly focused on odontocetes, with baleen whales currently being restricted to just three described taxa. Here, we report a new Late Miocene rorqual (family Balaenopteridae), Incakujira anillodefuego gen. et sp. nov., based on two exceptionally preserved specimens from the Pisco Formation exposed at Aguada de Lomas, Sacaco Basin, southern Peru. Incakujira overall closely resembles modern balaenopterids, but stands out for its unusually gracile ascending process of the maxilla, as well as a markedly twisted postglenoid process of the squamosal. The latter likely impeded lateral (omega) rotation of the mandible, in stark contrast with the highly flexible craniomandibular joint of extant lunge-feeding rorquals. Overall, Incakujira expands the still meagre Miocene record of balaenopterids and reveals a previously underappreciated degree of complexity in the evolution of their iconic lunge-feeding strategy.

Multiple origins of gigantism in stem baleen whales.

Living baleen whales (Mysticeti) include the world's largest animals to have ever lived-blue whales (Balaenoptera musculus) can reach more than 30 m. However, the gigantism in baleen whales remains little explored. Here, we compiled all published stem mysticetes from the Eocene and Oligocene and then mapped the estimated body size onto different phylogenies that suggest distinct evolutionary histories of baleen whales. By assembling all known stem baleen whales, we present three novel findings in early mysticete evolution. Results show that, regardless of different phylogenetic scenarios, large body size (more than 5-m long) evolved multiple times independently in their early evolutionary history. For example, the earliest known aetiocetid (Fucaia buelli, 33-31 Ma) was small in size, about 2 m, and a later aetiocetid (Morawanocetus-like animal, 26-23 Ma) can reach 8-m long-almost four times the size of Fucaia buelli-suggesting an independent gigantism in the aetiocetid lineage. In addition, our reconstruction of ancestral state demonstrates that the baleen whales originated from small body size (less than 5 m) rather than large body size as previously acknowledged. Moreover, reconstructing the evolution of body size in stem baleen whales suggests that the initial pulse of mysticete gigantism started at least back to the Paleogene and in turn should help to understand the origin, pattern, and process of the extreme gigantism in the crown baleen whales. This study illustrates that Cope's rule is insufficient to explain the evolution of body size in a group that comprises the largest animals in the history of life, although currently the lack of exact ancestor-descendant relationships remains to fully reveal the evolutionary history of body size.

Evaluating the Phylogenetic Status of the Extinct Japanese Otter on the Basis of Mitochondrial Genome Analysis.

The Japanese otter lived throughout four main Japanese islands, but it has not been observed in the wild since 1979 and was declared extinct in 2012. Although recent taxonomic and molecular phylogenetic studies suggest that it should be treated as an independent species, International Union for Conservation of Nature Red List considers it as subspecies of Lutra lutra. Therefore, the taxonomic status of this species needs to be resolved. Here we determined the complete mitochondrial genome of two Japanese otters caught in Kanagawa and Kochi prefectures and five Eurasian otters (L. lutra). We reconstructed a molecular phylogenetic tree to estimate the phylogenetic position of the Japanese otter in Lutrinae using the Japanese otters and the other 11 Lutrinae species on the basis of ND5 (692 bp) and cytochrome b (1,140 bp) sequences. We observed that the two Japanese otters had close relationships with Eurasian otters, forming a monophyletic group (100% bootstrap probability). To elucidate detailed phylogenetic relationships among the Japanese and Eurasian otters, we reconstructed a maximum likelihood tree according to mitochondrial genome sequences (14,740 bp). The Japanese otter (JO1) collected in Kanagawa was deeply nested in the Eurasian otter clade, whereas the Japanese otter (JO2) collected in Kochi formed a distinct independent lineage in the Lutra clade. The estimated molecular divergences time for the ancestral lineages of the Japanese otters was 0.10 Ma (95%: 0.06-0.16 Ma) and 1.27 Ma (95%: 0.98-1.59 Ma) for JO1 and JO2 lineages, respectively. Thus, JO1 was identified as a member of L. lutra; JO2 represented the old Japanese otter lineage, which may be a distinct new species or subspecies of Lutra. We suggest that the ancestral population of the JO2 lineage migrated to Japan via the land bridge that existed between western Japanese islands and Asian continent at 1.27 Ma.

Phylogeographic and Demographic Analysis of the Asian Black Bear (Ursus thibetanus) Based on Mitochondrial DNA.

The Asian black bear Ursus thibetanus is widely distributed in Asia and is adapted to broad-leaved deciduous forests, playing an important ecological role in the natural environment. Several subspecies of U. thibetanus have been recognized, one of which, the Japanese black bear, is distributed in the Japanese archipelago. Recent molecular phylogeographic studies clarified that this subspecies is genetically distantly related to continental subspecies, suggesting an earlier origin. However, the evolutionary relationship between the Japanese and continental subspecies remained unclear. To understand the evolution of the Asian black bear in relation to geological events such as climatic and transgression-regression cycles, a reliable time estimation is also essential. To address these issues, we determined and analyzed the mt-genome of the Japanese subspecies. This indicates that the Japanese subspecies initially diverged from other Asian black bears in around 1.46Ma. The Northern continental population (northeast China, Russia, Korean peninsula) subsequently evolved, relatively recently, from the Southern continental population (southern China and Southeast Asia). While the Japanese black bear has an early origin, the tMRCAs and the dynamics of population sizes suggest that it dispersed relatively recently in the main Japanese islands: during the late Middle and Late Pleistocene, probably during or soon after the extinction of the brown bear in Honshu in the same period. Our estimation that the population size of the Japanese subspecies increased rapidly during the Late Pleistocene is the first evidential signal of a niche exchange between brown bears and black bears in the Japanese main islands. This interpretation seems plausible but was not corroborated by paleontological evidence that fossil record of the Japanese subspecies limited after the Late Pleistocene. We also report here a new fossil record of the oldest Japanese black bear from the Middle Pleistocene, and it supports our new evolutionary hypothesis of the Japanese black bear.

A New Late Miocene Odobenid (Mammalia: Carnivora) from Hokkaido, Japan Suggests Rapid Diversification of Basal Miocene Odobenids.

The modern walrus, Odobenus rosmarus, is specialized and only extant member of the family Odobenidae. They were much more diversified in the past, and at least 16 genera and 20 species of fossil walruses have been known. Although their diversity increased in the late Miocene and Pliocene (around 8-2 Million years ago), older records are poorly known. A new genus and species of archaic odobenid, Archaeodobenus akamatsui, gen. et sp. nov. from the late Miocene (ca. 10.0-9.5 Ma) top of the Ichibangawa Formation, Hokkaido, northern Japan, suggests rapid diversification of basal Miocene walruses. Archaeodobenus akamatsui is the contemporaneous Pseudotaria muramotoi from the same formation, but they are distinguishable from each other in size and shape of the occipital condyle, foramen magnum and mastoid process of the cranium, and other postcranial features. Based on our phylogenetic analysis, A. akamatsui might have split from P. muramotoi at the late Miocene in the western North Pacific. This rapid diversification of the archaic odobenids occurred with a combination of marine regression and transgression, which provided geological isolation among the common ancestors of extinct odobenids.

Metal-free hydrogen evolution with nanoparticles derived from pyrene via two-photon ionization induced by laser irradiation.

Laser irradiation of a cyclohexane solution containing pyrene resulted in hydrogen evolution as pyrene was converted to a metal-free nanoparticle photocatalyst. When C6H12 was replaced by C6D12, D2 was mainly evolved. This result suggests that the hydrogen source is cyclohexane used as a solvent. Photocatalytic hydrogen evolution was also observed in an aqueous solution by using a water-soluble pyrene derivative.

Singlet oxygen generation from Li⁺@C⁺60 nano-aggregates dispersed by laser irradiation in aqueous solution.

Laser pulse irradiation of a deaerated aqueous solution containing the solid state lithium ion-encapsulated fullerene resulted in the formation of highly dispersed nano-aggregates (Li(+)@C60)n. Photoirradiation of an O2-saturated D2O solution containing (Li(+)@C60)n gave singlet oxygen with 55% quantum yield, leading to efficient double-stranded DNA cleavage.