Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations.

Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is  characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.

The prehistoric peopling of Southeast Asia.

The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the "two-layer" hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jomon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.

Osteological and genetic analysis of the extinct Ezo wolf (Canis lupus hattai) from Hokkaido Island, Japan.

The Ezo wolf (Canis lupus hattai Kishida, 1931 ) is an extinct subspecies that inhabited Hokkaido in Japan until the middle of the Meiji Period. Because there are very few preserved skeletons, no osteological and/or genetic analyses of the Ezo wolf have been conducted. In this study, 20 cranial and eight mandibular characters were measured on Ezo wolf skeletons, and mitochondrial DNA (mtDNA) was analyzed to assess genetic relationships between the Ezo wolf and other wolf lineages, including the Japanese wolf on Honshu. The morphological study showed that the Ezo wolf is larger than the Japanese wolf and similar in size to the grey wolf of the Asian and American Continents. MtDNA control sequences (751 bp) from two Ezo wolves were identical to those from the Canadian grey wolf. The morphological and genetic characters indicate that the ancestor of the Ezo wolf was genetically related to that of the grey wolf in Canada.

Mitochondrial DNA analysis of the Japanese wolf (Canis lupus hodophilax Temminck, 1839) and comparison with representative wolf and domestic dog haplotypes.

Mitochondrial DNA (mtDNA) D-loop control region sequences ranging In length from 583 to 598 bp were determined for eight Japanese wolf specimens (Canis lupus hodophilax Temminck, 1839) collected from several sites and compared with 105 haplotypes from the domestic dog (C. lupus familiaris) and continental grey wolf (C. lupus lupus). Also, a 197-bp mtDNA sequence was amplified from archaeological wolf specimens and two continental wolf specimens (C. lupus chanco) as reference sequences for analysis. The mtDNA haplotypes from the eight Japanese wolf specimens were closely related to each other and grouped in a single lineage with an 88% bootstrap value in a neighbor-Joining analysis. The results provide valuable Information for understanding the taxonomic and phylogenetic relationships of the Japanese wolf, which have long been controversial.

Meaning of the canine sexual dimorphism in fossil owl monkey, Aotus dindensis from the middle Miocene of La Venta, Colombia.

The owl monkey, Aotus, is the only modern nocturnal anthropoid with monogamous social structure. It has been demonstrated by the fossil species, Aotus dindensis, discovered from La Venta, Colombia, that the Aotus lineage had emerged as early as the middle Miocene (12-15 Ma). The type specimen of A. dindensis, which was discovered in 1986, preserves extremely large orbits, indicating a nocturnal habit. However, a few anatomical traits in living Aotus, such as the lack of a tapetum lucidum, indicates that nocturnality is a secondary adaptation from diurnal ancestry in this genus. Here we report new fossil specimens of A. dindensis from La Venta. The specimens include maxillary teeth and a mandibular fragment preserving lower molars. The detailed analysis of the specimen suggests that A. dindensis exhibits strong sexual dimorphism in the maxillary canine and premolars, which is traditionally associated with intense intermale competition for mates and/or food resources in non-monogamous, diurnal societies. As a result, the new fossil materials of A. dindensis demonstrate the first osteological evidence for the diurnal ancestry of the night monkey, Aotus. Moreover, the coexistence of large orbits and canine dimorphism suggests the presence of mosaic evolution in the craniodental characters of the Aotus lineage.

Reconstruction of human exposure to heavy metals using synchrotron radiation microbeams in prehistoric and modern humans.

OBJECTIVE: Teeth can serve as records of environmental exposure to heavy metals during their formation. We applied a new technology - synchrotron radiation microbeams (SRXRF) - for analysis of heavy metals in human permanent teeth in modern and historical samples. METHODS: Each tooth was cut in half. A longitudinal section 200 mum in thickness was subjected to the determination of the heavy metal content by SRXRF or conventional analytical methods (ICP-MS analysis or reduction-aeration atomic absorption spectrometry). The relative concentrations of Pb, Hg, Cu and Zn measured by SRXRF were translated in concentrations (in g of heavy metal/g of enamel) using calibration curves by the two analytical methods. RESULTS: Concentrations in teeth in the modern females (n = 5) were 1.2 +/- 0.5 mug/g (n = 5) for Pb; 1.7 +/- 0.2 ng/g for Hg; 0.9 +/- 1.1 mug/g for Cu; 150 +/- 24.6 mug/g for Zn. The levels of Pb were highest in the teeth samples obtained from the humans of the Edo era (1603-1868 AD: ) (0.5-4.0 mug/g, n = 4). No trend was observed in this study in the Hg content in teeth during 3,000 years. The concentrations of Cu were highest in teeth of two medieval craftsmen (57.0 and 220 mug/g). The levels of Zn were higher in modern subjects (P < 0.05) than those in the Jomon (~1000 BC: ) to Edo periods [113.2 +/- 27.4 (mug/g, n = 11)]. Reconstruction of developmental exposure history to lead in a famous court painter of the Edo period (18th century) revealed high levels of Pb (7.1-22.0 mug/g) in his childhood. CONCLUSIONS: SRXRF is useful a method for reconstructing human exposures in very long trends.

Additional materials of Myanmarpithecus yarshensis (Amphipithecidae, Primates) from the middle Eocene Pondaung Formation.

Myanmarpithecus yarshensis is an amphipithecid primate from the middle Eocene Pondaung Formation in Myanmar. It was previously known based on maxillary fragments with P(4)-M(3) and mandibular fragments with C-P(3) and M(2-3). This study reports new materials for the genus, including a humeral head fragment, a lingual fragment of the right M(2), a lingual fragment of the right M(3), and a left I(1). These new materials were collected from approximately the same point, and likely belonged to the same individual. The upper molar morphology and size of the new materials show similarity to those of the type specimen, indicating that the new materials can be assigned to M. yarshensis. The humeral head is the first postcranial element that is associated with dental materials for amphipithecids. The morphological similarity between the previously reported larger humerus and this specimen confirms the assignment of the former specimen to Amphipithecidae and suggests common locomotor adaptations in the family. The upper central incisor is large relative to the molar fragments, but is within the variation among extant platyrrhines. The tooth is spatulate-shaped and high crowned, and lacks the mesial process, indicating similarity to I(1) of haplorhines and clear differences from that of adapoids. It has been suggested that amphipithecids, including Myanmarpithecus, have affinities with notharctine adapoids, but the morphology of I(1) does not support the notharctine hypothesis of the Amphipithecidae.

A morphometric analysis of the Japanese macaque (Macaca fuscata) mandibular cheek teeth from the Torihama Shell-midden, Early Jomon Period, Fukui Prefecture, Japan.

We quantitatively examined the differences in the size and proportion of the Japanese macaque (Macaca fuscata) by comparing the Early Jomon specimens from Torihama shell-midden, Fukui Prefecture and modern specimens from Fukui Prefecture. The purpose of this study was to explore the temporal change in the proportion and size of teeth of the Japanese macaques based on the quantified data. The result of measurements of lower premolars and molars demonstrated that sexual dimorphism was evident only among the modern specimens where the females were significantly smaller than males. The size of male Torihama specimens was within the range of the modern population, whereas the size of the female Torihama specimens was significantly larger than the modern female population. The proportional pattern of premolars and molars for male and female Torihama specimens also differed. The results may suggest a possible difference in the degree of size reduction between males and females since the last glacial period.

Variation in maxillary sinus anatomy among platyrrhine monkeys.

Variations in the maxillary sinus anatomy of extant and fossil catarrhine primates have been extensively examined using computed tomography (CT), and have potential utility for phylogenetic analyses. This approach has also been used to demonstrate its anatomical variation in eight of the 16 extant genera of platyrrhines and the absence of the sinus in Saimiri and Cacajao. We used this approach to evaluate the three-dimensional anatomy of the maxillary sinus in all extant platyrrhine genera, and here argue the phylogenic implications of this variation. This study confirms, for the most part, previous CT studies and augments them with the six genera not studied previously: Ateles, Lagothrix, Callithrix, Cebuella, Pithecia and Chiropotes. The entire maxilla is pneumatized by the sinus in the atelines, Cebus, and Callicebus, whereas the sinus pneumatizes only the medial part of the maxilla in the callitrichines and Aotus. Pithecia has a unique conformation in which the maxillary sinus and the expanded inferior meatus pneumatize the posteromedial and anterolateral parts of the entire maxilla, respectively. Chiropotes has no sinus, and the inferior meatus possibly expands into the area between the middle meatus and medial surface of the maxilla to disturb sinus formation, as in the case of its close relative Cacajao. Finally, we argue that the sinus that pneumatizes the entire maxilla is a primitive feature in extant platyrrhines and was probably shared by the last common ancestor of the anthropoids.

The paleobiology of Amphipithecidae, South Asian late Eocene primates.

Analysis of the teeth, orbital, and gnathic regions of the skull, and fragmentary postcranial bones provides evidence for reconstructing a behavioral profile of Amphipithecidae: Pondaungia, Amphipithecus, Myanmarpithecus (late middle Eocene, Myanmar) and Siamopithecus (late Eocene, Thailand). At 5-8 kg, Pondaungia, Amphipithecus, and Siamopithecus are perhaps the largest known Eocene primates. The dental and mandibular anatomy suggest that large-bodied amphipithecids were hard-object feeders. The shape of the mandibular corpus and stiffened symphysis suggest an ability to resist large internal loads during chewing and to recruit significant amounts of muscle forces from both the chewing and non-chewing sides of the jaw so as to increase bite force during mastication. The large spatulate upper central incisor of Pondaungia and projecting robust canines of all the larger amphipithecids suggest that incisal food preparation was important. The molars of Siamopithecus, Amphipithecus, and Pondaungia have weak shearing crests. This, and the thick molar enamel found in Pondaungia, suggests a diet of seeds and other hard objects low in fiber. In contrast, Myanmarpithecus was smaller, about 1-2 kg; its cheek teeth suggest a frugivorous diet and do not imply seed eating. Postcranial bones (humerus, ulna, and calcaneus) of a single large amphipithecid individual from Myanmar suggest an arboreal quadrupedal locomotor style like that of howler monkeys or lorises. The humeral head is rounded, proximally oriented, and the tuberosities are low indicating an extremely mobile glenohumeral joint. The great thickness of the midshaft cortical bone of the humerus implies enhanced ability to resist bending and torsion, as seen among slow moving primate quadrupeds. The elbow joint exhibits articular features for enhanced stability in habitually flexed positions, features also commonly found in slow moving arboreal quadrupeds. The short distal load arm of the calcaneus is consistent with, but not exclusive to, slow, arboreal quadrupedalism, and suggests no reliance on habitual leaping.

Endocranial cast and morphology of the olfactory bulb of Amphipithecus mogaungensis (latest middle Eocene of Myanmar).

A detailed endocranial cast of the olfactory bulb of Amphipithecus mogaungensis, a latest middle Eocene primate from the Pondaung Formation (Myanmar), was studied in comparison with some Paleogene primates, the olfactory bulb of which has been reported. The olfactory bulb of Amphipithecus is located just anterior to the postorbital constriction, that is, within the interorbital septum. It is relatively large and pedunculate, not overlapped by the frontal lobe, and consists of two parallel aligned bodies. The relative volume of the olfactory bulb shows the same pattern as in adapiforms, but the location and bilobed form are more similar to those of omomyoids than of adapiforms.

Variation in mitochondrial DNA of Vietnamese pigs: relationships with Asian domestic pigs and Ryukyu wild boars.

Mitochondrial DNA (mtDNA) sequences (574 bp) of 30 Vietnamese pigs (large and small) were examined and compared with those of 61 haplotypes from wild boars and domestic pigs from various locations in Asia. The large Vietnamese pigs had genetic links to Ryukyu wild boars in southern Japan. The small Vietnamese pigs were closely related to other East Asian domestic pigs. These results indicate that Vietnamese pigs are genetically diverse and may be descendents of wild and domestic pigs from other regions of Asia.

The upper dentition and face of Pondaungia cotteri from central Myanmar.

A specimen of Pondaungia from the late middle Eocene Pondaung Formation in central Myanmar includes maxillary fragments and parts of the dentition, some hitherto undocumented, including the upper central incisor, canine, premolars and molars. Pondaungia has a large spatulate I1 closely resembling that of crown anthropoids. It possesses a stout projecting upper canine (like anthropoids) but differs from that tooth of crown anthropoids in lacking a strong mesial groove. There are three upper premolars of which P2 is distinctly smaller than P3 or P4. P3 has a buccolingually oriented mesial profile and an inflated distal profile resembling that of parapithecids and crown anthropoids. The distolingual molar cusp is a hypocone and is not homologus with the "pseudohypocone" of notharctines because the cusp is neither twinned with the protocone nor attached to a Nannopithex-fold. Pondaungia has a stout zygomatic root with a strongly demarcated muscle scar for the superficial masseter situated well above the occlusal plane. The inferior orbital margin is not preserved but the inflated suborbital region allows for the inference that the orbit was small. This specimen is not sufficiently well preserved to identify if there was postorbital closure. However, a specimen of the frontal bone of Amphipithecus shows that its orbital septum was absent or poorly developed. If, as commonly supposed, Pondaungia andAmphipithecus are sister taxa, postorbital closure was probably absent in Pondaungia. The large incisors, molars with poorly developed crests and thick enamel, together with the stoutly developed and strong dorsal component of the force vector of the superficial masseter muscle suggest that Pondaungia had a diet low in fiber, but that included hard food objects like nuts or seeds. The present material adds to the structural similarities between Pondaungia and anthropoids, but whether these similarities are due to shared descent or functional and adaptive convergence remains unresolved.