We report the sequencing at 131× coverage, de novo assembly and analyses of the genome of a female Tibetan wild boar. We also resequenced the whole genomes of 30 Tibetan wild boars from six major distributed locations and 18 geographically related pigs in China. We characterized genetic diversity, population structure and patterns of evolution. We searched for genomic regions under selection, which includes genes that are involved in hypoxia, olfaction, energy metabolism and drug response. Comparing the genome of Tibetan wild boar with those of neighboring Chinese domestic pigs further showed the impact of thousands of years of artificial selection and different signatures of selection in wild boar and domestic pig. We also report genetic adaptations in Tibetan wild boar that are associated with high altitudes and characterize the genetic basis of increased salivation in domestic pig.

BackgroundMost turtles from the Middle and Late Jurassic of Asia are referred to the newly defined clade Xinjiangchelyidae, a group of mostly shell-based, generalized, small to mid-sized aquatic froms that are widely considered to represent the stem lineage of Cryptodira. Xinjiangchelyids provide us with great insights into the plesiomorphic anatomy of crown-cryptodires, the most diverse group of living turtles, and they are particularly relevant for understanding the origin and early divergence of the primary clades of extant turtles.ResultsExceptionally complete new xinjiangchelyid material from the ?Qigu Formation of the Turpan Basin (Xinjiang Autonomous Province, China) provides new insights into the anatomy of this group and is assigned to Xinjiangchelys wusu n. sp. A phylogenetic analysis places Xinjiangchelys wusu n. sp. in a monophyletic polytomy with other xinjiangchelyids, including Xinjiangchelys junggarensis, X. radiplicatoides, X. levensis and X. latiens. However, the analysis supports the unorthodox, though tentative placement of xinjiangchelyids and sinemydids outside of crown-group Testudines. A particularly interesting new observation is that the skull of this xinjiangchelyid retains such primitive features as a reduced interpterygoid vacuity and basipterygoid processes.ConclusionsThe homology of basipterygoid processes is confidently demonstrated based on a comprehensive review of the basicranial anatomy of Mesozoic turtles and a new nomenclatural system is introduced for the carotid canal system of turtles. The loss of the basipterygoid process and the bony enclosure of the carotid circulation system occurred a number of times independently during turtle evolution suggesting that the reinforcement of the basicranial region was essential for developing a rigid skull, thus paralleling the evolution of other amniote groups with massive skulls.

The earliest evolution of mammals and origins of mammalian features can be traced to the mammaliaforms of the Triassic and Jurassic periods that are extinct relatives to living mammals. Here we describe a new fossil from the Middle Jurassic that has a mandibular middle ear, a gradational transition of thoracolumbar vertebrae and primitive ankle features, but highly derived molars with a high crown and multiple roots that are partially fused. The upper molars have longitudinal cusp rows that occlude alternately with those of the lower molars. This specialization for masticating plants indicates that herbivory evolved among mammaliaforms, before the rise of crown mammals. The new species shares the distinctive dental features of the eleutherodontid clade, previously represented only by isolated teeth despite its extensive geographic distribution during the Jurassic. This eleutherodontid was terrestrial and had ambulatory gaits, analogous to extant terrestrial mammals such as armadillos or rock hyrax. Its fur corroborates that mammalian integument had originated well before the common ancestor of living mammals.

Inference of colour patterning in extinct dinosaurs has been based on the relationship between the morphology of melanin-containing organelles (melanosomes) and colour in extant bird feathers. When this relationship evolved relative to the origin of feathers and other novel integumentary structures, such as hair and filamentous body covering in extinct archosaurs, has not been evaluated. Here we sample melanosomes from the integument of 181 extant amniote taxa and 13 lizard, turtle, dinosaur and pterosaur fossils from the Upper-Jurassic and Lower-Cretaceous of China. We find that in the lineage leading to birds, the observed increase in the diversity of melanosome morphologies appears abruptly, near the origin of pinnate feathers in maniraptoran dinosaurs. Similarly, mammals show an increased diversity of melanosome form compared to all ectothermic amniotes. In these two clades, mammals and maniraptoran dinosaurs including birds, melanosome form and colour are linked and colour reconstruction may be possible. By contrast, melanosomes in lizard, turtle and crocodilian skin, as well as the archosaurian filamentous body coverings (dinosaur 'protofeathers' and pterosaur 'pycnofibres'), show a limited diversity of form that is uncorrelated with colour in extant taxa. These patterns may be explained by convergent changes in the key melanocortin system of mammals and birds, which is known to affect pleiotropically both melanin-based colouration and energetic processes such as metabolic rate in vertebrates, and may therefore support a significant physiological shift in maniraptoran dinosaurs.

Very little is known about nonavian dinosaur population biology. Multi-individual sampling and longevity estimation using growth line counts can be used to construct life tables-the foundation for population analyses in ecology. Here we have determined the size and age distribution for a sample consisting of 80 individuals of the small ornithischian, Psittacosaurus lujiatunensis from the early Cretaceous Yixian Formation of China. Their ages ranged from less than a year to eleven years and the distribution was strongly right-skewed. This is consistent with taphonomic interpretations that these animals derive from a catastrophic death assemblage. The static life table analysis revealed the same general pattern of survivorship as tyrannosaurs including increased attrition before the attainment of full adult size. This may reflect increased physiological demands and/or predation exposure associated with reproduction. Collectively these findings suggest that most nonavian dinosaurs may have had a similar life history strategy. Anat Rec, 292:1514Rec, 292: -1521Rec, 292: , 2009. V V C 2009 Wiley-Liss, Inc.

Mandarin (Citrus reticulata) is one of the most important citrus crops worldwide. Its domestication is believed to have occurred in South China, which has been one of the centers of mandarin cultivation for four millennia. We collected natural wild populations of mandarin around the Nanling region and cultivated landraces in the vicinity. We found that the citric acid level was dramatically reduced in cultivated mandarins. To understand genetic basis of mandarin domestication, we de novo assembled a draft genome of wild mandarin and analyzed a set of 104 citrus genomes. We found that the Mangshan mandarin is a primitive type and that two independent domestication events have occurred, resulting in two groups of cultivated mandarins (MD1 and MD2) in the North and South Nanling Mountains, respectively. Two bottlenecks and two expansions of effective population size were identified for the MD1 group of cultivated mandarins. However, in the MD2 group there was a long and continuous decrease in the population size. MD1 and MD2 mandarins showed different patterns of interspecific introgression from cultivated pummelo species. We identified a region of high divergence in an aconitate hydratase (ACO) gene involved in the regulation of citrate content, which was possibly under selection during the domestication of mandarin. This study provides concrete genetic evidence for the geographical origin of extant wild mandarin populations and sheds light on the domestication and evolutionary history of mandarin.

Morphological phylogenies stand in a major conflict with molecular hypotheses regarding the phylogeny of Cryptodira, the most diverse and widely distributed clade of extant turtles. However, molecular hypotheses are often considered a better estimate of phylogeny given that it is more consistent with the stratigraphic and geographic distribution of extinct taxa. That morphology fails to reproduce the molecular topology partly originates from problematic character polarization due to yet another contradiction around the composition of the cryptodiran stem lineage. Extinct sinemydids are one of these problematic clades: they have been either placed among stem-cryptodires, stem-chelonioid sea turtles, or even stem-turtles. A new sinemydid from the Early Cretaceous Jehol Biota (Yixian Formation, Barremian-Early Aptian) of China, Xiaochelys ningchengensis gen. et sp. nov., allows for a reassessment of the phylogenetic position of Sinemydidae. Our analysis indicates that sinemydids mostly share symplesiomorphies with sea turtles and their purported placement outside the crown-group of turtles is an artefact of previous datasets. The best current phylogenetic estimate is therefore that sinemydids are part of the stem lineage of Cryptodira together with an array of other Jurassic to Cretaceous taxa. Our study further emphasises the importance of using molecular scaffolds in global turtle analyses.

BackgroundMagnetic resonance imaging (MRI) plays an irreplaceable role in the preoperative diagnosis of glioma, and its imaging features are the base of making treatment decisions in patients with glioma, but it is still controversial whether peritumoral edema shown by MRI from preoperative routine scans are associated with patient survival. The aim of this study was to assess the prognostic value of preoperative MRI features in patients with glioblastoma.MethodsA retrospective review of 87 patients with newly diagnosed supratentorial glioblastoma was performed using medical records and MRI data from routine scans. The Kaplan-Meier method and COX proportional hazard model were applied to evaluate the prognostic impact on overall survival of pretreatment MRI features (including peritumoral edema, edema shape, necrosis, cyst, enhancement, tumor crosses midline, edema crosses midline, and tumor size).ResultsIn addition to patient age, Karnofsky performance status (KPS) and postoperative chemoradiotherapy, peritumoral edema extent and necrosis on preoperative MRI were independent prognostic indicator for poor survival. Furthermore, patients with two unfavorable conditions (major edema and necrosis) had a shorter overall survival compared with the remainder.ConclusionsOur data confirm that peritumoral edema extent and necrosis are helpful for predicting poor clinical outcome in glioblastoma. These features were easy to determine from routine MRI scans postoperatively and therefore could provide a certain instructive significance for clinical activities.