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This paper addresses the Phanerozoic tectonic evolution of the western Tarim Basin based on an integrated stratigraphic, structural and tectonic analysis. P-wave velocity data show that the basin has a stable and rigid basement. The western Tarim Basin experienced a complex tectonic evolutionary history, and this evolution can be divided into six stages: Neoproterozoic to Early Ordovician, Middle Ordovician to Middle Devonian, Late Devonian to Permian, Triassic, Jurassic to Cretaceous and Paleogene to Quaternary. The western Tarim Basin was a rift basin in the Neoproterozoic to Early Ordovician. From the Middle Ordovician to Middle Devonian, the basin consisted of a flexural depression in the south and a depression that changed from a rift depression to a flexural depression in the north during each period, i.e., the Middle–Late Ordovician and the Silurian to Middle Devonian. During the Late Devonian to Permian, the basin was a depression basin early and then changed into a flexural basin late in each period, i.e., the Late Devonian to Carboniferous and the Permian. In the Triassic, the basin was a foreland basin, and from the Jurassic to Cretaceous, it was a downwarped basin. After the Paleogene, the basin became a rejuvenated foreland basin. Based on two cross sections, we conclude that the extension and shortening in the profile reflect the tectonic evolution of the Tarim Basin. The Tarim Basin has become a composite and superimposed sedimentary basin because of its long-term and complicated tectonic evolutionary history, highly rigid and stable basement and large size. [ABSTRACT FROM AUTHOR]

Plagiognathops microlepis is an economic freshwater fish in the subfamily Xenocyprinae of Cyprinidae. It is widely distributed in the freshwater ecosystem of China, with moderate economic value and broad development prospects. However, the lack of genomic resources has limited our understanding on the genetic basis, phylogenetic status and adaptive evolution strategies of this fish. Here, we assembled a chromosome-level reference genome of P. microlepis by integrating Pacbio HiFi long-reads, Illumina short-reads and Hi-C sequencing data. The size of this genome is 1004.34 Mb with a contig N50 of 38.80 Mb. Using Hi-C sequencing data, 99.59% of the assembled sequences were further anchored to 24 chromosomes. A total of 578.91 Mb repeat sequences and 28,337 protein-coding genes were predicted in the current genome, of which, 26,929 genes were functionally annotated. This genome provides valuable information for investigating the phylogeny and evolutionary history of cyprinid fishes, as well as the genetic basis of adaptive strategies and special traits in P. microlepis. [ABSTRACT FROM AUTHOR]

The Ediacaran Period (~635–539 Ma) is marked by the emergence and diversification of complex metazoans linked to ocean redox changes, but the processes and mechanism of the redox evolution in the Ediacaran ocean are intensely debated. Here we use mercury isotope compositions from multiple black shale sections of the Doushantuo Formation in South China to reconstruct Ediacaran oceanic redox conditions. Mercury isotopes show compelling evidence for recurrent and spatially dynamic photic zone euxinia (PZE) on the continental margin of South China during time intervals coincident with previously identified ocean oxygenation events. We suggest that PZE was driven by increased availability of sulfate and nutrients from a transiently oxygenated ocean, but PZE may have also initiated negative feedbacks that inhibited oxygen production by promoting anoxygenic photosynthesis and limiting the habitable space for eukaryotes, hence abating the long-term rise of oxygen and restricting the Ediacaran expansion of macroscopic oxygen-demanding animals. Using Hg isotopes, the authors find that repeated invasion of toxic, H2S-rich water into the marine photic zone of the Ediacaran ocean may have inhibited the rise of oxygen and delayed the expansion of early animals. [ABSTRACT FROM AUTHOR]

Porcine coronavirus SADS-CoV has been identified from suckling piglets with severe diarrhea in southern China in 2017. The SADS-CoV genome shares ~95% identity to that of bat α-coronavirus HKU2, suggesting that SADS-CoV may have emerged from a natural reservoir in bats. Here we report the cryo-EM structures of HKU2 and SADS-CoV spike (S) glycoprotein trimers at 2.38 Å and 2.83 Å resolution, respectively. We systematically compare the domains of HKU2 spike with those of α-, β-, γ-, and δ-coronavirus spikes, showing that the S1 subunit N- and C-terminal domains of HKU2/SADS-CoV are ancestral domains in the evolution of coronavirus spike proteins. The connecting region after the fusion peptide in the S2 subunit of HKU2/SADS-CoV adopts a unique conformation. These results structurally demonstrate a close evolutionary relationship between HKU2/SADS-CoV and β-coronavirus spikes and provide insights into the evolution and cross-species transmission of coronaviruses. Several coronaviruses infecting humans and animals have emerged in recent years. Here, the authors provide structures of the spike proteins of the porcine coronavirus SADS-CoV and closely related bat coronavirus HKU2, providing insights into evolution of coronavirus spike proteins. [ABSTRACT FROM AUTHOR]

Two case studies were conducted in the Shennan mining area of Shaanxi Province, China to evaluate the surrounding rock deformation and stress evolution in pre-driven longwall recovery rooms. These studies mainly monitored the surrounding rock deformation and coal pillar stress in the recovery rooms of the N1206 panel of 2−2 coal seam at Ningtiaota Coal Mine and the 15205 panel of 5−2 coal seam at Hongliulin Coal Mine. The monitoring results showed that the surrounding rock deformation of the main recovery room and the coal pillar stress in the N1206 and 15205 panels began to increase significantly when the face was 36 m and 42 m away from the terminal line, respectively. After the face entered the main recovery room, the maximum roof-to-floor convergence in the N1206 and 15205 panels was 348.03 mm and 771.24 mm, respectively, and the coal pillar stresses increased more than 5 MPa and 7 MPa, respectively. In addition, analysis of the periodic weighting data showed that the main roof break position of the N1206 and 15205 panels after the longwall face entered the main recovery room was − 3.8 m and − 8.2 m, respectively. This research shows that when the main roof breaks above the coal pillar, the surrounding rock deformation of the main recovery room and the coal pillar stress increase sharply. The last weighting is the key factor affecting the stability of the main recovery room and the coal pillar; main roof breaks at disadvantageous positions are the main cause of the support crushing accidents. [ABSTRACT FROM AUTHOR]

Orchid classification has undergone a series of significant changes during the past decade as molecular phylogenetic studies have examined relationships at all taxonomic levels in the family. Today, the 750 genera and 25,000 species of Orchidaceae are organized into five subfamilies, the two largest of which (Epidendroideae and Orchidoideae) are further divided into 19 tribes and 43 subtribes. Whereas some of these groups are relatively small in terms of total species numbers, and may be of little horticultural or medicinal value, they are especially important for understanding orchid evolution and may deserve to be conserved for this reason alone. The question of which orchids to conserve is a complex one, but the science of systematics, including taxonomy and phylogenetics, has an undeniable role to play in answering that question. Among the many ways that phylogenetic trees can assist biologists in setting conservation priorities are by: 1) guiding taxonomists in naming species, which is essential for creating checklists within floras, monographs, and inventories; 2) discovering overlooked, rare or cryptic species that deserve recognition and protection; 3) determining whether or not a taxon is actually a species or simply a variant or hybrid; 4) predicting species that may be of value to humans for economic value; 5) identifying species that may have particularly important scientific value for better understanding the biology of plants. In the same way that we cannot protect all habitats, we may not be able to save every orchid species. Priorities must be established. The Yachang Orchid Reserve has been recognized as important not only because of the number of individual orchid plants that grow there, but also because of its great orchid diversity. Diversity is a product of evolution by natural selection, and the science of phylogenetics has a role to play in better understanding that process. [ABSTRACT FROM AUTHOR]

The early evolution of the major groups of derived non-avialan theropods is still not well understood, mainly because of their poor fossil record in the Jurassic. A well-known result of this problem is the ‘temporal paradox’ argument that is sometimes made against the theropod hypothesis of avian origins. Here we report on an exceptionally well-preserved small theropod specimen collected from the earliest Late Jurassic Tiaojishan Formation of western Liaoning, China. The specimen is referable to the Troodontidae, which are among the theropods most closely related to birds. This new find refutes the ‘temporal paradox’ and provides significant information on the temporal framework of theropod divergence. Furthermore, the extensive feathering of this specimen, particularly the attachment of long pennaceous feathers to the pes, sheds new light on the early evolution of feathers and demonstrates the complex distribution of skeletal and integumentary features close to the dinosaur–bird transition. [ABSTRACT FROM AUTHOR]

The cyprinid fish genus Sinocyclocheilus, as the most cavefish rich genus, includes many species showing striking adaptation to caves and convergent reduction or even loss of eyes and pigmentation. RH1 is responsible for dim vision. In order to explore the evolution of RH1 gene in this genus, we sequenced the complete gene from 28 individuals of 16 representative species of Sinocyclocheilus, with cave and surface species included. Phylogenetic analyses supported the monophyly of Sinocyclocheilus and polyphyly of the cave species. Codon models implemented in PAML were used to infer the evolution of RH1. We found that Sinocyclocheilus had a significantly higher evolutionary rate for amino acids than other cyprinid fishes compared, which might be the result of relaxation of purifying selection and could be ascribed to cave habit of this genus. In contrast to previous hypotheses, both cave and surface lineages exhibited a similar rate of molecular evolution, so the RH1 of cave species may still be functional, although these species were highly adapted to cave environment. Two amino acid substitutions (D83G and E122V) that were not reported before were found, which may be useful for site-directed mutagenesis in the future. [ABSTRACT FROM AUTHOR]

The origin of the turtle body plan remains one of the great mysteries of reptile evolution. The anatomy of turtles is highly derived, which renders it difficult to establish the relationships of turtles with other groups of reptiles. The oldest known turtle, Proganochelys from the Late Triassic period of Germany, has a fully formed shell and offers no clue as to its origin. Here we describe a new 220-million-year-old turtle from China, somewhat older than Proganochelys, that documents an intermediate step in the evolution of the shell and associated structures. A ventral plastron is fully developed, but the dorsal carapace consists of neural plates only. The dorsal ribs are expanded, and osteoderms are absent. The new species shows that the plastron evolved before the carapace and that the first step of carapace formation is the ossification of the neural plates coupled with a broadening of the ribs. This corresponds to early embryonic stages of carapace formation in extant turtles, and shows that the turtle shell is not derived from a fusion of osteoderms. Phylogenetic analysis places the new species basal to all known turtles, fossil and extant. The marine deposits that yielded the fossils indicate that this primitive turtle inhabited marginal areas of the sea or river deltas. [ABSTRACT FROM AUTHOR]

An evolutionary trend of decreasing size is present along the line to birds in coelurosaurian theropod evolution, but size increases are seen in many coelurosaurian subgroups, in which large forms are less bird-like. Here we report on a new non-avian dinosaur, Gigantoraptor erlianensis, gen. et sp. nov., from the Late Cretaceous Iren Dabasu Formation of Nei Mongol, China. Although it has a body mass of about 1,400 kg, a phylogenetic analysis positions this new taxon within the Oviraptorosauria, a group of small, feathered theropods rarely exceeding 40 kg in body mass. A histological analysis suggests that Gigantoraptor gained this size by a growth rate considerably faster than large North American tyrannosaurs such as Albertosaurus and Gorgosaurus. Gigantoraptor possesses several salient features previously unknown in any other dinosaur and its hind limb bone scaling and proportions are significantly different from those of other coelurosaurs, thus increasing the morphological diversity among dinosaurs. Most significantly, the gigantic Gigantoraptor shows many bird-like features absent in its smaller oviraptorosaurian relatives, unlike the evolutionary trend seen in many other coelurosaurian subgroups. [ABSTRACT FROM AUTHOR]

The timing of early human dispersal to Asia is a central issue in the study of human evolution. Excavations in predominantly lacustrine sediments at Majuangou, Nihewan basin, north China, uncovered four layers of indisputable hominin stone tools. Here we report magnetostratigraphic results that constrain the age of the four artefact layers to an interval of nearly 340,000?yr between the Olduvai subchron and the Cobb Mountain event. The lowest layer, about 1.66 million years old (Myr), provides the oldest record of stone-tool processing of animal tissues in east Asia. The highest layer, at about 1.32?Myr, correlates with the stone tool layer at Xiaochangliang, previously considered the oldest archaeological site in this region. The findings at Majuangou indicate that the oldest known human presence in northeast Asia at 40°N is only slightly younger than that in western Asia. This result implies that a long yet rapid migration from Africa, possibly initiated during a phase of warm climate, enabled early human populations to inhabit northern latitudes of east Asia over a prolonged period. [ABSTRACT FROM AUTHOR]

Rubella remains a significant burden in mainland China. In this report, 667 viruses collected in 24 of 31 provinces of mainland China during 2010-2012 were sequenced and analyzed, significantly extending previous reports on limited numbers of viruses collected before 2010. Only viruses of genotypes 1E and 2B were found. Genotype 1E viruses were found in all 24 provinces. Genotype 1E viruses were likely introduced into mainland China around 1997 and endemic transmission of primarily one lineage became established. Viruses reported here from 2010-2012 are largely in a single cluster within this lineage. Genotype 2B viruses were rarely detected in China prior to 2010. This report documents a previously undetected 2B lineage, which likely became endemic in eastern provinces of China between 2010 and 2012. Bayesian analyses were performed to estimate the evolutionary rates and dates of appearance of the genotype 1E and 2B viral linages in China. A skyline plot of viral population diversity did not provide evidence of reduction of diversity as a result of vaccination, but should be useful as a baseline for such reductions as vaccination programs for rubella become widespread in mainland China. [ABSTRACT FROM AUTHOR]