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Genetic and fragmented palaeoanthropological data suggest that Denisovans were once widely distributed across eastern Eurasia 1-3 . Despite limited archaeological evidence, this indicates that Denisovans were capable of adapting to a highly diverse range of environments. Here we integrate zooarchaeological and proteomic analyses of the late Middle to Late Pleistocene faunal assemblage from Baishiya Karst Cave on the Tibetan Plateau, where a Denisovan mandible and Denisovan sedimentary mitochondrial DNA were found 3,4 . Using zooarchaeology by mass spectrometry, we identify a new hominin rib specimen that dates to approximately 48-32 thousand years ago (layer 3). Shotgun proteomic analysis taxonomically assigns this specimen to the Denisovan lineage, extending their presence at Baishiya Karst Cave well into the Late Pleistocene. Throughout the stratigraphic sequence, the faunal assemblage is dominated by Caprinae, together with megaherbivores, carnivores, small mammals and birds. The high proportion of anthropogenic modifications on the bone surfaces suggests that Denisovans were the primary agent of faunal accumulation. The chaîne opératoire of carcass processing indicates that animal taxa were exploited for their meat, marrow and hides, while bone was also used as raw material for the production of tools. Our results shed light on the behaviour of Denisovans and their adaptations to the diverse and fluctuating environments of the late Middle and Late Pleistocene of eastern Eurasia., (© 2024. The Author(s).)

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe 1 . Local hybridization between the two groups occurred 2 , but not on all occasions 3 . Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups 4 . One such technocomplex for which the makers are unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which has been described in northwestern and central Europe 5-8 . Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period., (© 2024. The Author(s).)

Introduction: Phytophthora ramorum is a quarantine pathogen that causes leaf blight and shoot dieback of the crown, bark cankers and death on a number of both ornamental and forest trees, especially in North America and northern Europe, where it has produced severe outbreaks. Symptoms caused by P. ramorum can be confused with those by other Phytophthora and fungal species. Early and accurate detection of the causal pathogen P. ramorum is crucial for effective prevention and control of Sudden Oak Death., Methods: In this study, we developed a P. ramorum detection technique based on a combination of recombinase polymerase amplification (RPA) with CRISPR/Cas12a technology (termed RPACRISPR/ Cas12a)., Results: This novel method can be utilized for the molecular identification of P. ramorum under UV light and readout coming from fluorophores, and can specifically detect P. ramorum at DNA concentrations as low as 100 pg within 25 min at 37°C., Discussion: We have developed a simple, rapid, sensitive, unaided-eye visualization, RPA CRISPR/Cas12a-based detection system for the molecular identification of P. ramorum that does not require technical expertise or expensive ancillary equipment. And this system is sensitive for both standard laboratory samples and samples from the field., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Guo, Xia, Dai, Liu, Shamoun and CuiPing.)

Polydactyly is one of the most common hereditary congenital limb malformations in chickens and other vertebrates. The zone of polarizing activity regulatory sequence (ZRS) is critical for the development of polydactyly. The causative mutation of polydactyly in the Silkie chicken has been mapped to the ZRS; however, the causative mutations of other chicken breeds are yet to be established. To understand whether the same mutation decides the polydactyly phenotype in other chicken breeds, we detected the single-nucleotide polymorphism in 26 different chicken breeds, specifically, 24 Chinese indigenous breeds and 2 European breeds. The mutation was found to have fully penetrated chickens with polydactyly in China, indicating that it is causative for polydactyly in Chinese indigenous chickens. In comparison, the mutation showed no association with polydactyly in Houdan chickens, which originate from France, Europe. Based on the different morphology of polydactyly in Chinese and European breeds, we assumed that the trait might be attributable to different genetic foundations. Therefore, we subsequently performed genome-wide association analysis (GWAS) to locate the region associated with polydactyly. As a result, a ~0.39 Mb genomic region on GGA2p was identified. The region contains six candidate genes, with the causative mutation found in Chinese indigenous breeds also being located in this region. Our results demonstrate that polydactyly in chickens from China and Europe is caused by two independent mutation events that are closely located in the chicken genome.

Crimean-Congo hemorrhagic fever virus (CCHFV) is a member of genus Nairovirus, family Bunyaviridae, which are distributed widely in Africa, Europe and Asia with several genotypes. As a BSL-4 level pathogen, the requirement of high-level biosafety facilities severely constrains researches on live virus manipulation. In this study, we developed a helper-virus-independent mini-genome rescue system for the Chinese YL04057 strain. Based on the enhanced green fluorescent protein (EGFP)-derived mini-genome plasmids, this polymerase I driven system permits easy observation and quantification. Unlike previous report, gradually reduced levels of activity of the CCHFV L, M and S untranslated regions (UTRs) were observed in our system. We also demonstrated that the UTRs at both ends were indispensable for mini-genome background expression. In addition, we phylogentically analyzed all six UTRs of CCHFV and showed that L-UTRs were clustered together approximately corresponding to their original geographical continents. The UTRs of M segment showed a similar branch structure to its open reading frames (ORFs), and nearly an identical tree was generated with 5' UTRs of S segment compared with its ORFs. However, the 3' UTRs of S segment formed new divergent groups. Compatibility tests of YL04057 strain nucleocapsid protein and L protein expression plasmids with Nigerian strain IbAr10200 mini-genomes revealed lower compatibility of L-UTRs without an obvious effect on M-UTRs. Moreover, we demonstrated that the L-UTRs could tolerate certain nucleotide mutations. This system may provide a foundation for future studies of the viral replication cycle, pathogenic mechanisms and evolutionary patterns of CCHFV., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Hepatitis E virus (HEV) has been detected in humans and in a broad range of animals, including pigs. For the first time the full-length genomic sequence of a HEV of European porcine origin, termed swX07-E1, was determined. Comparative analysis of 76 complete or nearly complete nucleotide sequences showed that swX07-E1 shares the highest nucleotide identity with Japanese swine HEV swJ8-5 and swJ12-4. The whole-genome phylogenetic analysis showed that swX07-E1 from Europe belongs to genotype-3 HEV, clusters with variants from Japan, Mongolia and Kyrgyzstan in subgroup 3c, but it is divergent from the prototype US HEV. Our analysis indicates that swX07-E1 represents a new subgroup of genotype-3 and that analysis of full-length sequences is necessary to discover new subgroups of HEV. According to our knowledge, swX07-E1 is the first full-length genome sequence of HEV from European swine. Knowledge about the full length HEV sequence from European swine is very important for understanding the HEV evolutionary events and the molecular mechanism of infection in human and in animals.