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Exploring the effects of orographic events and climatic shifts on the geographic distribution of organisms in the Himalayas-Hengduan Mountains (HHM) region and Qinghai-Tibetan Plateau (QTP) is crucial to understand the impact of environmental changes on organism evolution. To gain further insight into these processes, we reconstructed the evolutionary history of nine Chamaesium species distributed across the HHM and QTP regions. In total, 525 individuals from 56 populations of the nine species were analyzed based on three maternally inherited chloroplast fragments ( rpl16 , trnT-trnL , and trnQ-rps16 ) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-two chloroplast DNA (cpDNA) and 47 ITS haplotypes were identified in nine species. All of the cpDNA and ITS haplotypes were species-specific. Phylogenetic analysis suggested that all nine species form a monophyletic clade with high support. Dating analysis and ancestral area reconstruction revealed that the ancestral group of Chamaesium originated in the southern Himalayan region at the beginning of the Paleogene (60.85 Ma). The nine species of Chamaesium then separated well during the last 25 million years started in Miocene. Our maxent modeling indicated the broad-scale distributions of all nine species remained fairly stable from LIG to the present and predicted that it will remain stable into the future. The initial split of Chamaesium was triggered by climate changes following the collision of the Indian plate with the Eurasia plate during the Eocene. Subsequently, divergences within Chamaesium may have been induced by the intense uplift of the QTP, the onset of the monsoon system, and Central Asian aridification. Long evolutionary history, sexual reproduction, and habitat fragmentation could contribute to the high level of genetic diversity of Chamaesium . The higher genetic differentiation among Chamaesium populations may be related to the drastic changes of the external environment in this region and limited seed/pollen dispersal capacity., 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 © 2021 Zheng, Guo, Price, He and Zhou.)

The fall armyworm ( Spodoptera frugiperda ) is one of the most significant agricultural pests in the world and invaded China in early 2019. We sampled and sequenced RNA-seq data from 15 individuals across different developmental stages. Developmental stages were the larval stage (5th instar larvae and 6th instar larvae), chrysalis stage, and adult stage (female adult and male adult). Individual samples were mainly clustered by developmental stages and we then identified variation between developmental stages of differentially expressed transcripts (DETs). There were 2136 upregulated DETs and 1391 downregulated DETs in the larval stage when comparing larval and chrysalis stages. In the comparison between the chrysalis and adult stages, there were 2033 upregulated DETs and 1391 downregulated DETs in the chrysalis stage. In total, 19,195 abundantly expressed transcripts were obtained and 10% of them were DETs. We then obtained stage-specific DETs to investigate the potential function of the fall armyworm during different developmental stages. We also constructed our annotation background set for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. This indicated that the fall armyworm may undergo active metabolism during its lifespan, even in the chrysalis stage. And it also may experience detoxifying and xenobiotic metabolism throughout its life, especially in the larval stage, which partially explains the difficulty to eradicate using chemical control. Our study is the first insight into the developmental patterns of the fall armyworm and we also provide the fundamental information about enhanced drug resistance at the level of transcriptome. These results are beneficial for a future investigation related to the eradication and/or control stage.

Physospermopsis (Apiaceae) comprises about 10 species, but its taxonomy and phylogeny are disputed. The genus is mostly distributed in the Himalayas and Hengduan Mountains at high elevation. Earlier molecular studies involving six species of Physospermopsis indicated that this genus is not monophyletic and is nested in the East Asia Clade. Therefore, the aims of this study were to re-assess the phylogenetic position of, and interspecific relationships within, Physospermopsis based on two chloroplast loci ( rpl16 , rps16 ) and one nuclear region, the internal transcribed spacers of ribosomal DNA (ITS). Eight species involving 13 populations of Physospermopsis were collected. These were sequenced and analyzed with the sequences of 31 other Apiaceae species obtained from the NCBI to determine phylogenetic relationships using Bayesian inference (BI) and Maximum likelihood (ML). Our study found that Physospermopsis is monophyletic, nested in Pleurospermeae of Apiaceae, sister to Pleurospermum . And we propose that the Physospermopsis clade should be replaced by the East Asia Clade. However, the interspecific relationships within Physospermopsis were not well resolved and the positioning of species was unclear. Diagnostic characteristics to distinguish Physospermopsis species in the field and laboratory are provided for future Physospermopsis phylogenetic studies., (Xin-Rui Xu, Xian-Lin Guo, Megan Price, Xing-Jin He, Song-Dong Zhou.)

Sinocarum is a Sino-Himalayan endemic genus of Apiaceae and distributed in high-elevations from Nepal to SW China. In this study, morphological characteristics were combined with nuclear internal transcribed spacer (ITS) and two chloroplast DNA (cpDNA) intron sequences ( rpl16 and rps16 ) to determine the phylogenetic placement of Sinocarum and the infrageneric relationships between five Sinocarum species. The results confirmed that Sinocarum was a polyphyletic group separated into two clades, Acronema and East Asia clades. S. coloratum , the generic type of Sinocarum , S. cruciatum , S. vaginatum and S. filicinum are in the Acronema clade. Among them, the first three species are clustered into a subclade and are closely related to the genus Acronema . While S. filicinum has a close affinity with Meeboldia . S. schizopetalum did not ally with its congeners we collected and is allied closely with members of the distantly related East Asia clade. In addition, the fruit of the Acronema clade Sinocarum species is usually oblong-ovoid or ovoid, and the pollen is super-rectangular, while the Sinocarum species in the East Asia clade have broad-ovoid fruit and sub-rhomboidal pollen. This study has furnished cumulative evidence to reduce phylogenetic uncertainty and provide a more comprehensive description of the plant morphology, fruit morphology and anatomy, and pollen morphology of these five Chinese Sinocarum species., (Yan-Ping Xiao, Xian-Lin Guo, Megan Price, Wei Gou, Song-Dong Zhou, Xing-Jin He.)

Olfaction is a complicated process that begins with the specific binding of volatile odorant molecules to dedicated olfactory receptors (ORs) in the olfactory epithelium and plays a pivotal role in the survival of mammals. The OR subgenome of the snow leopard has remained largely unexplored, and thus, investigation of the OR system would shed light on the evolutionary dynamics of the snow leopard OR repertoires and genetic evidence for environmental adaptation. In this study, we conducted genome-wide identification and characterization of OR genes in the snow leopard and compared them to all other Panthera species. A total of 213, 294, 624, 305, and 253 functional OR genes were identified in the snow leopard, lion, jaguar, leopard, and tiger, respectively. The phylogenetic relationships of functional Panthera OR genes were illustrated, which comprised 69 families and 350 subfamilies distributed in two classes (Class I and Class II). Comparative analysis of the five Panthera species indicated 115 shared and 5 snow leopard-specific clusters. The potential odorant specificity of certain snow leopard OR genes was identified by similarities to human protein sequences and we identified odorants such as eugenol methyl ether that had the most OR genes. Since our references for odorants were from human studies, possible odorants from snow leopard-specific OR genes need further investigation. The lowest number of OR genes for the snow leopard among Panthera species possibly revealed the association between OR gene family contraction and high-altitude adaptation, which needed further and deeper investigation. This systematic study of OR genes in the snow leopard will provide a solid foundation for further study of olfactory function and variation in the snow leopard.

Clubhouse communities rapidly responded to the COVID-19 pandemic to keep members connected as psychosocial rehabilitation programs were globally disrupted. This investigation aims to elucidate how Clubhouse directors responded to the pandemic and their members' needs, while also directly assessing the needs and well-being of members. This study utilized secondary data from Director and Member surveys designed to capture Clubhouse status, member engagement, and measures of well-being. Descriptive statistics and correlation coefficients were computed across data from directors (n = 140) and members (n = 1136). Directors across 19 countries indicated that the majority of Clubhouses closed and were engaging with members using a variety of technologies, primarily Zoom videoconferencing. For members, greater levels of virtual Clubhouse engagement were positively correlated with physical and mental well-being and negatively correlated with hospitalization rates. This study provides support for an association between virtual Clubhouse engagement and well-being. Repeated measures studies are needed to further investigate this association., Competing Interests: Conflict of interestOn behalf of all authors, the corresponding author states that there is no conflict of interest., (© The Author(s), under exclusive licence to Springer Nature India Private Limited 2021.)

Hansenia Turcz., Haplosphaera Hand.-Mazz. and Sinodielsia H.Wolff are three Apiaceae genera endemic to the Hengduan Mountains and the Himalayas, which usually inhabit elevations greater than 2000 m. The phylogenetic relationships between and within the genera were uncertain, especially the placement of Hap. himalayensis and S. microloba . Therefore, we aimed to conduct comparative (simple sequence repeat (SSR) structure, codon usage bias, nucleotide diversity (Pi) and inverted repeat (IR) boundaries) and phylogenetic analyses of Hansenia , Haplosphaera and Sinodielsia (also compared with Chamaesium and Bupleurum ) to reduce uncertainties in intergeneric and interspecific relationships. We newly assembled eight plastid genomes from Hansenia , Haplosphaera and Sinodielsia species, and analyzed them with two plastid genomes from GenBank of Hap. phaea, S. yunnanensis . Phylogenetic analyses used these ten genomes and another 22 plastid genome sequences of Apiaceae. We found that the newly assembled eight genomes ranged from 155,435 bp to 157,797 bp in length and all had a typical quadripartite structure. Fifty-five to 75 SSRs were found in Hansenia , Haplosphaera and Sinodielsia species, and the most abundant SSR was mononucleotide, which accounted for 58.47% of Hansenia , 60.21% of Haplosphaera and 48.01% of Sinodielsia. There was no evident divergence of codon usage frequency between the three genera, where codons ranged from 21,134 to 21,254. The Pi analysis showed that trnE(UUC)-trnT(GGU) , trnH(GUG)-psbA and trnE(UUC)-trnT(GGU) spacer regions had the highest Pi values in the plastid genomes of Hansenia (0.01889), Haplosphaera (0.04333) and Sinodielsia (0.01222), respectively. The ndhG-ndhI spacer regions were found in all three genera to have higher diversity values (Pi values: 0.01028-0.2), and thus may provide potential DNA barcodes in phylogenetic analysis. IR boundary analysis showed that the length of rps19 and ycf1 genes entering IRs were usually stable in the same genus. Our phylogenetic tree demonstrated that Hap. himalayensis is sister to Han. weberbaueriana ; meanwhile, Haplosphaera and Hansenia are nested together in the East Asia clade, and S. microloba is nested within individuals of S. yunnanensis in the Acronema clade. This study will enrich the complete plastid genome dataset of the Apiaceae genera and has provided a new insight into phylogeny reconstruction using complete plastid genomes of Hansenia , Haplosphaera and Sinodielsia .

Aging is a very complicated biological process that can change gene expressions. The Chinese rhesus macaque (Macaca mulatta lasiota; CR) is closely related to humans. We explored gene expression with increasing age and DNA methylation changes in young and old CRs. Results showed blood transcriptome and DNA methylome significantly changed from young to old CRs. The age-associated differentially expressed genes (DEGs) and differentially methylated regions (DMRs) were associated with age-related biological features, such as immunity, blood coagulation, and biosynthetic process. The measurements of coagulation indicators confirmed old CRs had shorter coagulation time than young CRs, and the activities of coagulation factor II (FII) and factor VIII (FVIII) were enhanced in old CRs. Humans and CRs exhibited the same enhanced blood coagulation with age phenotype. Our study found aging is a critical factor affecting gene expression in CRs, and also provided new insights into the blood coagulation changes in non-human primates., (Copyright © 2020 Elsevier Inc. All rights reserved.)

MicroRNAs (miRNAs) are key in the post-transcriptional regulation of gene expression and thus characterization of miRNAs and investigation of the relative abundance and specificity of tissue expression are essential for understanding gene expression in the golden snub-nosed monkey (GSM, Rhinopithecus roxellanae). Here, we report the first dataset of GSM miRNAs where we identified 460 miRNAs in seven tissues, with 246 conserved known mature miRNAs and 214 novel mature miRNAs. We determined miRNA abundance and expression in the seven tissues using a Tissue Specificity Index score and found that most novel GSM miRNAs showed a highly tissue-specific expression pattern. In particular, 67 novel miRNAs and the miR-34 family were expressed in abundance only in the lung. Five known miRNAs were highly abundant in digestive organs such as the pancreas and liver, and four novel miRNAs were highly expressed in the heart and muscle. Annotation of target genes of GSM miRNAs indicated that target genes were enriched in many important pathways, such as the HIF-1 signaling pathway and xenobiotic biodegradation-related pathways. Collectively, these results emphasize that miRNAs play important roles in GSM diet and high-elevation adaptation regulation. In summary, this study provides essential information on GSM miRNAs and will benefit further investigations of the function and mechanism of miRNAs in controlling gene expression in the GSM.

The Tibetan chicken is a native Chinese breed that lives at high elevations and has adapted to the extreme environmental conditions of the Tibetan Plateau. However, its hypoxic adaptation at the gene expression level is unclear. Here, we sequenced nine lung transcriptomes of the Tibetan chicken at three developmental stages (5 and 42 weeks and 4.5 years). A total of 1.02 billion clean reads were obtained. We identified 16 012 mRNAs and 6898 lncRNAs. The expression of mRNA showed that nine samples were significantly divided into three clusters, with higher correlation and closer relationship between the 5 and 42 week groups. We identified 399 differentially expressed genes (DEGs) between the 5 and 42 week groups, 3532 DEGs between the 5 week and 4.5 year groups, and 3909 DEGs between the 42 week and 4.5 year groups. The up-regulated DEGs in the 5 week group, compared with 42 week and 4.5 year groups, were enriched in GO terms associated with growth and development, whereas the up-regulated DEGs in the 4.5 year group were mainly enriched in many metabolic-related categories. Moreover, the enrichment results with up-regulated DEGs in the 5 and/or 42 week groups, compared with the 4.5 year group, were associated with hypoxic adaptation, such as oxygen transport, oxygen binding and oxygen carrier activity, and calcium signaling pathway. In addition, we identified 978 high-correlation lncRNA and protein-coding gene pairs, and 524 significant neighboring protein-coding genes were also DEGs. Our results provide new insights into gene expression of lung tissue in Tibetan chickens during the aging process., (© 2020 Stichting International Foundation for Animal Genetics.)

Hyenas (family Hyaenidae) occupy a variety of different niches, of which the striped hyena ( Hyaena hyaena ) scavenges mainly on the carcasses of animals. We compared its genome with the genomes of nine other mammals, focusing on similarities and differences in chemoreception, detoxification, digestive, and immune systems. The results showed that the striped hyena's immune and digestive system-related gene families have significantly expanded, which was likely to be an adaptive response to its scavenging lifestyle. In addition, 88 and 26 positive selected genes (PSGs) were identified in the immune system and digestive system, respectively, which may be the molecular basis for immune defense system to effectively resist pathogen invasion. Functional enrichment analysis of PSGs revealed that most of them were involved in the immune regulation process. Among them, eight specific missense mutations were found in two PSGs ( MHC class II antigen DOA and MHC class II antigen DOB ), suggesting important reorganization of the immune system in the striped hyena. Moreover, we identified one cathelicidin gene and four defensin genes in the striped hyenas by genome mining, which have high-efficiency and broad-spectrum antimicrobial activity. Of particular interest, a striped hyena-specific missense mutation was found in the cathelicidin gene. PolyPhen-2 classified the missense mutation as a harmful mutation, which may have aided in immune adaptation to carrion feeding. Our genomic analyses on the striped hyena provided insights into its success in the adaptation to the scavenging lifestyle.

Chamaesium H. Wolff (Apiaceae, Apioideae) is a small genus mainly distributed in the Hengduan Mountains and the Himalayas. Ten species of Chamaesium have been described and nine species are distributed in China. Recent advances in molecular phylogenetics have revolutionized our understanding of Chinese Chamaesium taxonomy and evolution. However, an accurate phylogenetic relationship in Chamaesium based on the second-generation sequencing technology remains poorly understood. Here, we newly assembled nine plastid genomes from the nine Chinese Chamaesium species and combined these genomes with eight other species from five genera to perform a phylogenic analysis by maximum likelihood (ML) using the complete plastid genome and analyzed genome structure, GC content, species pairwise Ka/Ks ratios and the simple sequence repeat (SSR) component. We found that the nine species' plastid genomes ranged from 152,703 bp ( C. thalictrifolium ) to 155,712 bp ( C. mallaeanum ), and contained 133 genes, 34 SSR types and 585 SSR loci. We also found 20,953-21,115 codons from 53 coding sequence (CDS) regions, 38.4-38.7% GC content of the total genome and low Ka/Ks (0.27-0.43) ratios of 53 aligned CDS. These results will facilitate our further understanding of the evolution of the genus Chamaesium .

The buff-throated partridge (Tetraophasis szechenyii) is a hypoxia-tolerant bird living in an extremely inhospitable high-altitude environment, which has high ultraviolet (UV) radiation as well as a low oxygen supply when compared with low-altitude areas. To further understand the molecular genetic mechanisms of the high-altitude adaptation of the buff-throated partridges, we de novo assembled the complete genome of the buff-throated partridge. Comparative genomics revealed that positively selected hypoxia-related genes in the buff-throated partridge were distributed in the HIF-1 signaling pathway (map04066), response to hypoxia (GO:0001666), response to oxygen-containing compound (GO:1901700), ATP binding (GO:0005524), and angiogenesis (GO:0001525). Of these positively selected hypoxia-related genes, one positively selected gene (LONP1) had one buff-throated partridge-specific missense mutation which was classified as deleterious by PolyPhen-2. Moreover, positively selected genes in the buff-throated partridge were enriched in cellular response to DNA damage stimulus (corrected P value: 0.028006) and DNA repair (corrected P value: 0.044549), which was related to the increased exposure of the buff-throated partridge to UV radiation. Compared with other avian genomes, the buff-throated partridge showed expansion in genes associated with steroid hormone receptor activity and contractions in genes related to immune and olfactory perception. Furthermore, comparisons between the buff-throated partridge genome and red junglefowl genome revealed a conserved genome structure and provided strong evidence of the sibling relationship between Tetraophasis and Lophophorus. Our data and analysis contributed to the study of Phasianidae evolutionary history and provided new insights into the potential adaptation mechanisms to the high altitude employed by the buff-throated partridge.

The monal genus (Lophophorus) is a branch of Phasianidae and its species inhabit the high-altitude mountains of the Qinghai-Tibet Plateau. The Chinese monal, L. lhuysii, is a threatened endemic bird of China that possesses high-altitude adaptability, diversity of plumage color and potentially low reproductive life history. This is the first study to describe the monal genome using next generation sequencing technology. The Chinese monal genome size is 1.01 Gb, with 16,940 protein-coding genes. Gene annotation yielded 100.93 Mb (9.97%) repeat elements, 785 ncRNA, 5,465,549 bp (0.54%) SSR and 15,550 (92%) genes in public databases. Compared to other birds and mammals, the genome evolution analysis showed numerous expanded gene families and positive selected genes involved in high-altitude adaptation, especially related to the adaptation of low temperature and hypoxia. Consequently, this gene data can be used to investigate the molecular evolution of high-altitude adaptation in future bird research. Our first published genome of the genus Lophophorus will be integral for the study of monal population genetic diversity and conservation, genomic evolution and Galliformes species differentiation in the Qinghai-Tibetan Plateau., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The black-necked crane (Grus nigricollis) which inhabits high-altitude areas has the largest body size of the world's 15 crane species, and is classified as threatened by the IUCN. To support further studies on population genetics and genomics, we present a high-quality genome assembly based on both Illumina and nanopore sequencing. In total, 54.59 Gb Illumina short reads and 116.5 Gb nanopore long reads were generated. The 1.23 Gb assembled genome has a high contig N50 of 17.89 Mb, and has a longest contig of 87.83 Mb. The completeness (97.7%) of the draft genome was evaluated with single-copy orthologous genes using BUSCO. We identified 17,789 genes and found that 8.11% of the genome is composed of repetitive elements. In total, 84 of the 2,272 one-to-one orthologous genes were under positive selection in the black-necked crane lineage. SNP-based inference indicated two bottlenecks in the recent demographic trajectories of the black-necked crane. The genome information will contribute to future study of crane evolutionary history and provide new insights into the potential adaptation mechanisms of the black-necked crane to its high-altitude habitat., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

The globally distributed American cockroach ( Periplaneta americana ) is considered a pest, but it has been widely used in traditional Chinese medicine. In the past, the American cockroach's genome and transcriptomes were sequenced, but the differential expression transcripts between developmental stages were unavailable. We performed the de novo assembly and analysis of American cockroach transcriptomes from four developmental stages. Approximately 200 million high-quality paired-end reads were generated by using Illumina Hiseq 2000 sequencer. The assembly produced 291,250 transcripts with an average length of 714 bp. In addition, 38,052 microsatellites and 11,060,020 transposable elements were identified. Based on sequence homology, 53,262 transcripts were annotated. After calculating the expression levels of all the transcripts, we found that 13 transcripts were highly expressed in all the samples and at least two, p10 and actin-related protein 1, played important roles during development. A total of 7954 differentially expressed transcripts (DETs) were identified. The adult had the largest number of DETs when compared to other samples (4818), while the 3rd and 8th larva had the least number of DETs (1332). We performed gene enrichment analysis with the DETs, and some interesting results were detected in the different groups. For example, chitin is the major component of the insect exoskeleton, and the chitin-related genes in larvae and new molted samples had higher expression levels than in adults. In addition, the enrichment analysis detected many chitin-related pathways. Our study performed the first large-scale comparative transcriptomics between the developmental stages of American cockroach, which could provide useful gene expression data for future studies.

The Sichuan partridge ( Arborophila rufipectus , Phasianidae, Galliformes) is distributed in south-west China, and classified as endangered grade. To examine the evolution and genomic features of Sichuan partridge, we de novo assembled the Sichuan partridge reference genome. The final draft assembly consisted of approximately 1.09 Gb, and had a scaffold N50 of 4.57 Mb. About 1.94 million heterozygous single-nucleotide polymorphisms (SNPs) were detected, 17,519 protein-coding genes were predicted, and 9.29% of the genome was identified as repetitive elements. A total of 56 olfactory receptor (OR) genes were found in Sichuan partridge, and conserved motifs were detected. Comparisons between the Sichuan partridge genome and chicken genome revealed a conserved genome structure, and phylogenetic analysis demonstrated that Arborophila possessed a basal phylogenetic position within Phasianidae. Gene Ontology (GO) enrichment analysis of positively selected genes (PSGs) in Sichuan partridge showed over-represented GO functions related to environmental adaptation, such as energy metabolism and behavior. Pairwise sequentially Markovian coalescent analysis revealed the recent demographic trajectory for the Sichuan partridge. Our data and findings provide valuable genomic resources not only for studying the evolutionary adaptation, but also for facilitating the long-term conservation and genetic diversity for this endangered species.

Cathartidae is a small family of large-bodied carrion-feeding birds, of which the turkey vulture (Cathartes aura, Cathartidae) is the most widespread distributed. To investigate the chemoreception system, detoxification system, and immune system in the turkey vulture, we compared its genome to 14 other avian genomes. Comparative genomics demonstrated the expansion in the chemoreception system, especially the olfactory receptors, while the genes in the detoxification system of the turkey vulture did not show apparent expansion. We identified five positively selected genes associated with the immune system in the turkey vulture, which was likely to strengthen the immune defense against pathogenic invasion. Functional enrichment analysis indicated that many positively selected genes were involved in the regulation of immune system processes, implying important reorganization of the immune system in the turkey vulture. The turkey vulture-specific missense mutations were found in one positively selected gene (BCL6), and all the missense mutations were classified as deleterious by PolyPhen-2, possibly contributing to immune adaptation to the carrion feeding. Furthermore, we identified four turkey vulture-specific missense mutations in three β-defensin genes of the turkey vulture, which was an indispensable part in the innate immunity (a natural barrier against invasive microbes including bacteria, fungi, and viruses). Our genomic analyses in the turkey vulture provided insights into the genetic signatures of the adaptation to the carrion feeding.

The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica ) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica . In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium .

Background: While acknowledged as one of social marketing's necessities, limited reporting of segmentation exists. The current study seeks to extend segmentation drawing on all four segmentation bases within the context of Queensland young adult sexual health behaviour., Methods: An online survey was used to collect data from 15 to 29 year old people in Queensland, Australia. Data collection was undertaken online to capture the broader population of young adults and in person on campuses to gather data from students who were currently enrolled at University. Quotas were set to ensure a broad representation was attained reflecting the States demography., Results: Two-step cluster analysis revealed three different segments. The most important variables in segment formation were age, household type, experience of risky sexual encounters and previously being tested or treated for sexually transmissible infections (STIs). The results suggest that demographic and behavioural variables were the most effective in segment definition., Conclusions: This study investigated young people aged 15-29 in Queensland, Australia to examine group differences drawing from four bases. This study revealed three distinct segments in a sexual health context and highlighted the importance of behavioural variables in segment formation, insight and understanding.

The Chinese forest musk deer (Moschus berezovskii; FMD) is an artiodactyl mammal and is both economically valuable and highly endangered. To investigate the genetic mechanisms of musk secretion and adaptive immunity in FMD, we compared its genome to nine other artiodactyl genomes. Comparative genomics demonstrated that eight positively selected genes (PSGs) in FMD were annotated in three KEGG pathways that were related to metabolic and synthetic activity of musk, similar to previous transcriptome studies. Functional enrichment analysis indicated that many PSGs were involved in the regulation of immune system processes, implying important reorganization of the immune system in FMD. FMD-specific missense mutations were found in two PSGs (MHC class II antigen DRA and ADA) that were classified as deleterious by PolyPhen-2, possibly contributing to immune adaptation to infectious diseases. Functional assessment showed that the FMD-specific mutation enhanced the ADA activity, which was likely to strengthen the immune defense against pathogenic invasion. Single nucleotide polymorphism-based inference showed the recent demographic trajectory for FMD. Our data and findings provide valuable genomic resources not only for studying the genetic mechanisms of musk secretion and adaptive immunity, but also for facilitating more effective management of the captive breeding programs for this endangered species., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Raptors are carnivorous birds including accipitrids (Accipitridae, Accipitriformes) and owls (Strigiformes), which are diurnal and nocturnal, respectively. To examine the evolutionary basis of adaptations to different light cycles and hunting behavior between accipitrids and owls, we de novo assembled besra (Accipiter virgatus, Accipitridae, Accipitriformes) and oriental scops owl (Otus sunia, Strigidae, Strigiformes) draft genomes. Comparative genomics demonstrated four PSGs (positively selected genes) (XRCC5, PRIMPOL, MDM2, and SIRT1) related to the response to ultraviolet (UV) radiation in accipitrids, and one PSG (ALCAM) associated with retina development in owls, which was consistent with their respective diurnal/nocturnal predatory lifestyles. We identified five accipitrid-specific and two owl-specific missense mutations and most of which were predicted to affect the protein function by PolyPhen-2. Genome comparison showed the diversification of raptor olfactory receptor repertoires, which may reflect an important role of olfaction in their predatory lifestyle. Comparison of TAS2R gene (i.e. linked to tasting bitterness) number in birds with different dietary lifestyles suggested that dietary toxins were a major selective force shaping the diversity of TAS2R repertoires. Fewer TAS2R genes in raptors reflected their carnivorous diet, since animal tissues are less likely to contain toxins than plant material. Our data and findings provide valuable genomic resources for studying the genetic mechanisms of raptors' environmental adaptation, particularly olfaction, nocturnality and response to UV radiation.

Purpose: To examine associations between patient perceptions that their provider was knowledgeable of their medical history and clinicians' early adoption of an application that presents providers with an integrated longitudinal view of a patient's electronic health records (EHR) from multiple healthcare systems., Method: This retrospective analysis utilizes provider audit logs from the Veterans Health Administration Joint Legacy Viewer (JLV) and patient responses to the Survey of Patient Healthcare Experiences Patient-Centered Medical Home (SHEP/PCMH) patient satisfaction survey (FY2016) to assess the relationship between the primary care provider being an early adopter of JLV and patient perception of the provider's knowledge of their medical history. Multivariate logistic regression models were used to control for patient age, race, sex education, health status, duration of patient-provider relationship, and provider characteristics., Results: The study used responses from 203,903 patients to the SHEP-PCMH survey in FY2016 who received outpatient primary care services from 11,421 unique providers. Most (91%) clinicians had no JLV utilization in the 6 months prior to the studied patient visit. Controlling for patient demographics, length of the patient-provider relationship, and provider and facility characteristics, being an early adopter of the JLV system was associated with a 14% (adj OR 1.14, p < 0.000) increased odds that patients felt their provider was knowledgeable about their medical history. When evaluating the interaction between duration of patient-provider relationship and being an early adopter of JLV, a greater effect was seen with patient-provider relationships that were greater than 3 years (adj OR 1.23, p < 0.000), compared to those less than 3 years., Conclusions: Increasing the interoperability of medical information systems has the potential to improve both patient care and patient experience of care. This study demonstrates that early adopters of an integrated view of electronic health records from multiple delivery systems are more likely to have their patients report that their clinician was knowledgeable of their medical history. With provider payments often linked to patient satisfaction performance metrics, investments in interoperability may be worthwhile.

Background: The forest musk deer, Moschus berezovskii, is one of seven musk deer (Moschus spp.) and is distributed in Southwest China. Akin to other musk deer, the forest musk deer has been traditionally and is currently hunted for its musk (i.e., global perfume industry). Considerable hunting pressure and habitat loss have caused significant population declines. Consequently, the Chinese government commenced captive breeding programs for musk harvesting in the 1950s. However, the prevalence of fatal diseases is considerably restricting population increases. Disease severity and extent are exacerbated by inbreeding and genetic diversity declines in captive musk deer populations. It is essential that knowledge of captive and wild forest musk deer populations' immune system and genome be gained in order to improve their physical and genetic health. We have thus sequenced the whole genome of the forest musk deer, completed the genomic assembly and annotation, and performed preliminary bioinformatic analyses., Findings: A total of 407 Gb raw reads from whole-genome sequencing were generated using the Illumina HiSeq 4000 platform. The final genome assembly is around 2.72 Gb, with a contig N50 length of 22.6 kb and a scaffold N50 length of 2.85 Mb. We identified 24,352 genes and found that 42.05% of the genome is composed of repetitive elements. We also detected 1,236 olfactory receptor genes. The genome-wide phylogenetic tree indicated that the forest musk deer was within the order Artiodactyla, and it appeared as the sister clade of four members of Bovidae. In total, 576 genes were under positive selection in the forest musk deer lineage., Conclusions: We provide the first genome sequence and gene annotation for the forest musk deer. The availability of these resources will be very useful for the conservation and captive breeding of this endangered and economically important species and for reconstructing the evolutionary history of the order Artiodactyla.

Urophysa is a Chinese endemic genus with only two species (U. rockii and U. henryi) distributed in Yungui Plateau (Guizhou Province) and adjacent regions (i.e., Provinces of Hunan, Hubei, Chongqing and Sichuan). The aim of this study was to determine the genetic diversity and population differentiation within Urophysa and investigate the effect of the Yungui Plateau uplift and climate oscillations on evolution of Urophysa. In this study, micro-morphological characteristics, nine microsatellite loci (SSR), two nuclear loci (ITS and ETS) and two chloroplast fragments (psbA-trnH and trnL-trnF) were used to analyze the phylogenetic relationships and assess genetic and phylogeographical structure of Urophysa. Isolation by distance (IBD) was performed to research the effects of geographical isolation. We detected high genetic diversity at the species level but low genetic diversity within populations. Striking genetic differentiation (AMOVA) among populations and a significant phylogeographical structure (NST > GST, p < 0.01) were detected among U. henryi populations, along with significant effects of isolation by distance (IBD). Molecular clock estimation using calibration strategy and cpDNA substitution rate indicated that the divergence of U. henryi occurred during late Miocene to early Quaternary, when the orogeny of Yungui Plateau was violent. U. rockii originated at the early Quaternary and further differentiated at early Pleistocene. Our results suggested that habitat fragmentation played an important role in the genetic diversity and population differentiation of U. rockii and U. henryi. Heterogenous geomorphological configuration and complicated environment resulted from rapid uplift of the Yungui Plateau were inferred as important incentives for the modern phylogeograhpical pattern and species divergence of Urophysa. The geographical isolation, limited gene flow, specialized morphologies and the Pleistocene climatic oscillation greatly contributed to the allopatric divergence of U. rockii. Significant genetic drift and inbreeding were detected in these two species, in situ measures should be implemented to protect them.

The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.

Over 50% of young people have dated by age 15. While romantic relationship concerns are a major reason for adolescent help-seeking from counselling services, we have a limited understanding of what types of relationship issues are most strongly related to mental health issues and suicide risk. This paper used records of 4019 counselling sessions with adolescents (10-18 years) seeking help from a national youth counselling service for a romantic relationship concern to: (i) explore what types and stage (pre, during, post) of romantic concerns adolescents seek help for; (ii) how they are associated with mental health problems, self-harm and suicide risk; and (iii) whether these associations differ by age and gender. In line with developmental-contextual theory, results suggest that concerns about the initiation of relationships are common in early adolescence, while concerns about maintaining and repairing relationships increase with age. Relationship breakups were the most common concern for both male and female adolescents and for all age groups (early, mid, late adolescence). Data relating to a range of mental health issues were available for approximately half of the sample. Post-relationship concerns (including breakups) were also more likely than pre- or during-relationship concerns to be associated with concurrent mental health issues (36.8%), self-harm (22.6%) and suicide (9.9%). Results draw on a staged developmental theory of adolescent romantic relationships to provide a comprehensive assessment of relationship stressors, highlighting post-relationship as a particularly vulnerable time for all stages of adolescence. These findings contribute to the development of targeted intervention and support programs.

Background: Recent research has proposed a new method for defining a favorable outcome in traumatic brain injury and stroke research., Purpose: This new method is called the sliding dichotomy, and it is suggested as a potential solution to the problem of underpowered clinical trials., Methods: We present a brief simulation study and graphical comparison of the power of each method to detect varying treatment effect sizes., Results: Simulations of a patient population similar to the National Acute Brain Injury Study: Hypothermia (NABISH) study indicate that the sliding dichotomy method does not result in higher power than traditional methods., Conclusions: Although the sliding dichotomy may present gains in power in some cases, several aspects of the patient population need to be considered in choosing between sliding dichotomy and traditional definitions of favorable outcomes.

Although mitochondria are key determinants of myocardial injury during ischemia-reperfusion (I/R), their interaction with critical cytoprotective signaling systems is not fully understood. Sphingosine-1-phosphate (S1P) produced by sphingosine kinase-1 protects the heart from I/R damage. Recently a new role for mitochondrial S1P produced by a second isoform of sphingosine kinase, SphK2, was described to regulate complex IV assembly and respiration via interaction with mitochondrial prohibitin-2. Here we investigated the role of SphK2 in cardioprotection by preconditioning. Littermate (WT) and sphk2 (-/-) mice underwent 45 min of in vivo ischemia and 24 h reperfusion. Mice received no intervention (I/R) or preconditioning (PC) via 5 min I/R before the index ischemia. Despite the activation of PC-cytoprotective signaling pathways in both groups, infarct size in sphk2 (-/-) mice was not reduced by PC (42 ± 3% PC vs. 43 ± 4% I/R, p = ns) versus WT (24 ± 3% PC vs. 43 ± 3% I/R, p < 0.05). sphk2 (-/-) mitochondria exhibited decreased oxidative phosphorylation and increased susceptibility to permeability transition (PTP). Unlike WT, PC did not prevent ischemic damage to electron transport or the increased susceptibility to PTP. To evaluate the direct contribution to the resistance of mitochondria to cytoprotection, SphK2, PHB2 or cytochrome oxidase subunit IV was depleted in cardiomyoblasts. PC protection was abolished by each knockdown concomitant with decreased PTP resistance. These results point to a new action of S1P in cardioprotection and suggest that the mitochondrial S1P produced by SphK2 is required for the downstream protective modulation of PTP as an effector of preconditioning protection.

Background: In the period immediately following hospital discharge, patients often experience difficulty with medication management. The problems related to patients' handling of discharge prescriptions are not well characterized., Methods: We conducted a large observational study of patients discharged from 170 community hospitals in 2005. By combining clinical, administrative, and call center data, we were able to examine independent predictors of prescription-related issues in the 48-72 hours after hospital discharge. Issues included: not picking up prescribed discharge medications, not knowing if these medications had been picked up, not taking discharge medications, and not understanding how to take the medications., Results: More than half (57.0%) of the 31,199 subjects in the study were women, and the mean age was 61.1 years. Overall, 7.2% of patients (n = 2253) reported prescription-related issues, most often not filling discharge prescriptions. In multivariable analyses, prescription-related issues were more common among adults age 35-49; women; patients with Medicare HMO coverage, Medicaid, or no insurance; adults with higher severity of illness ratings; and patients prescribed 6 or more medications or an inhaler. Predictors of fewer problems were being age 65 or older; having HMO or commercial insurance; being prescribed antibiotics, anticoagulants, or angiotensin II receptor blockers; and having a major diagnosis in the skin or musculoskeletal categories., Conclusions: About 7% of patients reported prescription-related issues within a few days of hospital discharge. High-risk patients should be identified and offered additional assistance prior to discharge and receive a follow-up phone call to assess if discharge prescriptions have been filled., ((c) 2008 Society of Hospital Medicine.)

Background: Professional organizations recommend that physicians discuss prostate cancer with patients to make individual screening decisions. However, few studies have tested strategies to encourage such discussions, particularly among high-risk populations. We examined the effects of two low-literacy interventions on the frequency of prostate cancer discussion and screening., Design: Randomized, blinded, controlled trial with concealed allocation., Setting/participants: Inner-city primary care clinic, serving a predominately African-American population. Participants were men aged 45-70 with no history of prostate cancer, presenting for a regular appointment., Interventions: While waiting to see their physician, patients received a patient education handout on prostate cancer screening (PtEd), a handout simply encouraging patients to talk to their doctor about prostate cancer (Cue), or a control handout. The interventions did not advocate for or against screening., Measures: Patient-reported discussion of prostate cancer with the physician and chart reviews determine prostate-specific antigen (PSA) test orders and performance of digital rectal examination (DRE). Adjusted odds ratios (aOR) and 95% confidence intervals (CI) were computed. Data were collected in 2003, and analyses were completed in 2006., Results: Most of the 250 subjects (90.4%) were African American and 78.8% read below the ninth grade level. Overall, 48.4% reported discussing prostate cancer during the appointment. Compared to the control group (37.3%), discussions were significantly more common in the Cue group (58.0%, aOR=2.39 [1.26-4.52]), as well as in the PtEd group (50.0%, aOR=1.92 [1.01-3.65]). When prostate cancer was discussed, patients in the intervention groups more commonly initiated the conversation (47.6% PtEd and 40.0% Cue, vs 9.7% control, p<0.01 for each comparison to control). Compared to the control group (2.4%), PSA test orders increased in the PtEd group (14.1%, aOR=7.62 [1.62-35.83]) and in the Cue group (12.3%, aOR=5.86 [1.24-27.81]). Documentation of DRE did not change significantly (4.7% PtEd, 6.2% Cue, and 6.0% control)., Conclusions: Two simple low-literacy interventions significantly increased discussion of prostate cancer and PSA test orders but not performance of DRE. Both interventions were effective in empowering low-literacy patients to initiate conversations about prostate cancer with their physician.

Objective: To compare the diagnostic efficiency of six index tests as predictors of juvenile bipolar disorder in two large outpatient samples, aged 5 to 10 and 11 to 17 years, gathered from 1997 to 2002., Method: DSM-IV diagnosis was based on a semistructured diagnostic interview (Schedule for Affective Disorders and Schizophrenia for School-Age Children) with the parent and youth sequentially, blind to scores on the index tests. Participants were 318 youths aged 5 to 10 (50% with bipolar diagnoses) and 324 youths aged 11 to 17 (41% with bipolar diagnoses). Areas under the curve (AUCs) from receiver operating characteristic analyses and multilevel likelihood ratios quantified test performance., Results: Parent report (AUCs from 0.78 to 0.84 in both age groups) outperformed teacher (AUCs 0.57 in the younger sample and 0.70 in the older sample) or adolescent measures (AUCs 0.67 [General Behavior Inventory] and 0.71 [Youth Self-Report]) at identifying bipolar disorders. Combining tests did not produce clinically meaningful classification improvement., Conclusions: Parent report was more useful than teacher report or adolescent self-report on the index tests studied. Results generally replicated across both age groups. Parent report on these instruments could facilitate differential diagnosis of bipolar disorder in youths aged 5 to 17 years, especially by decreasing the rate of false-positive diagnoses., (Copyright 2004 American Academy of Child and Adolescent Psychiatry)