A comprehensive survey of bat sarbecoviruses across China for the origin tracing of SARS-CoV and SARS-CoV-2

Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 have been thought to originate from bat, but whether the cross-species transmission occurred directly from bat to human or through an intermediate host remains elusive. In this study, we performed CoV screening of 102 samples collected from animal-selling stalls of Wuhan Huanan Market (WHM) and pharyngeal and anal swabs from13,064 bats collected at 703 locations across China, covering almost all known southern hotspots for sarbecovirus, between 2016 and 2021. This is the first systematic survey of bat CoV in China during the outbreak of Corona Virus Disease 2019. We found four non-sarbeco CoVs in samples of WHM, and 142 SARS-CoV related CoVs (SARSr-CoV) and 4 recombinant CoVs in bats, of which YN2020B-G share the highest sequence identity with SARS-CoV among all known bat CoVs, suggesting endemic SARSr-CoVs in bats in China. However, we did not find any SARS-CoV-2 related CoVs (SC2r-CoV) in any samples, including specimens collected from the only two domestic places where RaTG13 and RmYN02 were previously reported (the Tongguan caves and the karst caves around the Xishuangbanna Tropical Botanical Garden), indicating that SC2r-CoVs might not actively circulate among bats in China. Phylogenetic analysis showed that there are three different lineages of sarbecoviruses, L1 (SARSr-CoV), L2 (SC2r-CoV), and L-R (a novel CoV lineage from L1 and L2 recombination), in China. Of note, L-R CoVs are only found in R. pusillus. Further macroscopical analysis of the genetic diversity, host specificity for colonization and accidental infection, and geographical characteristics of available CoVs in database revealed the presence of a general geographical distribution pattern for bat sarbecoviruses, with the highest genetic diversity and sequence homology to SARS-CoV or SARS-CoV-2 along the southwest border of China, the least in the northwest of China. Considering the receptor binding motifs for spike gene of sarbecoviruses in Indochina Peninsula show the greatest diversity, our data provide the rationale that extensive surveys in further south and southwest to or of China might be needed for finding closer ancestors of SARS-CoV and SARS-CoV-2.

The Evaluation of Agronomic Traits of Wild Soybean Accessions (Glycine soja Sieb. and Zucc.) in Heilongjiang Province, China

Wild soybean germplasm is distributed widely in China, particularly in Heilongjiang Province. In this study, 242 wild soybean accessions from four agricultural divisions in Heilongjiang Province were evaluated based on six qualitative and eight quantitative traits. Results showed that a large amount of variation occurred in these evaluated traits. Abundant qualitative traits included the wild type (78.51%), purple flowers (90.50%), needle leaf (39.26%), black seed (83.88%), brown hilum (52.07%), and mud film (87.60). Results of multivariate analysis based on quantitative traits showed that 100-seed weight, seeds weight per plant, number of seeds per plant, number of effective pods, and number of invalid pods were significantly different among samples (p < 0.05). A total of 27 germplasms were screened. Cluster analysis identified the 242 accessions into two groups, not following the geographical distribution pattern, with rich wild soybean resources revealed in the northern site. The present study indicated that wild soybean in Heilongjiang Province should be conserved in situ. The rich genetic diversity revealed in soybeans of different sites in Heilongjiang Province suggested its significant potential utilization in genetic improvement and breakthrough for soybean breeding. This information will help to exploit and conserve wild soybean accessions in Heilongjiang Province.

Potential geographical distribution and environmental explanations of rare and endangered plant species through combined modelling: A case study of Northwest Yunnan, China

In recent decades, due to the effect of climate change and the interference of human activities, the species habitat index fallen 2%. Studying the geographical distribution pattern and predicting the potential geographical distribution of species are of great significance for developing scientific and effective biodiversity conservation strategies. The purpose of this research is to predict the potential geographical distribution of 25 rare and endangered plant species in Northwest Yunnan, China on the grid map with a resolution of 0.05° × 0.05° and analyze the explanation capabilities of various environmental factors on the potential geographical distribution patterns of these species, and explore the main restrictive environmental factors. Initially, we employed the ecological niche model MaxEnt to predict the potential geographical distribution of target species. Following that, we overlaid the potential geographical distribution of each species, and we obtained the potential geographical distribution pattern of species richness on the spatial scale of the ecological niche model with a resolution of 0.05° × 0.05°. Ultimately, we also adopted geographically weighted regression (GWR) model to investigate the explanation capabilities of various environmental parameters on the potential distribution patterns. The results showed that the average AUC value of each species was between 0.80 and 1.00, which indicated that the simulation precision of the MaxEnt model for each species was good or excellent. Besides, the potential distribution areas of these species were between 826.33 km2 and 44,963.53 km2. In addition, the average contribution values of the annual precipitation (Bio12), precipitation of coldest quarter (Bio19) and population density (Pop) were 25.92%, 15.86% and 17.95%, respectively. Moreover, the goodness of fit R2 and AIC value of the water model were 0.88 and 7,703.82, respectively, which indicated the water factor largely influenced the potential distribution of these species. The results of this study would be helpful for implementing long-term conservation and reintroduction for these species.

Molecular phylogeny of the limacoid snail family Dyakiidae in Southeast Asia, with the description of a new genus and species

Members of the terrestrial snail family Dyakiidae from Southeast Asia show a distinct geographical distribution pattern and possess different degrees of complexity in their amatorial organ gland. This study is the first molecular phylogeny of ten of the 12 genera in this family, performed to provide insights into the origin of Dyakiidae and the evolution of their shells and amatorial organ gland structure. A new genus and new species, Pseudoquantula lenticularis Jirapatrasilp & Panha gen. & sp. nov., was uncovered based on its distinct morphological characters and molecular divergence. All other genera were retrieved as monophyletic except for Dyakia. Mainland Southeast Asia was inferred to be the ancestral range of the Dyakiidae, and the lineages then dispersed to and diversified in Borneo. Cladistic analysis showed that all 14 morphological characters used in this study were homoplastic. These results disagree with the previous amatorial organ transformation series, in which neither Pseudoplecta nor Quantula was ancestral to the other genera. The enigmatic genus Pseudoplecta, which lacks an amatorial organ gland, exhibited secondary loss.

Survey of Low Birthweight and Extremely Low Birthweight Events in a High Environmental Risk Area of Apulia, Italy

The association between environmental conditions and pregnancy outcome has been under investigation for a long time, but results appear to be inconclusive regarding damage to either the newborn or the mother. The aim of this study was to evaluate the distribution of hospitalization of newborns with low birthweight (< 2500 g) and extremely low birthweight (< 1000 g) in the geographical area of Taranto, Italy, which is characterized by high environmental risk because of industrial pollution. We analyzed the database of hospital discharge forms for the years 2001–2013 regarding hospital admission of newborns in the region of Apulia. The relative risk (RR) of hospitalization, adjusted for the deprivation index, was estimated using the Besag–York–Molliè Bayesian model. The city of Taranto, which has the highest environmental risk, had the highest RR for newborns with low birthweight (1.47, 95% uncertainty interval 1.38–1.56). Other geographical areas with high environmental pollution had higher RRs for low birth weight compared with the regional average. We found no geographical distribution pattern of extremely low birthweight that would suggest an association with environmental pollution.

Genetic delimitation of Oreocharis species from Hainan Island

Hainan Island harbours an extraordinary diversity of Gesneriaceae with 14 genera and 23 species, amongst which two species and one variety are recognised in the genus Oreocharis. These three Oreocharis taxa are all Hainan-endemics and show a complex geographical distribution pattern with considerable morphological intermixtures. In this study, we combined DNA (nuclear ITS sequences and cpDNAtrnL-trnF and ycf1b) to evaluate genetic delimitation for 12 Oreocharis populations from the island, together with morphological similarity analysis using 16 morphological traits. The results showed Hainan Oreocharis taxa were monophyletic with relative low genetic diversity within populations, highly significant genetic differentiation amongst populations and a significant phylogeographical structure. The 12 populations formed three genetically distinct groups, roughly correspondent to the currently recognised two species and one unknown lineage. The PCA analyses of morphological traits indicate three distinctive groups, differing mainly in petal colour and corolla shapes. The roles of river and mountain isolations in the origin and distribution of these three lineages are discussed.

A new molecular method for the exploration of hybrid zones between two toad species of conservation interest

Analyzing hybrid zones between previously isolated lineages allows insight into processes determining the fate of re-encounter of these taxa. The distributions of Fire-bellied (Bombina bombina) and Yellow-bellied toads (B. variegata) meet in the Carpathian Basin resulting in a narrow contact zone in the foothill regions, where hybrids often appear. Our aim was to explore a transient zone between B. bombina and B. variegata within the Carpathian Basin along a transect including the Börzsöny Hills in Hungary and Krupinská Planina in Slovakia. We visited 28 locations in these areas and collected altogether 230 specimens, photographed and sampled them using buccal swabs. In order to distinguish between the two species and determine hybrid individuals, we used mitochondrial markers and designed a novel technique based on the restriction of the Ncx-1 gene. The geographical distribution pattern of these two species delivered unexpected results, as Börzsöny Hills was completely colonised by B. bombina including locations which can be classified as typical habitats of B. variegata. Moreover, in Krupinská Planina many locations were also colonised by B. bombina, including high altitude ponds. The most remote sites still harbour B. variegata populations, but seven of these were found with hybrid individuals. This pattern may indicate the northward and altitudinal range expansion of B. bombina and the colonisation of habitats of its sister species in these areas. Our results warrant enhanced attention to hybrid zones, where introgression and changes in population composition may reflect recent rapid environmental alterations and redirect conservation focus.

A Global Analysis of Y-STR INRA189 Polymorphism in Chinese Domestic Yak Breeds/Populations

The objective of this study was to probe into the polymorphism of Y-STR INRA189 and identify the geographical distribution pattern of its alleles in the Chinese domestic yak gene pool. We examined the variation at INRA189 locus in 682 male yaks representing 15 breeds/populations in China. The results showed that six alleles, including five reported previously (149, 155, 157, 159, and 161 bp) and a new one identified in this study (139 bp), were detected at INRA189 locus based on genotyping analysis. The frequencies of six alleles varied among the 15 yak breeds/populations with a clear phylogeographical pattern, which revealed the paternal genetic difference among Chinese yak breeds/populations. The average polymorphism information content (PIC) among the 15 yak breeds/populations was 0.32, indicating INRA189 to be an intermediate polymorphic Y-STR marker (0.25 < PIC < 0.5) in yak. Sequence alignment revealed that the variations among six alleles at INRA189 were defined by a TG dinucleotide repeat motif, which repeated for 12, 17, 20, 21, 22, and 23 times, corresponding to the alleles of 139, 149, 155, 157, 159, and 161 bp, respectively. Therefore, we believe that the polymorphic yak Y-STR INRA189 can be used to characterize male-mediated genetic events, including paternal genetic origin, diversity, and evolution.

Integrating Phylogeographic Analysis and Geospatial Methods to Infer Historical Dispersal Routes and Glacial Refugia of Liriodendron chinense

Liriodendron chinense (Hemsl.), a Tertiary relic tree, is mainly distributed in subtropical China. The causes of the geographical distribution pattern of this species are poorly understood. In this study, we inferred historical dispersal routes and glacial refugia of this species by combining genetic data (chloroplast DNA (cpDNA), nuclear ribosomal DNA (nrDNA), and nuclear DNA (nDNA)) and geospatial data (climate and geology) with the methods of landscape genetics. Additionally, based on sequence variation at multiple loci, we employed GenGIS and Barrier software to analyze L. chinense population genetic structure. Dispersal corridors and historical gene flow between the eastern and western populations were detected, and they were located in mountainous regions. Based on species distribution model (SDMs), the distribution patterns in paleoclimatic periods were consistent with the current pattern, suggesting the presence of multiple refuges in multiple mountainous regions in China. The genetic structure analysis clustered most eastern populations into a clade separated from the western populations. Additionally, a genetic barrier was detected between the eastern and western populations. The dispersal corridors and historical gene flow detected here suggested that the mountains acted as a bridge, facilitating gene flow between the eastern and western populations. Due to Quaternary climatic fluctuations, the habitats and dispersal corridors were frequently inhabited by warm-temperate evergreen forests, which may have fragmented L. chinense habitats and exacerbated the differentiation of eastern and western populations. Ultimately, populations retreated to multiple isolated mountainous refugia, shaping the current geographical distribution pattern. These dispersal corridors and montane refugia suggested that the mountains in subtropical China play a crucial role in the conservation of genetic resources and migration of subspecies or related species in this region.