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With the increasing importance of X-chromosome (Chr-X) genotyping in kinship identification, the exploitation of X chromosome genetic marker multiplex kits is increasing. The Human X-InDels amplification kit is a novel developed system which contained 38 X-chromosomal Insertion/deletion markers (X-InDels) and Amelogenin. Herein, we investigated the genetic diversity of the 38 X-InDels in the Tibetan ethnic minority (n = 792) from seven regions and evaluated the application potential of this novel panel. The rs16368 was the least variable locus, whereas the most polymorphic locus was the rs59605609 in Tibetan population. We confirmed three linkage groups with the haplotype diversities ranged from 0.5032 to 0.5976. The overall combined power of discrimination (PD) in males and females were 0.999999999582066 and 0.999999999999993, respectively. And the overall combined mean exclusion chance (MEC) values were not lower than 0.999125526990159. In addition, we explored the genetic relationships among the Tibetans in seven different regions via series of population comparison analyses, finding that the genetic relationship between the Ngari Tibetan and Chamdo Tibetan was the farthest, which was consistent with geographical distribution., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Objectives: To characterize the presence and genetic environment of the multiresistance gene cfr in bacterial isolates from a swine farm.Methods: A total of 97 bacterial isolates, recovered from 32 faecal swabs obtained on one farm, were tested for the presence of the cfr gene by PCR. Species identification of the one cfr-positive strain was conducted using the BD PhoenixTM 100 Automated Microbiology System. Susceptibility testing was carried out by broth microdilution. The genetic environment of the cfr gene was analysed by WGS.Results: The Morganella morganii isolate BCMM24 was the only cfr-positive strain. The cfr gene, as well as 15 other resistance genes, is located on a novel 111238 bp transposon derived from Tn7, designated as Tn6451, which comprises various genetic materials including a novel class 1 integron with five gene cassettes. The cfr-containing region consists of a novel genetic structure IS26-cfr-ΔTn554 tnpB-ΔTn3 family tnpA-IS26, differing from previous reports. Two-step PCR results show that the structure can be looped out and that Tn6451 cannot be excised from the chromosome.Conclusions: To the best of our knowledge, we report the cfr gene in M. morganii for the first time. The cfr gene and 15 other resistance genes are located on a novel Tn7 transposon derivative, suggesting that the Tn7 transposon may act as a reservoir for various antimicrobial resistance genes and more Tn7 derivatives carrying multiple resistance genes are likely to be discovered in Gram-negative bacteria of both animal and human origin. [ABSTRACT FROM AUTHOR]

Background: Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos is one of the few wild orchids with high ornamental value in northern China. However, over the past decade, excessive collection, trading, tourism development, habitat fragmentation, deceptive pollination, and seed germination difficulties have all caused a sharp decline in the number of C. macranthos individuals and its population. In order to propose a scientific and effective conservation strategy, the genetic diversity, genetic structure and gene flow of the current CM population are urgent scientific issues to be clarified., Results: Here, 99 individuals of C. macranthos from north and northeast China were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gb high-quality clean reads and 41,154 SNPs were obtained. Our data based on bioinformatics methods revealed that C. macranthos has lower genetic diversity, high levels of historical gene flow, and moderate-to-high genetic differentiation between populations. The gene migration model revealed that the direction of gene flow was mainly from northeast populations to north populations in China. The results of genetic structure analysis showed that 11 C. macranthos populations can be considered as two groups, and further divided into four subgroups. Moreover, the Mantel test detected no significant "Isolation by Distance" between populations., Conclusions: Our study demonstrates that the present genetic diversity and genetic structure of C. macranthos populations were mainly caused by biological characteristics, human interference, habitat fragmentation, and restricted gene flow. Finally, constructive measures, which can provide a basis for the proposal of conservation strategies, have been suggested., (© 2023. The Author(s).)

Background: Mosquito control is needed to prevent dengue fever, which is mainly spread by Aedes albopictus in China. Application of insecticides is one of the main mosquito control methods; however, this approach can fail due to the knockdown resistance (kdr) gene mutation that causes decreased sensitivity to insecticides in Ae. albopictus. The kdr mutation patterns among different regions in China differ significantly. However, the underlying mechanism and factors that influence kdr mutation remain unclear. To explore the potential influence of genetic background on the development of insecticide resistance in Ae. albopictus, we analyzed the genetic structure of Ae. albopictus populations in China and its correlation with major kdr mutations., Methods: We collected Ae. albopictus from 17 sites in 11 provinces (municipalities) across China from 2016 to 2021 and extracted the genomic DNA from individual adult mosquitoes. We selected eight microsatellite loci for genotyping, and based on microsatellite scores, we estimated intraspecific genetic diversity, population structure, and effective population size. The association between the intrapopulation genetic variation and F1534 mutation rate was evaluated by the Pearson correlation coefficient., Results: Based on variation analysis of the microsatellite loci of 453 mosquitoes representing 17 populations throughout China, more than 90% of the variation occurred within individuals, whereas only about 9% of the variation occurred among populations, indicating that field populations of Ae. albopictus are highly polymorphic. The northern populations tended to belong to gene pool I (BJFT 60.4%, SXXA 58.4%, SDJN 56.1%, SXYC 46.8%), the eastern populations tended to belong to pool III (SH 49.5%, JZHZ 48.1%), and the southern populations tended to belong to three different gene pools. Moreover, we observed that the greater the fixation index (F ST ), the lower the wild-type frequency of F1534 of VSGC., Conclusions: The degree of genetic differentiation among Ae. albopictus populations in China was low. These populations were divided into three gene pools, in which the northern and eastern pools are relatively homogeneous, while the southern gene pool is heterogeneous. The possible correlation between its genetic variations and kdr mutations is also noteworthy., (© 2023. The Author(s).)

Massive actions have been and are being taken into protecting the world's primates from extinction, while the study of the properties of genetic diversity, demographic history, and ecological relationships will benefit the understanding of the long-term survival of a species. The Taihangshan macaque (Macaca mulatta tcheliensis), a subspecies of rhesus macaque (Macaca mulatta), is endemic to China and currently restricted to southern Mt. Taihangshan area. Herein, we evaluated the genetic diversity, population structure, and demographic history of this subspecies using mitochondrial (Cytb and high variable region I: HVR I) and nuclear markers (microsatellite loci) of 131 individuals collected from 9 localities covering the distribution range of this subspecies. Both phylogenetic analyses and genetic assignment revealed that the wild populations of Taihangshan macaques could be divided into 2 major highly divergent clades, THS-east and THS-west. Low genetic diversity (π: 0.00266 ± 0.00016) but high haplotype diversity (H d : 0.80352 ± 0.015) were detected in the Taihangshan macaques, particularly in THS-east. Analyses of demographic history suggested that the Taihangshan macaques experienced first a stable historical population size from Holocene to early 19th century but a subtle decline and then slight growth in the recent 200 years. We suggest that bridging the neighbor populations (i.e. setting corridors) would facilitate the male-mediated gene flow and subsequently increase the genetic diversity of the Taihangshan macaque populations., (© 2022 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.)

Background: The evergreen broadleaved forest (EBLF) is an iconic vegetation type of East Asia, and it contributes fundamentally to biodiversity-based ecosystem functioning and services. However, the native habitat of EBLFs keeps on decreasing due to anthropogenic activities. Ormosia henryi is a valuable rare woody species in EBLFs that is particularly sensitive to habitat loss. In this study, ten natural populations of O. henryi in southern China were sampled, and then genotyping by sequencing (GBS) was applied to elucidate the standing genetic variation and population structure of this endangered species., Results: In ten O. henryi populations, 64,158 high-quality SNPs were generated by GBS. Based on these markers, a relatively low level of genetic diversity was found with the expected heterozygosity (He) ranging from 0.2371 to 0.2901. Pairwise F ST between populations varied from 0.0213 to 0.1652, indicating a moderate level of genetic differentiation. However, contemporary gene flow between populations were rare. Assignment test and principal component analysis (PCA) both supported that O. henryi populations in southern China could be divided into four genetic groups, and prominent genetic admixture was found in those populations located in southern Jiangxi Province. Mantel tests and multiple matrix regression with randomization (MMRR) analyses suggested that isolation by distance (IBD) could be the possible reason for describing the current population genetic structure. In addition, the effective population size (Ne) of O. henryi was extremely small, and showed a continuous declining trend since the Last Glacial Period., Conclusions: Our results indicate that the endangered status of O. henryi is seriously underestimated. Artificial conservation measures should be applied as soon as possible to prevent O. henryi from the fate of extinction. Further studies are needed to elucidate the mechanism that leading to the continuous loss of genetic diversity in O. henryi and help to develop a better conservation strategy., (© 2023. The Author(s).)

Gekko japonicus , i.e., Schlegel's Japanese Gecko, is an important species which is widely distributed in East Asia. However, the information about population genetics of this species from China remains unclear. To address this issue, we used sequences from a fragment of the mitochondrial protein-coding gene cytochrome c oxidase I to estimate genetic diversity, genetic structure, and historical demography of G. japonicus populations from China. Phylogenetic analysis indicated that G. japonicus had a close relationship with Gekko wenxianensis . A total of 14 haplotypes were obtained, of which haplotype 1 was the most common and widely distributed. The genetic diversity of G. japonicus was comparatively low across different geographic populations. The populations of G. japonicus were divided into four groups which exhibited low levels of genetic differentiation, and expressed an unclear pattern of population structuring. In addition, potential population expansion of G. japonicus has occurred as well. Overall, these results demonstrate that the populations of G. japonicus reveal low genetic diversity in China, which is attributed to the founder and bottleneck events among populations. Our results will provide meaningful information on the population genetics of G. japonicus and will provide some insights into the study of origin of populations.

Introduction: Since the second half of the 20th century, Aedes albopictus , a vector for more than 20 arboviruses, has spread worldwide. Aedes albopictus is the main vector of infectious diseases transmitted by Aedes mosquitoes in China, and it has caused concerns regarding public health. A comprehensive understanding of the spatial genetic structure of this vector species at a genomic level is essential for effective vector control and the prevention of vector-borne diseases., Methods: During 2016-2018, adult female Ae. albopictus mosquitoes were collected from eight different geographical locations across China. Restriction site-associated DNA sequencing (RAD-seq) was used for high-throughput identification of single nucleotide polymorphisms (SNPs) and genotyping of the Ae. albopictus population. The spatial genetic structure was analyzed and compared to those exhibited by mitochondrial cytochrome c oxidase subunit 1 ( cox 1) and microsatellites in the Ae. albopictus population., Results: A total of 9,103 genome-wide SNP loci in 101 specimens and 32 haplotypes of cox 1 in 231 specimens were identified in the samples from eight locations in China. Principal component analysis revealed that samples from Lingshui and Zhanjiang were more genetically different than those from the other locations. The SNPs provided a better resolution and stronger signals for novel spatial population genetic structures than those from the cox 1 data and a set of previously genotyped microsatellites. The fixation indexes from the SNP dataset showed shallow but significant genetic differentiation in the population. The Mantel test indicated a positive correlation between genetic distance and geographical distance. However, the asymmetric gene flow was detected among the populations, and it was higher from south to north and west to east than in the opposite directions., Conclusions: The genome-wide SNPs revealed seven gene pools and fine spatial genetic structure of the Ae. albopictus population in China. The RAD-seq approach has great potential to increase our understanding of the spatial dynamics of population spread and establishment, which will help us to design new strategies for controlling vectors and mosquito-borne diseases., 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 © 2022 Wei, He, Wang, Fan, He, Hu, Chen, Zhou, Zhong and Zheng.)

The aim of the study was to better understand the genetic characteristics of the Miao group in China. Herein, genetic characteristics and forensic application values of 57 autosomal insertion-deletion (InDel) loci were investigated in 210 unrelated healthy individuals from the Chinese Yunnan Miao (YM) group. Meanwhile, the genetic differences in these InDels were compared among the YM group and 26 reference populations. The results of forensic statistical analyses showed that all 57 autosomal InDels were in accordance with the Hardy-Weinberg and linkage equilibria of pairwise loci in the Chinese YM group. Moreover, the combined probability of discrimination and probability of exclusion in the YM group were 0.9999999999999999999999801 and 0.999928, respectively, which indicated that the multiplex amplification including 57 autosomal InDels was suitable for forensic individual identification and paternity testing in the Chinese YM group. In addition, the results of allelic frequency distribution differential analyses, principal component analyses, phylogenetic tree reconstruction, and genetic structure analyses between the Chinese YM group and 26 reference populations revealed that the genetic similarities between the YM group and East Asian populations were more than that between the YM group and other geographical populations. This 57 autosomal InDels system can also effectively distinguish East Asian, European, and African populations., (© 2022 Wiley-VCH GmbH.)

Alternaria alternata is an opportunistic human fungal pathogen and a ubiquitous phytopathogen capable of causing diseases to >100 agricultural crops and ornamental plants. To control plant diseases caused by A. alternata, triazole fungicides have been widely used both in open crop and vegetable fields and in indoor growth facilities such as greenhouses. At present, the effect of fungicide use on triazole resistance development in A. alternata populations is not known. Here, we isolated 237 A. alternata strains from nine greenhouses around metropolitan Kunming in Yunnan, southwest China, determined their genotypes using 10 short tandem repeat markers, and quantified their susceptibility to four triazoles (difenoconazole, tebuconazole, itraconazole, and voriconazole). Abundant allelic and genotypic diversities were detected among these A. alternata strains. Significantly, over 17% of the strains were resistant to difenoconazole, and both known and new drug-resistance mutations were found in the triazole target gene cyp51 . Our findings of high-level genetic variation of A. alternata in greenhouses coupled with high-frequency fungicide resistance call for greater attention to continued monitoring and to developing alternative plant fungal disease management strategies in greenhouses. IMPORTANCE Alternaria alternata is among the most common fungi in our environments, such as indoor facilities, the soil, and outdoor air. It can cause diseases in >100 crop and ornamental plants. Furthermore, it can cause human infections. However, our understanding of its genetic diversity and antifungal susceptibility is very limited. Indeed, the critical threshold values for resistance have not been defined for most antifungal drugs in this species. Greenhouses are known to have heavy applications of agricultural fungicides. In this study, we analyzed strains of A. alternata from nine greenhouses near metropolitan Kunming in southwestern China. Our study revealed very high genetic diversity and identified strains with high MIC values against two agricultural and two medical triazole antifungals within each of the nine greenhouses. Our study calls for greater attention to this emerging threat to food security and human health.

Living in the heart of Eurasia, the Kyrgyz ethnic minority have a complex human evolutionary and migration history. However, the genetic architecture of the Kyrgyz population has not been fully explored. We studied 526 Kyrgyz samples from Kizilsu Kirghiz Autonomous Prefecture in Xinjiang using the Investigator® DIPplex kit. All loci followed Hardy-Weinberg equilibrium (HWE). The combined power of discrimination (CPD) and combined power of paternity exclusion (CPE) was 0.9999999999988 and 0.9936, respectively. Compared with 90 reference populations, five InDels (HLD99, HLD81, HLD64, HLD118, and HLD111) have the potential to distinguish the Kyrgyz/Uyghur/Kazak population from other East Asian populations. Our results suggested a close genetic relationship between the Kyrgyz population and the Uyghur/Kazak populations, followed by South Asian populations. This was in accordance with the inland migration hypothesis or modern human migration influenced by warfare. Overall, this system can be used as a powerful tool in forensic individual identification and as a complementary tool in paternity cases and biogeographic ancestry analyses., (© 2020. Springer-Verlag GmbH Germany, part of Springer Nature.)

Understanding the genetic diversity and habitat adaptation patterns of different geographic populations of marine organisms is essential for the rational maintenance, development, and utilization of their resources. Pampus minor Liu and Li 1998 is an economically valuable marine fish species. To determine the population genetic structure and elucidate the genetic mechanism underlying the habitat adaptation of this species, restriction site-associated DNA sequencing (RAD-seq) was used to scan the whole genomes of three P. minor putative populations along the coast of China for single-nucleotide polymorphism (SNPs) and outlier SNPs. Our population genetic structure analysis based on 2388 SNPs and 731 outlier SNPs throughout the genome revealed no significant genetic differentiation among the three populations. Results suggested that the life-cycle characteristics of P. minor, its relatively large population sizes, and ocean current transport might have shaped its current genetic pattern. The annotation information of both assembled sequences (which included outlier SNPs) and candidate loci associated with adaptations indicated that genes involved in many processes, including ion exchange, osmotic pressure regulation, metabolism, and the immune response, have been very important in the adaptations of P. minor to its heterogeneous habitats. Against the background of increased human activities, increased fishing intensity, and destruction of marine habitats, the results of this study provide basic genetic information for the accurate division of protection units of P. minor., (Copyright © 2021. Published by Elsevier Inc.)

The demersal brown banded bamboo shark Chiloscyllium punctatum is a major component of sharks landed in Malaysia. However, little is known about their population structure and the effect of high fishing pressure on these weak swimming sharks. Both mitochondrial DNA control region (1072 bp) and NADH dehydrogenase subunit 2 (1044 bp) were used to elucidate the genetic structure and connectivity of C. punctatum among five major areas within the Sundaland region. Our findings revealed (i) strong genetic structure with little present day mixing between the major areas, (ii) high intra-population genetic diversity with unique haplotypes, (iii) significant correlation between genetic differentiation and geographical distance coupled with detectable presence of fine scale geographical barriers (i.e. the South China Sea), (iv) historical directional gene flow from the east coast of Peninsular Malaysia towards the west coast and Borneo, and (v) no detectable genetic differentiation along the coastline of east Peninsular Malaysia. Genetic patterns inferred from the mitochondrial DNA loci were consistent with the strong coastal shelf association in this species, the presence of contemporary barriers shaped by benthic features, and limited current-driven egg dispersal. Fine scale population structure of C. punctatum highlights the need to improve genetic understanding for fishery management and conservation of other small-sized sharks., (© 2021. The Author(s).)

In this issue of Cell, Wang et al. harness ancient DNA methods to produce and analyze new genomic data from 31 individuals from South China, dated between 500 and 10,000-12,000 years ago. The study reveals a complex interplay between groups of three different genetic ancestries and provides a new perspective on interactions and agricultural dispersals in South China and Southeast Asia., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Ancestry informative markers have extensive uses and advantages in inferring ancestral origins and estimating ancestral genetic information components of admixed populations. With the characteristics of highly cultural exchange and the admixed genetic structure of the Kyrgyz group, it is essential to enrich the genetic data of the Kyrgyz group. In this study, we used a self-developed ancestry informative marker-deletion/insertion polymorphic (AIM-DIP) panel to explore ancestral components of Chinese Kyrgyz group and population genetic relationships between the Kyrgyz group and reference populations. Results showed that all AIM-DIP loci were conformed to Hardy-Weinberg equilibrium. There were 36 AIM-DIP loci that contributed significantly to genetic information inference. Multiple statistical analyses revealed that Chinese Kyrgyz group had a closer genetic relationship with Chinese Uyghur group. The ancestral components of the Kyrgyz group, being mostly composed of genetic components of European and East Asian populations, were more similar to the ancestral components of Chinese Uyghur group., (Copyright © 2021 Elsevier Inc. All rights reserved.)

With the rapid degradation of coral reefs due to global warming and anthropogenic impacts, relatively high-latitude areas, such as the northern South China Sea (SCS), are likely to become refuges for tropical coral species. Here we investigated the genetic features and adaptability of one dominant scleractinian coral species, Turbinaria peltata, in the northern SCS. A total of 81 samples from 5 sites were studied to explore potential mechanisms of adaptability to environmental stress as a result of climate change. Ten microsatellite markers developed in this study, one nuclear gene (internal transcribed spacer, ITS), and one mitochondrial gene (mitochondrial cytochrome oxidase subunit I gene, mtDNA COI) were used. Our results indicated that the genetic diversity of T. peltata in the northern SCS is low (A r  = 1.403-2.011, H o  = 0.105-0.248, H e  = 0.187-0.421) with the lowest in Dongfang population (DF) (A r  = 1.403, H o  = 0.22, H e  = 0.187). These results indicate that T. peltata has insufficient genetic adaptability and may unable to handle increasingly complex global changes. A significantly moderate genetic differentiation was observed among T. peltata populations (Φ ST  = 0.167), in addition to a high genetic differentiation between DF and other populations (F ST  = 0.272-0.536 > 0.25). The DF population near a fishing port was exposed to severe anthropogenic environmental stress, which may drive the extraordinarily high genetic differentiation between DF and other populations. Furthermore, the Mantel test results showed that the genetic differentiation of the other four populations was strongly correlated with the average sea surface temperature (SST) (R 2  = 0.82, Mantel test P < 0.05) and geographical distance (R 2  = 0.57, Mantel test P < 0.05). Our results suggest that the genetic structure of T. peltata in the relatively high-latitude of the SCS was significantly affected by average SST, geographical isolation, and anthropogenic activities. These findings provide a theoretical foundation for the protection of relatively high-latitude coral reefs., Competing Interests: Declaration of competing interest We declare we have no competing interests., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Background: Strongyllodes variegatus (Fairmaire) is a major insect pest of oilseed rape in China. Despite its economic importance, the contribution of its population genetics in the development of any suitable protection control strategy for the management of oilseed rape crops is poorly studied. It is a much urgent need to prevent its spread to the rest of the world., Results: Using the sequences of mitochondrial DNA cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) as genetic markers, we analyzed the population genetic diversity and structure of 437 individuals collected from 15 S. variegatus populations located in different oilseed rape production areas in China. In addition, we estimated the demographic history using neutrality test and mismatch distribution analysis. The high level of genetic diversity was detected among the COI and Cytb sequences of S. variegatus. The population structure analyses strongly suggested three distinct genetic and geographical regions in China with limited gene flow. The Mantel test showed that the genetic distance was greatly influenced by the geographical distance. The demographic analyses showed that S. variegatus had experienced population fluctuation during the Pleistocene Epoch, which was likely to be related to the climatic changes., Conclusion: Overall, these results demonstrate that the strong genetic structure of S. variegatus populations in China, which is attributed by the isolation through the geographical distance among populations, their weak flight capacity and subsequent adaptation to the regional ecological conditions.

Background: Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim. (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants., Results: In this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity, and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of a north to south migration pattern in history., Conclusions: This study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve. In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.

A total of 64 haplotypes were obtained from the complete Cytochrome b gene (Cyt b) of 77 Sorex isodon collected from three populations (Daxing'anling, Xiaoxing'anling, and Changbai Mountains) in Northeast China. The haplotype diversity was 0.9920 and the nucleotide diversity was 0.0105, indicating high genetic diversity. The genetic diversity of Changbai Mountains population was significantly higher than that of Daxing'anling and Xiaoxing'anling populations. The F-statistics, the number of migrants per generation and the genetic distance results showed that the genetic distances among the populations and among the sampling sites were generally consistent with geographical distance. Analysis of molecular variance showed that the differentiation among populations, among sampling sites, and within sampling site accounted for 33.4%, 10.2% and 56.4% of total variation, respectively. The analysis of population history showed that S. isodon in Northeast China experienced no population expansion. The reported complete sequence of Cyt b gene of S. isodon (GenBank) of Europe and other parts of Asia was downloaded to examine the genetic structure of S. isodon. The phylogenetic tree was divided into two large branches. One branch consisted mainly of Daxing'anling and Xiaoxing'anling samples. The other branch was departed into two sub-branches. Median-joining network analysis showed that there were three lineages: one lineage mainly consisted of haplotypes from Daxing'anling and Xiaoxing'anling, and also four haplotypes of Changbai Mountains, while the other lineage included a few haplotypes of three populations in Northeast China, and those from Baikal Lake, Russia and Finland. The last lineage was entirely composed of haplotypes from Changbai Mountains. The results of genetic diversity, phylogenetic tree and median-joining network all suggested that the Changbai Mountains was the refuge for S. isodon during last glacial.

Objective: To describe the genetic structure of populations in different areas of China, and explore the effects of different strategies to control the confounding factors of the genetic structure in cohort studies. Methods: By using the genome-wide association study (GWAS) on data of 4 500 samples from 10 areas of the China Kadoorie Biobank (CKB), we performed principal components analysis to extract the first and second principal components of the samples for the component two-dimensional diagram generation, and then compared them with the source of sample area to analyze the characteristics of genetic structure of the samples from different areas of China. Based on the CKB cohort data, a simulation data set with cluster sample characteristics such as genetic structure differences and extensive kinship was generated; and the effects of different analysis strategies including traditional analysis scheme and mixed linear model on the inflation factor (λ) were evaluated. Results: There were significant genetic structure differences in different areas of China. Distribution of the principal components of the population genetic structure was basically consistent with the geographical distribution of the project area. The first principal component corresponds to the latitude of different areas, and the second principal component corresponds to the longitude of different areas. The generated simulation data showed high false positive rate (λ=1.16), even if the principal components of the genetic structure was adjusted or the area specific subgroup analysis was performed, λ could not be effectively controlled (λ>1.05); while, by using a mixed linear model adjusting for the kinship matrix, λ was effectively controlled regardless of whether the genetic structure principal component was further adjusted (λ=0.99). Conclusions: There were large differences in genetic structure among populations in different areas of China. In molecular epidemiology studies, bias caused by population genetic structure needs to be carefully treated. For large cohort data with complex genetic structure and extensive kinship, it is necessary to use a mixed linear model for association analysis.

X-chromosome short tandem repeat markers (X-STRs), due to their special inheritance models, physical location on a single chromosome and the absence of recombination in male meiosis, play an important role in forensic and population genetics. While a series of genetic analyses focusing on the genetic diversity and forensic characteristics of X-STRs are well studied for ethnically/linguistically diverse and demographically large Chinese populations, genetic evidence from Gelao ethnicity is still sparse. Here, we genotyped the first batch of 19 X-STRs in 513 Chinese Gelao individuals (265 females and 248 males), and reported genetic polymorphisms, forensic characteristics based on the single locus and seven linkage groups. DXS10135 with the highest PIC (0.9106) and LG1 (DXS10148-DXS10135-DXS8378) with the largest HD (0.9970) are polymorphic and informative. The CPDs in Gelao males and females are respectively larger than 0.999999999997095 and 0.99999999999999999999918, and the combined MECs are larger than 0.999999975715109. Subsequently, we investigated the population relationships among 14 Chinese populations based on 19 X-STRs and among 23 populations based on 11 overlapped X-STRs. Our results revealed genetic differentiations among Tibeto-Burman, Altaic and other Chinese homogenous populations, and demonstrated that Guizhou Gelao has the genetically closer relationships with Han Chinese and geographically close Guizhou Miao.

Harmonia axyridis, one of the most important insect predators, has been widely used in biological control in agriculture. In this study, the mitochondrial COII gene was used as genetic marker to investigate the genetic structure and diversity of H. axyridis geographic populations distributed in Shaanxi Province. Level of genetic differentiation and gene flow among different populations of H. axyridis were analyzed. For all the 529 H. axyridis individuals from 21 populations, 15 haplotypes were observed (named as Hap1-Hap15). Hap1 and Hap2 were dominant haplotypes in all sampled individuals, accounting for 34.4% and 37.6% respectively. The overall haplotype diver-sity was 0.732, and it ranged from 0.652 to 0.786 within population. The average gene flow (N m ) among 21 populations was 10.13, and the overall F ST value was 0.024, implying low genetic diffe-rentiation among all populations. Results from neutrality tests suggested that H. axyridis populations followed the neutral evolution model and the population size remained stable. Molecular variance analysis (AMOVA) showed high proportion of total genetic variance attributed to variations within populations. Phylogenetic tree based on Nei's genetic distance of different geographic populations showed clear divergence between northern, central, and southern Shaanxi groups. Results from Mantel test suggested that the genetic distance was weakly correlated with geographical distance between populations. Geographical pattern of genetic structure and diversity in populations from different regions indicated weak gene flow between northern, central, and southern Shaanxi due to Qinling Mountains barrier and climate difference.

The phylogeographic structure of the land snail Camaena cicatricosa was analyzed in this study based on mitochondrial gene (COI and 16srRNA, mt DNA) and internal transcribed spacer (ITS2) sequences in 347 individuals. This snail is the vector of the zoonotic food-borne parasite Angiostrongylus cantonensis and one of the main harmful snails distributed exclusively in China. The results revealed significant fixation indices of genetic differentiation and high gene flow between most populations except several populations. An isolation-by-distance test showed no significant correlation between genetic distance and geographical distance among C. cicatricosa populations, which suggested that gene flow was not restricted by distance. The levels of haplotype and nucleotide diversity of C. cicatricosa were generally high, except those in some special populations, according to the mt DNA and ITS2 data. Furthermore, the phylogenetic trees and asteroid networks of haplotypes indicated nonobvious genetic structure, the same as results got based on the synonymous and non synonymous sites of 347 sequences of the COI gene. All lines of evidence indicated that climatic changes and geographical and human barriers do not substantially affect the current population structure and distribution of the investigated snails.

Background: Turnip mosaic virus (TuMV) is one of the most widespread and economically important virus infecting both crop and ornamental species of the family Brassicaceae. TuMV isolates can be classified to five phylogenetic lineages, basal-B, basal-BR, Asian-BR, world-B and Orchis., Results: To understand the genetic structure of TuMV from radish in China, the 3'-terminal genome of 90 TuMV isolates were determined and analyzed with other available Chinese isolates. The results showed that the Chinese TuMV isolates from radish formed three groups: Asian-BR, basal-BR and world-B. More than half of these isolates (52.54%) were clustered to basal-BR group, and could be further divided into three sub-groups. The TuMV basal-BR isolates in the sub-groups I and II were genetically homologous with Japanese ones, while those in sub-group III formed a distinct lineage. Sub-populations of TuMV basal-BR II and III were new emergent and in a state of expansion. The Chinese TuMV radish populations were under negative selection. Gene flow between TuMV populations from Tai'an, Weifang and Changchun was frequent., Conclusions: The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China.

Water chestnut beetle (Galerucella birmanica Jacoby) is a pest of the water chestnut (Trapa natans L.). To analyze the phylogeny and biogeography of the beetle and provide evidence for the origin of T. natans in China, we conducted this by using three mitochondrial genes (COI, COII and Cytb) and nuclear ITS2 ribosomal DNA of G. birmanica. As for mtDNA genes, the beetle could be subdivided into three groups: northeastern China (NEC), central-northern-southern China (CC-NC-SC) and southwestern China (SWC) based on SAMOVA, phylogenetic analyses and haplotype networks. But for ITS2, no obvious lineages were obtained but individuals which were from NEC region clustered into one clade, which might be due to sequence conservation of ITS2. Significant genetic variation was observed among the three groups with infrequent gene flow between groups, which may have been restricted due to natural barriers and events in the Late Pleistocene. Based on our analyses of genetic variation in the CC-NC-SC geographical region, the star-like haplotype networks, approximate Bayesian computation, niche modelling and phylogeographic variation of the beetle, we concluded that the beetle population has been lasting in the lower, central reaches of the Yangtze River Basin with its host plant, water chestnut, which is consistent with archaeological records. Moreover, we speculate that the CC-NC-SC population of G. birmanica may have undergone a period of expansion coincident with domestication of the water chestnut approximately 113,900-126,500 years ago.

Puccinia striiformis f. sp. tritici is the causal pathogen of interregional epidemics of wheat stripe rust in China via long-distance migration. Gansu Province serves as putative inoculum center providing oversummering inoculum, while Sichuan Basin area serves as a region providing huge amounts of overwintering inoculum. Thus, the relationship between these two regions in population exchange and migration become important in prediction of interregional epidemics. In this study, we compared the population genetic structure and race composition between Gansu and Sichuan Basin populations to infer their migration relationships. A total of 526 isolates, spanning 3 years, were genotyped using eight pairs of amplified fragment length polymorphism markers, and a subset of 98 isolates were inoculated onto 19 Chinese differentials to perform the race analysis. Twenty-three common races and 26 shared genotypes supplied molecular evidence for migration between Gansu and Sichuan Basin populations. Bayesian assignment and principal component analysis revealed that the genetic group assignment of the Sichuan Basin populations (10SB and 11SB) changed in the spring to align with the fall Gansu populations in the prior seasons (09GS and 10GS), which indicated an asymmetric migration from Gansu Province to the Sichuan Basin area. The linkage disequilibrium and the parsimony tree length permutation test revealed a strong annual recombination signal in the Gansu populations and an inconsistent signal in the Sichuan Basin populations.

The maternally inherited obligate bacteria Wolbachia is known for infecting the reproductive tissues of a wide range of arthropods. In this study, we surveyed Wolbachia infections in Polytremis nascens (Lepidoptera: Hesperiidae) from 14 locations in China by amplifying the 16S rRNA gene with a nested PCR method and revealed the effect of Wolbachia on host mitochondrial DNA. The results show that 31% (21/67) are Wolbachia positive among all specimens and mainly prevails in southern populations in China. No significant difference in the prevalence is found between the sexes. Notably, the nucleotide diversity of Wolbachia infected butterflies is smaller compared to that of uninfected butterflies. The mitochondrial DNA of infected group appear to be not evolving neutrally (Tajima's D value=-2.3303 and Fu's F values=-3.7068). The analysis of molecular variance shows significant differentiation of mitochondrial haplotypes between infected and uninfected specimens (FST=0.6064). The mismatch analysis speculated the different expansion pattern in Wolbachia infected specimens and all P. nascens specimens. These results suggest that the populations of P. nascens may have recently been subjected to a Wolbachia-induced sweep. Additionally, phylogenetic analysis differentiated the mitochondrial haplotypes of P. nascens into three major clades. The clades are in perfect agreement with the pattern of Wolbachia infection. One of the clades grouped with the butterflies infected with Wolbachia. The remaining two clades grouped with uninfected butterflies from the central-west of China populations and Eastern and Southern China populations respectively, which are isolated mainly by the Yangtze River. The analysis of haplotype networks, geographic distribution and population size change shows that Haplotype 1 in central-west of China is the ancestral haplotype and the populations of P. nascens are expanded., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Tick-borne encephalitis virus (TBEV) is transmitted to vertebrates by taiga or forest ticks through bites, inducing disease of variable severity. The reasons underlying these differences in the severity of the disease are unknown. In order to identify genetic factors affecting the pathogenicity of virus strains, we have sequenced and compared the complete genomes of 34 Far-Eastern subtype (FE) TBEV strains isolated from patients with different disease severity (Primorye, the Russian Far East). We analyzed the complete genomes of 11 human pathogenic strains isolated from the brains of dead patients with the encephalitic form of the disease (Efd), 4 strains from the blood of patients with the febrile form of TBE (Ffd), and 19 strains from patients with the subclinical form of TBE (Sfd). On the phylogenetic tree, pathogenic Efd strains formed two clusters containing the prototype strains, Senzhang and Sofjin, respectively. Sfd strains formed a third separate cluster, including the Oshima strain. The strains that caused the febrile form of the disease did not form a separate cluster. In the viral proteins, we found 198 positions with at least one amino acid residue substitution, of which only 17 amino acid residue substitutions were correlated with the variable pathogenicity of these strains in humans and they authentically differed between the groups. We considered the role of each amino acid substitution and assumed that the deletion of 111 amino acids in the capsid protein in combination with the amino acid substitutions R16K and S45F in the NS3 protease may affect the budding process of viral particles. These changes may be the major reason for the diminished pathogenicity of TBEV strains. We recommend Sfd strains for testing as attenuation vaccine candidates.

Premise of the Study: Both historical and contemporary microevolutionary processes greatly influence the genetic patterns of East Asian plant endemics, but the spatial and temporal contexts of these processes remain poorly understood. Here, we investigate the relative influences of historical and contemporary gene flow and drift on the population genetic structure of Kirengeshoma palmata, a perennial herb from East China and South Japan., Methods: We used data from nine polymorphic microsatellite loci to assess the levels of genetic diversity, effective population size, and contemporary and historical gene flow for six of the seven known populations., Key Results: We found high levels of inbreeding and allelic diversity within populations. Both contemporary and historical migration rates among populations were low, and a test of alternate models of population history strongly favored a model of long-term drift-migration equilibrium. We inferred declines in population size ca. 10,000-100,000 yr ago, but failed to detect recent declines. Bayesian clustering divided K. palmata populations into three genetic clusters, two of which were consistent with a glacial refugium hypothesis for two mountain ranges in East China., Conclusions: These results suggest that anthropogenic fragmentation has had little effect on the genetic characteristics of Chinese K. palmata. Rather, past decline in population size due to Late Pleistocene climate change as well as restricted pollen and seed dispersal may have contributed to low levels of both historical and contemporary gene flow, resulting in high genetic differentiation between adjacent mountain ranges due to genetic drift and inbreeding.

To study the population genetic structure and forces driving the evolution of Wheat yellow mosaic virus (WYMV), the nucleotide sequences encoding the coat protein (CP) (297 sequences) or the genome-linked virion protein (VPg) (87 sequences) were determined from wheat plants growing at 11 different locations distributed in five provinces in China. There were close phylogenetic relationships between all sequences but clustering on the phylogenetic trees was congruent with their provenance, suggesting an origin-dependent population genetic structure. There were low levels of genetic diversity, ranging from 0.00035 ± 0.00019 to 0.01536 ± 0.00043 (CP), and 0.00086 ± 0.00039 to 0.00573 ± 0.00111 (VPg), indicating genetic stability or recent emergence of WYMV in China. The results may suggest that founder effects play a role in shaping the genetic structure of WYMV. Between-population diversity was consistently higher than within-population diversity, suggesting limited gene flow between subpopulations (average FST 0.6241 for the CP and 0.7981 for the VPg). Consistent amino acid substitutions correlated with the provenance of the sequences were observed at nine positions in the CP (but none in the VPg), indicating an advanced stage in population structuring. Strong negative (purifying) selection was implicated on both the CP and VPg but positive selection on a few codons in the CP, indicating an ongoing molecular adaptation.

Airborne bacteria emissions from oxidation ditch with rotating aeration brushes were investigated in a municipal wastewater treatment plant in Beijing, China. Microbial samples were collected at different distances from the rotating brushes, different heights above the water surface, and different operation state over a 3-month period (April, May, and June) in order to estimate the seasonal variation and site-related distribution characteristics of the microorganisms present. The concentration of bacterial aerosol was analyzed by culture methods, while their dominant species, genetic structure and diversity were assayed using bio-molecular tools. Results showed that total microbial concentrations were highest in June and lowest in April. The mechanical rotation caused remarkable variation in concentration and diversity of culturable airborne bacteria before and after the rotating brushes. The highest concentration was observed near the rotating brushes (931 ± 129-3,952 ± 730 CFU/m(3)), with concentration decreasing as distance and height increased. Bacterial community polymerase chain reaction and denaturing gradient gel electrophoresis indicated that diversity decreased gradually with increasing height above the water surface but remained relatively constant at the same height. All dominant bacteria identified by DNA sequence analysis belonged to Firmicutes. Pathogenic species such as Moraxella nonliquefaciens and Flavobacterium odoratum were isolated from the bioaerosols. Due to the serious health risks involved, exposure of sewage workers to airborne microorganisms caused by brush aerators should be monitored and controlled.

Objective: Revealed the genetic diversity level and genetic structure characteristics in Sinopodophyllum emodi, a rare and endangered species in China., Method: We detected the genetic polymorphism within and among six wild populations (45 individuals) by the approach of Start Codon Targeted (SCoT) Polymorphism. The associated genetic parameters were calculated by POP-GENE1.31 and the relationship was constructed based on UPGMA method., Result: A total of 350 bands were scored by 27 primers and 284 bands of them were polymorphic. The average polymorphic bands of each primer were 10.52. At species level, there was a high level of genetic diversity among six populations (PPB = 79.27%, N(e) = 1.332 7, H = 0.210 9 and H(sp) = 0.328 6). At population level, the genetic diversity level was low (PPB = 10.48% (4.00% -23.71%), N(e) = 1.048 7 (1.020 7-1.103 7), H = 0.029 7 (0.012 9-0.063 1), H(pop) = 0.046 2 (0.019 9-0.098 6). The Nei's coefficient of genetic differentiation was 0.841 1, which was consistent with the Shannon's coefficient of genetic differentiation (0.849 4). Two calculated methods all showed that most of the genetic variation existed among populations. The gene flow (N(m) = 0.094 4) was less among populations, indicating that the degree of genetic differentiation was higher. Genetic similarity coefficient were changed from 0.570 8 to 0.978 7. By clustering analysis, the tested populations were divided into two classes and had a tendency that the same geographical origin or material of similar habitats clustered into one group., Conclusion: The genetic diversity of samples of S. emodi is high,which laid a certain foundation for effective protection and improvement of germplasm resources.

Chinese cherry (Cerasus pseudocerasus Lindl.) is one of the most economically domestic fruit trees in China. The rich variation of wild Chinese cherry is the most important breeding resource for existing cultivars. In order to reveal the levels and distribution of genetic variation within wild Chinese cherry of Sichuan Province, China, where is rich in wild Chinese cherry, the sequence variation of chloroplast DNA trnQ-rps16 intergenic spacer was analyzed in 145 individuals of all nine existing populations (seven from Sichuan, two from Shanxi and Guizhou provinces) of China. The results showed that trnQ-rps16 sequence were aligned with 13 polymorphic sites (1.87%), including 3 substitutions and 10 indels in 145 individuals, which revealed a low level of genetic diversity (h= 0.562, π= 0.00184). Compared to other regions (h= 0.733, π= 0.00243), a rather lower genetic diversity (h= 0.544, π= 0.00203) was found in the populations from Sichuan, and a large scale of genetic diversity among the seven populations was detected (h= 0-0.708; π= 0-0.00298), ranging from EM (h=0.000, π=0.000) to TL (h=0.708, π=0.00298). The low genetic diversity of populations may be strongly affected by founder effect and bottleneck effect because of the marginal nature, recent reduction, and consequent genetic drift of these populations. In addition, a fairly low genetic differentiation (FST= 0.21573) was found among the studied populations. This suggest that gene flow seems to originate from pronounced seed dispersal abilities of the species and it may play a significant role in shaping such a genetic structure. The long generation cycle of the species may also contribute to this structure. Based on these findings, a conservational plan for sampling or preserving fewer populations but more individuals from each population for the species was proposed.

Premise of the Study: The possible persistence of wild Ginkgo biloba populations in China has long been debated but never scientifically confirmed. We test our hypothesis that the extant Ginkgo populations in the Dalou Mountains (SW China) represent fragments of the original natural Ginkgo range and offer a range of pertinent perspectives on the living fossil Ginkgo's history, prehistory, ecology, and place in human culture-all important aspects of this highly valued species., Methods: We analyzed the vegetation of the study area, determined the population age structure of Ginkgo, and compared it to existing fossil records. For supporting material, we also examined records of the lack of human presence before the mid-17th century in the area, the local people's beliefs regarding preservation of the forests and existing genetic studies., Key Results: Current species composition of Ginkgo forests in the Dalou Mountains agrees closely with floristic assemblages from fossil records bearing G. biloba. Current populations are found in habitats similar to those of fossil Ginkgo, which, as today, favored rock crevices. Female to male ratios are 3:2. Estimated ages for many of the trees show that Ginkgo was present in this area prior to human settlement and indigenous peoples of this area are unlikely to have planted Ginkgo because of traditional beliefs. Our results agree with existing genetic studies that show that these mountains were glacial refugia for G. biloba., Conclusions: The corroborative evidence confirms the finding that these populations represent fragments of the original natural Ginkgo in the valley and lower mountain slopes of the Dalou Mountains.

The endangered perennial plant Saruma henryi Oliv. is endemic to China and has phylogenetic, ecological, and medicinal value. We used 10 microsatellite (SSR) loci to investigate genetic diversity and differentiation in 16 natural populations. Genetic diversity was high at the species level (H(E) = 0.9427, h = 0.9410, I = 3.0213) and low at the population level (H(E) = 0.4441, h = 0.4307, I = 0.6822). Pronounced genetic differentiation was detected among populations (G(ST) = 0.5428, F(ST) = 0.5524), in line with the limited among-population gene flow (Nm = 0.21). The significant isolation-by-distance pattern revealed by a Mantel test (r = 0.311, P = 0.001) suggested a clear geographic tendency in the distribution of genetic variability. Bayesian assignment and principal coordinates analyses supported the clustering of 16 populations into three groups. The present SSR results were also compared with previously published ISSR results. These results have significant implications for conservation of the species.

Michelia coriacea, a critically endangered tree, has a restricted and fragmented distribution in Southeast Yunnan Province, China. The genetic diversity, genetic structure and gene flow in the three extant populations of this species were detected by 10 inter-simple sequence repeat (ISSR) markers and 11 simple sequence repeat (SSR) markers. Examination of genetic diversity revealed that the species maintained a relatively high level of genetic diversity at the species level (percentage of polymorphic bands) PPB = 96.36% from ISSRs; PPL (percentage of polymorphic loci) = 95.56% from SSRs, despite several fragmental populations. Low levels of genetic differentiation among the populations of M. coriacea were detected by Nei's G(st) = 0.187 for ISSR and Wright's F(st) = 0.090 for SSR markers, which is further confirmed by Bayesian model-based STRUCTURE and PCoA analysis that could not reveal a clear separation between populations, although YKP was differentiated to other two populations by ISSR markers. Meanwhile, AMOVA analysis also indicated that 22.84% and 13.90% of genetic variation existed among populations for ISSRs and SSRs, respectively. The high level of genetic diversity, low genetic differentiation, and the population, structure imply that the fragmented habitat and the isolated population of M. coriacea may be due to recent over-exploitation. Conservation and management of M. coriacea should concentrate on maintaining the high level of genetic variability through both in and ex-situ conservation actions.

Objective: To explore the features of genetic differentiation and gene flow of ten minorities in Yunnan province according to nine CODIS short tandem repeat(STR) loci (CSF1PO, FGA, THO1, TPOX, v WA, D3S1358, D5S818, D7S820 and D13S317)., Methods: Heterozygosity and parameters of population differentiation such as F, theta, f and Gst at each locus were calculated. DA genetic distance and fixation index Fst were calculated by Phylip 3.6 and Arlequin 3.0 software, respectively. Phylogenetic trees were constructed by Mega 3.0, and the patterns of gene flow were analyzed by R-matrix model., Results: It showed that average genetic heterogeneity in ten minorities was above 0.7. Significant difference was found for most of the loci in genetic differentiation. Phylogenetic tree analysis showed that the ten minorities were divided into two clusters. The results of the R-matrix analysis showed that the gene flow of Yi and Dai minorities were higher than that of other minorities, while the pattern of gene flow of Dulong minority demonstrated some of the isolation., Conclusion: Nine STR loci commonly used in forensic identification show a high polymorphism. Heterozygosity can be used for investigating genetic differentiation and gene flow of minority. The ten minorities in Yunnan are independent populations, while the level of differentiation is not high. The relationship in evolution is not far from each other and shows a widely gene flow among the minorities.

White muscardine caused by Beauveria bassiana is an important factor affecting sericulture. In the present study, a total of 124 B. bassiana isolates were obtained from the silkworm cadavers, rearing rooms and appliances, surrounding mulberry orchards, pine plantations, and croplands in Jingxian County of south Anhui and Qishan County of southwest Anhui. Together with the mass production strains, the isolates were analyzed for population genetic structure by ISSR markers to trace the origin and the spreading track of the muscardine. The results showed that the two B. bassiana populations in Jingxian County and Qishan County were heterogenic, being monophyletic in Jingxian and polyphyletic in Qishan. Both the Jingxian population and the Qianshan predominant subpopulation were characterized typically by enzootic nature, i.e., low incidence and frequent occurrence, but the Qianshan non-predominant subpopulation could spread among some alternate hosts outside the rearing rooms. The groups prevailing in pine caterpillar populations in the pine plantations of Qianshan and Jingxian, the production strains, and the epizootic strain prevailing in surrounding mantids were all not associated to the silkworm muscardine, displaying safety to sericulture.

Apricot was introduced into the Mediterranean Basin from China and Asian mountains through the Middle-East and the Central Europe. Traditionally present in Tunisia, we were interested in accessing the origin of apricot species in the country, and in particular in the number and the location of its introductions. A set of 82 representative apricot accessions including 49 grafted cultivars and 33 seed propagated 'Bargougs' were genotyped using 24 microsatellite loci revealing a total of 135 alleles. The model-based Bayesian clustering analysis using both Structure and InStruct programs as well as the multivariate method revealed five distinct genetic clusters. The genetic differentiation among clusters showed that cluster 1, with only four cultivars, was the most differentiated from the four remaining genetic clusters, which constituted the largest part of the studied germplasm. According to their geographic origin, the five identified groups (north, centre, south, Gafsa oasis and other oases groups) enclosed a similar variation within group, with a low level of differentiation. Overall results highlighted the distinction of two apricot gene pools in Tunisia related to the different mode of propagation of the cultivars: grafted and seed propagated apricot, which enclosed a narrow genetic basis. Our findings support the assumption that grafting and seed propagated apricots shared the same origin.

China is one of the largest centers of genetic diversity of Oryza sativa L. in the world. Using a genetically representative primary core collection of 3,024 rice landraces in China, we analyzed the genetic structure and intraspecific differentiation of O. sativa, and the directional evolution of SSR. The genetic structure was investigated by model-based structure analysis and construction of neighbor-joining phylogenetic tree. Comparison between genetic structure and predefined populations according to Ting's taxonomic system revealed a hierarchical genetic structure: two distinct subspecies, each with three ecotypes and different numbers of geo-ecogroups within each ecotype. Two subspecies evidently resulted from adaptation to different environments. The different cropping systems imposed on the subspecies led to further differentiation, but the variation within each subspecies resulted from different causes. Indica, under tropical-like or lowland-like environments, exhibited clear differentiation among seasonal ecotypes, but not among soil-watery ecotypes; and japonica showed clear differences between soil water regime ecotypes, but not among seasonal ecotypes. Chinese cultivated rice took on evident directional evolution in microsatellite allele size at several aspects, such as subspecies and geographical populations. Japonica has smaller allele sizes than indica, and this may partly be the result of their different domestication times. Allele size was also negatively correlated with latitude and altitude, and this may be interpreted by different mutation rates, selection pressures, and population size effects under different environments and cropping systems.

Background: Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis) to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow., Results: Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains., Conclusion: The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high elevations, which may significantly contribute to the diminishing barrier effect of mountain ridges. Additionally, a significant decrease in genetic diversity in the peripheral populations supports Mayr's central-peripheral population hypothesis.

General and genetic statistical methods are commonly used to deal with microsatellite data (highly variable neutral genetic markers). In this paper, the self-organizing map (SOM) that belongs to the unsupervised artificial neural networks (ANNs) was applied to analyse the structure of 58 European and two Chinese pig populations (Sus scrofa) including commercial lines, local breeds and cosmopolitan breeds. Results were compared with other unsupervised classification or ordination methods such as factorial correspondence analysis, hierarchical clustering from an allele sharing distance and the Bayesian genetic model and with principal components analysis and neighbour joining from allelic frequencies and genetic distances between populations. Like other methods, SOMs were able to classify individuals according to their breed origin and to visualize similarities between breeds. They provided additional information on the within- and between-population diversity, allowed differences between similar populations to be highlighted and helped differentiate different groups of populations.

Objective: To assess the population genetic diversity and genetic structure and screen species-specific bands for identification of Changium smyrnioides and Chuanminshen violaceum., Method: Seven wild populations of Changium smyrnioides and one cultivated population of Chuanminshen violaceum were studied by ISSR analysis. The population genetic diversity and population genetic structure were assessed by using POPGENE software., Result: A total of 152 ISSR markers were scored, among which 136 (90.8%) were polymorphic. The values of Gst tended to be high (mean Gst = 0.575). The level of genetic divesity of Changium smyrnioides (A = 1.272; P = 27.26%; I = 0.132; H = 0.087) was higher than that of Chuanminshen violaceum (A = 1.217; P = 21.7; I = 0.103; H = 0.067)., Conclusion: The genetic variation of Changium smyrnioides is high and the majority of genetic variation occur among populations. Substantial genetic divergence is shown by cluster analysis (UPGMA) to befound between Changium smyrnioides and Chuanminshen violaceum at DNA level. In addition, one species-specific marker has been obtained in Chuanminshen violaceum. The phylogenetic relationship of two species has also been discussed.