The mussel is one of the main cultivated species in the world.A significant challenge faced by suspension-cultured mussels is the high incidence of mussel fall-off from cultivation ropes,adversely impacting harvest yi...The mussel is one of the main cultivated species in the world.A significant challenge faced by suspension-cultured mussels is the high incidence of mussel fall-off from cultivation ropes,adversely impacting harvest yields,which have been documented at commercial mussel farms in the United Kingdom,the United States of America,Canada,Spain,New Zealand and China.Byssus is an important attachment structure for marine mussels,and weakness in byssal thread attachment is a major factor leading to mussel detachment from ropes.To investigate the relationship between genetic variability and byssal thread phenotypic characteristics in the hard-shelled mussel(Mytilus coruscus),we collected three wild populations of M.coruscus from different latitudes in the East China Sea,including the Shengsi(SS),Jiaojiang(JJ),and Fuding(FD)populations.The genetic diversity and structure of these populations were investigated using 10 microsatellite loci.The mean observed heterozygosity(Ho)in the SS population was 0.44,higher than the mean Ho values of the JJ(0.40)and FD(0.39)populations.The mean inbreeding coefficients(F_(is))in the SS population was 0.20,lower than the mean F_(is)values of the JJ(0.33)and FD populations(0.40).These results revealed that the SS population exhibited higher genetic diversity compared to the other two populations.The different numbers of private alleles(P_(a))in the three populations,ranging from 10 to 17,suggest that these populations have experienced selective pressures from various environments.Moreover,genetic differentiation was observed in the genetic distance between the SS population and the other two populations.We also examined the phenotypic characteristics of their byssal threads.There were significant differences in byssus attachment strength among the three populations,with the SS population located at the highest latitude secreting more byssal threads and exhibiting greater byssal breaking force and plaque adhesion strength,while the Fuding(FD)population located at the lowest latitude had the weakest byssal attachment.The observed differentiation in private alleles and byssus phenotypes might suggest that the three wild populations have experienced different environmental selective pressures.This study provides insight for future genetic enhancement programs aimed at improving byssus attachment in M.coruscus.展开更多
Introduction Tibetan sheep,economically important animals on the Qinghai–Tibet Plateau,have diversified into numerous local breeds with unique characteristics through prolonged environmental adaptation and selective ...Introduction Tibetan sheep,economically important animals on the Qinghai–Tibet Plateau,have diversified into numerous local breeds with unique characteristics through prolonged environmental adaptation and selective breeding.However,most current research focuses on one or two breeds,and lacks a comprehensive representa-tion of the genetic diversity across multiple Tibetan sheep breeds.This study aims to fill this gap by investigating the genetic structure,diversity and high-altitude adaptation of 6 Tibetan sheep breeds using whole-genome rese-quencing data.Results Six Tibetan sheep breeds were investigated in this study,and whole-genome resequencing data were used to investigate their genetic structure and population diversity.The results showed that the 6 Tibetan sheep breeds exhibited distinct separation in the phylogenetic tree;however,the levels of differentiation among the breeds were minimal,with extensive gene flow observed.Population structure analysis broadly categorized the 6 breeds into 3 distinct ecological types:plateau-type,valley-type and Euler-type.Analysis of unique single-nucleotide polymor-phisms(SNPs)and selective sweeps between Argali and Tibetan sheep revealed that Tibetan sheep domestication was associated primarily with sensory and signal transduction,nutrient absorption and metabolism,and growth and reproductive characteristics.Finally,comprehensive analysis of selective sweep and transcriptome data sug-gested that Tibetan sheep breeds inhabiting different altitudes on the Qinghai–Tibet Plateau adapt by enhancing cardiopulmonary function,regulating body fluid balance through renal reabsorption,and modifying nutrient diges-tion and absorption pathways.Conclusion In this study,we investigated the genetic diversity and population structure of 6 Tibetan sheep breeds in Qinghai Province,China.Additionally,we analyzed the domestication traits and investigated the unique adapta-tion mechanisms residing varying altitudes in the plateau region of Tibetan sheep.This study provides valuable insights into the evolutionary processes of Tibetan sheep in extreme environments.These findings will also contribute to the preservation of genetic diversity and offer a foundation for Tibetan sheep diversity preservation and plateau animal environmental adaptation mechanisms.展开更多
To assess the population development of submerged plant species in disturbed lake ecosystems,we need to better understand the genetic diversity and spatial genetic structure at a fine scale,as well as the impact of di...To assess the population development of submerged plant species in disturbed lake ecosystems,we need to better understand the genetic diversity and spatial genetic structure at a fine scale,as well as the impact of disturbances on the populations.Caohai Lake,in southwest China,is a suitable natural sampling lake because of its abundance of submerged plants and the intense human disturbance.Three widely distributed species,Potamogeton lucens,Ceratophyllum demersum,and Myriophyllum spicatum,were sampled;the spatial position of each individual was recorded in two-dimensional coordinates;and the species were analyzed genetically using microsatellite markers.Among the species studied,M.spicatum exhibited the highest genetic and clonal diversities.All P.lucens subpopulations but one showed a significant fine-scale spatial genetic structure(FSGS),which may result from the limited gene dispersal.However,M.spicatum and C.demersum,with a relatively large distance of gene dispersal,had no significant FSGS.The FSGS pattern of P.lucens at the dock site with intense boat disturbance was significantly different from that at other sites.Our results imply that the FSGS of submerged plants is affected by many factors including seed dispersal,vegetative reproduction and disturbance from birds and boats.Most subpopulations of the three species hadσ_(sex)^(2)/σ_(veg)^(2)values greater than one,implying that the sexual dispersal contributes more than vegetative dispersal to total gene dispersal.Therefore,it is worth paying attention to the importance of seed dispersal for population development of submerged plants in lake ecosystems.展开更多
The present investigation aims at unveiling the main causes of the recorded disparate phylogeographic patterning among the two highly dispersive coastal crab species Carcinus aestuarii and Pachygrapsus marmoratus in t...The present investigation aims at unveiling the main causes of the recorded disparate phylogeographic patterning among the two highly dispersive coastal crab species Carcinus aestuarii and Pachygrapsus marmoratus in the Mediterranean Sea.For this purpose,available mitochondrial and nuclear data for both species were re-analyzed and investigated for genetic polymorphism and differentiation patterns across three defined geographic scales in their distribution ranges,but also across the same locations in the Mediterranean Sea.The temporal frame of genetic diversification was also determined for both species in order to check whether observed differences in phylogeographic patterns among these coastal decapods could be attributed to different evolutionary histories.The obtained results revealed a more variable and diversified gene pool in the green crab C.aestuarii than the one recorded in the marbled crab P.marmoratus.Lack of significant correlation between pairwise genetic dissimilarities observed among C.aestuarii populations and those detected for P.marmoratus was notably discerned across the same defined Mediterranean locations.This finding indicates that the pattern of pairwise genetic differentiation does not vary in the same way in both examined crab species.Significant outputs of population genetic differentiation,retrieved within both species,were shown to be differently associated with the potential effects of various kinds of isolation processes(related to geography,environment and biogeographic boundary).Evolutionary history reconstruction showed older genetic diversification event in C.aestuarii than the one recorded in P.marmoratus.These recorded temporal frames suggest different modes of genetic diversification in both crab species(glacial vicariance for C.aestuarii and interglacial dispersal for P.marmoratus).They may also provide an explanation for the recorded differences in variation of patterns of population genetic diversity and structure,when integrated with species ecological requirements and life-history traits.展开更多
Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is...Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and genetic structure between them by specific length amplified fragment sequencing(SLAF-seq).Finally,470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained.Phylogenetic analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(p<0.001),this suggested that the genetic variation in the T.cuspidata is mainly attributed to within-population factors.In conclusion,the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations,and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations.As evident,the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T.cuspidata species.These developed SNP markers can provide a molecular foundation for T.cuspidata breeding,construction of genetic maps,variety identification,and association analysis of agronomic traits.展开更多
China is a hotspot of relict plant species that were once widespread throughout the Northern Hemisphere.Recent research has demonstrated that the occurrence of long-term stable refugia in the mountainous regions of ce...China is a hotspot of relict plant species that were once widespread throughout the Northern Hemisphere.Recent research has demonstrated that the occurrence of long-term stable refugia in the mountainous regions of central and south-western China allowed their persistence through the late Neogene climate fluctuations.One of these relict lineages is Dipteronia,an oligotypic tree genus with a fossil record extending to the Paleocene.Here,we investigated the genetic variability,demographic dynamics and diversification patterns of the two currently recognized Dipteronia species(Dipteronia sinensis and D.dyeriana).Molecular data were obtained from 45 populations of Dipteronia by genotyping three cpDNA regions,two single copy nuclear genes and 15 simple sequence repeat loci.The genetic study was combined with niche comparison analyses on the environmental space,ecological niche modeling,and landscape connectivity analysis.We found that the two Dipteronia species have highly diverged both in genetic and ecological terms.Despite the incipient speciation processes that can be observed in D.sinensis,the occurrence of long-term stable refugia and,particularly,a dispersal corridor along Daba Shan-west Qinling,likely ensured its genetic and ecological integrity to date.Our study will not only help us to understand how populations of Dipteronia species responded to the tectonic and climatic changes of the Cenozoic,but also provide insight into how Arcto-Tertiary relict plants in East Asia survived,evolved,and diversified.展开更多
Understanding the intra-population genetic diversity and population genetic structure is beneficial for plant protection and breeding.Dendrobium huoshanense is an endangered authentic medicinal herb.To analyze the pop...Understanding the intra-population genetic diversity and population genetic structure is beneficial for plant protection and breeding.Dendrobium huoshanense is an endangered authentic medicinal herb.To analyze the population differentiation and genetic diversity in D.huoshanense,simple sequence repeat(SSR)markers were obtained by high-throughput transcriptome sequencing,and 10 expressed sequence tag(EST)-SSRs were studied in 182 Dendrobium individual samples from 15 populations distributed in Huoshan County,southwest Anhui Province.After deep sequencing of D.huoshanense transcriptome,a total of 58202 unigenes were obtained,and 7781 SSRs with 1~6 base repeats were detected.Among them,dinucleotide SSRs were the dominant repeating motifs(3119,40.085%),and the most common was AG/CT(2666,54.01%).Ten SSR primers were screened out from the designed 120 primer pairs for further polymorphism verification.The results showed that 75 alleles were detected,and the number of alleles at each locus ranged from 4 to 11,with an average of 7.5.The mean expected heterozygosity(H_(e)),observed heterozygosity(H_(o))and polymorphism information content(C_(pi))of the 10 SSR loci were 0.646,0.574,and 0.607,respectively.D.huoshanense populations exhibited a high level of genetic diversity(H_(o)=0.591,H_(e)=0.557)and a moderate level of differentiation(F_(ST)=0.10069),and the genetic variation mainly existed within populations.The results of Structure and neighbour-joining(NJ)analysis based on 10 polymorphic primers showed that D.huoshanense populations were clustered into 2 groups,and the populations KS,HSD,and JXZ had rich genetic diversity and multiple private alleles,suggesting that these populations could be used for genetic improvement of the species.The study revealed frequency distribution of D.huoshanense SSR loci,and successfully developed microsatellite genetic markers,which are expected to expand the repertoire of DNA markers for genetic study of D.huoshanense.展开更多
One hundred and nine Malus sieversii accessions from four geographical populations located at Kuerdening in Mohe town, Gongliu County, Jiaowutuohai, in Xinyuan County, Daxigou in Houcheng County of Ily State, and Baer...One hundred and nine Malus sieversii accessions from four geographical populations located at Kuerdening in Mohe town, Gongliu County, Jiaowutuohai, in Xinyuan County, Daxigou in Houcheng County of Ily State, and Baerluke Mountain in Yumin County of Tacheng State, Xinjiang Uygur Autonomous Region of China were studied by SSR markers. The purpose of the study was to determine the genetic structure and diversity in these eco-geographical populations with eight pair SSR primers of apple. The results indicated that： an average of 16 bands was detected in the four populations. The percentage of polymorphic bands in Gongliu population （89.06%） was the highest in the four populations. The average Nei＇s gene diversity index was 0.257 for all the loci. Totally, 128 polymorphic loci were detected and the percentage of polymorphic loci （P） was 100%, 88.28%, 84.83%, 87.50%, and 87.12%, respectively, at the species level and Gongliu, Xinyuan, Huocheng, and Yumin population levels. The Nei＇s gene diversity index （H = 0.2619） and Shannon＇s information index （1 = 0.4082） in the species level were higher than in the population level. The Nei＇s gene diversity index and Shannon＇s information index in the four populations were Gongliu 〉 Huocheng 〉 Xinyuan 〉 Yumin. Gongliu population and Xinyuan population were the highest in genetic identity and the closest in genetic distance. Gene flow between the populations was 7.265 based on genetic differentiation coefficient （GST = 0.064）. The UPGMA cluster analysis indicated that the genetic relationships between the Gongliu and Xinyuan population were the closest, and the Yumin population were the farthest with the other three populations. The UPGMA cluster analysis indicated that the four geographical populations located in Gongliu, Xinyuan, Huocheng, and Yumin were relatively independent populations. Concurrently, there was also mild gene exchange between the populations. On the basis of the study of population genetic structure and the highest genetic diversity, Gongliu population should be given a high priority consideration in Malus sieversii population＇s in situ germplasm conservation.展开更多
Eighty-five pomegranate （Punica granatum L.） cultivars from six geographical populations located at Shandong, Anhui, Shaanxi, Henan, Yunnan, and Xinjiang Provinces were studied for its population genetic diversity b...Eighty-five pomegranate （Punica granatum L.） cultivars from six geographical populations located at Shandong, Anhui, Shaanxi, Henan, Yunnan, and Xinjiang Provinces were studied for its population genetic diversity by means of fluorescent-AFLP markers. The results indicated that 135-185 polymorphic loci were amplified by eight pairs of primers at species level. An average of 158.25 polymorphic loci was amplified for each primer combination. The polymorphism percentage ranged from 62.5% to 86.11%, and the average polymorphism percentage was 73.26%. This indicated that there was plentiful genetic diversity in pomegranate cultivars. The genetic diversity at the species level was higher than that at the population level. The order of the genetic diversity was Henan population 〉 Xinjiang population 〉 Shaanxi population 〉 Anhui population 〉 Shandong population 〉 Yunnan population. Variance analysis showed that there was significant difference between populations in genetic diversity. The genetic differentiation coefficient between populations （Gsr） was 0.2018, which indicated that gene differentiation was mainly within the population, and between populations, it accounted for 20.18% of the total variation. Gene flow （Nm） between the populations measured was 1.9027 based on the genetic differentiation coefficient between populations, indicating that there was mild gene flow between populations. The UPGMA cluster analysis showed that most accessions from the same population were clustered together, but there was partly gene exchange. All genetic parameters indicated that there was plentiful genetic diversity in pomegranate cultivars in China, of which Henan population was significantly higher than the other populations, and it had wide application foreground in pomegranate breeding in China.展开更多
Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot （Prunus armeniaca L.） cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous R...Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot （Prunus armeniaca L.） cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous Region of China. The purpose of this study was to determine the genetic structure and genotypic diversity among the different eco-geographical populations. Based on the results from this study, 8 pairs of fluorescent-AFLP primers showed clear electrophoregram and high polymorphism amongst the 64 pairs of EcoR Ⅰ/Mse Ⅰ （Mse Ⅰ - a FAM fluorescent marked primer） primers screened. There was a significant polymorphic difference for the same primer pair in different populations and for the same population with different primer pairs. The percentage of polymorphic loci （P） at species level was higher than Kuche, Hetian, Kashi population levels, respectively. The Nei＇s gene diversity index （H） and Shannon＇s information index （I） at species level were higher than those of Kuche, Hetian, and Kashi at population level, respectively. H and I of Kuche population were the highest amongst the three populations. Apricot population genetic diversity was found mainly within the population, Genetic differentiation coefficient between populations （GST） was 0.0882. Gene flow Nm between the populations was 5.1689. Population genetic identity was between 0.9772-0.9811 and genetic distance was between 0.0191-0.0232. These results further indicated that the similarity between populations was higher and the genetic distance between populations was smaller. The UPGMA cluster analysis indicates that the geographical populations at Kuche, Kashi, Hetian were relatively independent Mendelian populations. Concurrently, there was also partial gene exchange between the populations. All the evidences indicated that the genetic diversity in Kuche population was the highest, suggesting that it could be a transition population from wild apricot to cultivated apricot. There were abundant genetic diversities in apricot cultivar populations in southern Xinjiang, China, which provide promising germplasm for further breeding and theoretical basis for biodiversity conservation and utilization for apricot population in this area.展开更多
Genetic structure and differentiation of Reaumuria soongorica (Pall.) Maxim population from the desert of Fukang, Xinjiang, were assessed by means of random amplified polymorphic DNA (RAPD) markers. High genetic diver...Genetic structure and differentiation of Reaumuria soongorica (Pall.) Maxim population from the desert of Fukang, Xinjiang, were assessed by means of random amplified polymorphic DNA (RAPD) markers. High genetic diversity and differentiation were revealed in the population of R soongorica by 15 random primers. One hundred and thirty-six individuals from seven subpopulations were sampled in the study. Seventy-one loci have been detected, and among them 69 were polymorphic. The mean proportion of polymorphic loci (PPB) was 97.18%. The analyses of Shannon information index (0.307 5), Nei's gene diversity (0.312 7) and G(ST)(0.312 0) indicated that there were more genetic variations within the subpopulations than those among the subpopulations. The results of AMOVA analysis showed that 61.58% of the genetic variations existed within subpopulations, and 38.02% among the subpopulations. The gene flow among the subpopulations of R soongorica (Nm = 1.102 8) was much less than that of the common anemophytes (Nm = 5.24), so genetic differentiation among the subpopulations occurred to some extent. Additionally, through the use of clustering and the correlation analyses, we found that the genetic structure of natural population of R soongorica was related to some ecological factors (soil factors mainly) of the oasis-desert transition zone. The genetic diversity level of R soongorica had negative correlation with the content of total soil P and Cl significantly (P < 0.05). On the contrary, it had significant positive correlation with CO32- (P < 0.05), showing that the distribution of the individuals of R soongorica in the sampled areas correlates with certain soluble salt. Furthermore, the genetic diversity of the natural population of R soongorica increased with the decreasing of the content of soil organic matters, water, total N and total P in soil. The paper concluded that the microenvironment ecological factors played an important role in the adaptive evolution of R soongorica population.展开更多
Genetic diversity and population genetic structure in 188 individuals from five natural populations of Castampsis fargesii Franch. were studied by RAPD markers. Three hundred and eighty-five loci were identified with ...Genetic diversity and population genetic structure in 188 individuals from five natural populations of Castampsis fargesii Franch. were studied by RAPD markers. Three hundred and eighty-five loci were identified with 41 oligonucleotide primers, out of which 157 loci were polymorphic and accounted for 40.78% of total genetic diversity at species level. Shannon's indices of diversity (I) and Nei's gene diversity ( h) were 0.459 7 and 0.296 at the species level, respectively. The result showed that genetic variation of C. fargesii populations mainly existed within populations. Genetic differentiation (Hsp-hpop)/Hsp estimated with Shannon's index of diversity and coefficient of gene differentiation (Gst) were 0.047 6 and 0.042 9 respectively, which were confirmed by the analysis of molecular variance (AMOVA). Therefore, it is apparent that within-population variation accounted for 94.97% and among-populations variation accounted for only 5.03% of the total genetic diversity. AMOVA also indicated that there was significant differentiation among populations as well as among individuals within a population.展开更多
The Hooded Crane (Grus monacha) is a waterbird wintering in the wetlands of the middle and lower reaches of the Yangtze River, China. The gradual habitat loss resulting from wetland degradation may have posed negative...The Hooded Crane (Grus monacha) is a waterbird wintering in the wetlands of the middle and lower reaches of the Yangtze River, China. The gradual habitat loss resulting from wetland degradation may have posed negative effects on the structure of our wintering populations. For its effective protection, it is important to conduct an intensive study on the genetic structure of this population. A total of 221 faecal samples, nine feather samples and four muscle samples of Hooded Cranes from four wintering populations, i.e., from Caizi Lake and Shengjin Lake in Anhui, Poyang Lake in Jiangxi and Chongming Dongtan in Shanghai, were collected for this study. Full-length 1103–1104 bp mtDNA D-loop sequences from 72 samples were amplified using PCR. Based on our amplified D-loop sequences and the sequences of two individual birds obtained from GenBank (AB017625 and AB023813), we analyzed the genetic structure of these four wintering Hooded Crane populations. Twenty six variable sites were found among 72 target sequences in the four wintering populations and 23 haplotypes were defined. Genetic diversity analyses showed that the haplotype diversity of Hooded Cranes was 0.823 ± 0.042 with a nucleotide diversity of 0.00157 ± 0.00021. The FST values of the four populations show that there is no significant genetic differentiation among the populations of Hooded Cranes wintering in the middle and lower reaches of the Yangtze River. Tajima’s D and Fu’s tests suggest that the Hooded Crane populations may have experienced population expansion in their evolutionary history.展开更多
In order to determine population genetic structure and pathogenicity of Ustilaginoidea virens in the major rice-growing areas of Anhui Province, total 92 U. virens strains were collected from 28 rice-planting counties...In order to determine population genetic structure and pathogenicity of Ustilaginoidea virens in the major rice-growing areas of Anhui Province, total 92 U. virens strains were collected from 28 rice-planting counties （cities） of Anhui Province. Their genetic diversity was analyzed by using REP-PCR （repetitive extragenic palindromic sequence PCR）, and pathogenicity was determined with artificial inoculation method. The results showed that U. virens in rice-growing regions of Anhui Province had a rich genetic diversity. At the similarity level of 0.76, the 92 U. virens strains could be classified into 7 groups. Significant differences were found in pathogenicity among the 24 U. virens strains belonging to different groups, which showed no association with territorial source of U. virens strain or cluster method adopted by this study. Strain pathogenicity and rice varieties showed significant specificity.展开更多
[Objective] This study aimed to analyze the genetic structure of eight populations of Spartina alterniflora in China at the nuclear DNA level.[Method] The EH277045-derived sequences were amplified from 75 samples in 8...[Objective] This study aimed to analyze the genetic structure of eight populations of Spartina alterniflora in China at the nuclear DNA level.[Method] The EH277045-derived sequences were amplified from 75 samples in 8 populations and directly sequenced.Nucleotide diversity,haplotype diversity,the mean value of Nei＇s genetic distance,genetic differentiation index FST and other genetic parameters were calculated to estimate the genetic diversity and genetic differentiation of S.alterniflora populations in China.[Result] 75 samples were divided into 25 haplotypes by 28 polymorphic sites.Relatively high nucleotide diversity（π=0.011） and haplotype diversity（Hd=0.794） were detected.The mean value of Nei＇s genetic distance and genetic differentiation index FST among eight populations were 0.056 and 0.222,respectively,the Nei＇s genetic distance ranged from 0.000 to 0.189 and FST ranged from 0.000 to 0.444 between each pair of the eight populations.AMOVA result revealed that 79% and 21% of the total genetic variation was partitioned within and among S.alterniflora populations,respectively.[Conclusion] At the nuclear DNA level,there were a relatively high level of genetic diversity and a relatively low level of genetic differentiation among S.alterniflora populations in China,and the genetic diversity existed mainly within rather than among populations.展开更多
Comprehensive phylogeographic insights require the integration of evidence across diverse taxa,ecosystems,and geographical regions.However,our understanding of the arid biota of the vast Asian drylands remains limited...Comprehensive phylogeographic insights require the integration of evidence across diverse taxa,ecosystems,and geographical regions.However,our understanding of the arid biota of the vast Asian drylands remains limited.Accordingly,this study combined phylogeographic analyses with ecological niche modeling to investigate patterns of diversification and demography of the Central Asian racerunner(Eremias vermiculata),a widespread lizard inhabiting arid eastern-Central Asia(AECA).Mitochondrial DNA(mtDNA)sequences were obtained from 876 individuals across 113 localities,while three nuclear genes-CGNL1,MAP1A,andβ-fibint7-were sequenced from 204,170,and 138 individuals,respectively.Analyses identified four distinct mtDNA lineages corresponding to specific geographic subregions within the AECA,reflecting the topographic and ecological heterogeneity of the region.The detection of mito-nuclear discordance indicated the presence of complex evolutionary dynamics.Divergence dating placed the initial lineage splits at approximately 1.18 million years ago,coinciding with major tectonic activity and climatic aridification that likely promoted allopatric divergence.In particular,lineage diversification within the Tarim Basin suggests that recent environmental shifts may have contributed to genetic divergence.Demographic reconstructions revealed signatures of population expansion or range shifts across all lineages during the Last Glacial Maximum,signifying the combined influence of the unique topography and climate dynamics of the AECA on diversification and demographic change.These results highlight the need for fine-scale genomic investigations to clarify the mechanisms underlying mito-nuclear discordance and local adaptation.Such efforts are essential for advancing understanding of how genetic diversity in dryland taxa responds to environmental change,providing insights into the evolutionary adaptability of species in dynamic landscapes.展开更多
In the field of calculating the attack area of air-to-air missiles in modern air combat scenarios,the limitations of existing research,including real-time calculation,accuracy efficiency trade-off,and the absence of t...In the field of calculating the attack area of air-to-air missiles in modern air combat scenarios,the limitations of existing research,including real-time calculation,accuracy efficiency trade-off,and the absence of the three-dimensional attack area model,restrict their practical applications.To address these issues,an improved backtracking algorithm is proposed to improve calculation efficiency.A significant reduction in solution time and maintenance of accuracy in the three-dimensional attack area are achieved by using the proposed algorithm.Furthermore,the age-layered population structure genetic programming(ALPS-GP)algorithm is introduced to determine an analytical polynomial model of the three-dimensional attack area,considering real-time requirements.The accuracy of the polynomial model is enhanced through the coefficient correction using an improved gradient descent algorithm.The study reveals a remarkable combination of high accuracy and efficient real-time computation,with a mean error of 91.89 m using the analytical polynomial model of the three-dimensional attack area solved in just 10^(-4)s,thus meeting the requirements of real-time combat scenarios.展开更多
Although a growing number of both sequence-based and microsatellite nuclear loci have been used to infer genetic structures, their relative efficiencies remain poorly understood. In our study, we used the Green-backed...Although a growing number of both sequence-based and microsatellite nuclear loci have been used to infer genetic structures, their relative efficiencies remain poorly understood. In our study, we used the Green-backed Tit (Parus monticolus) to explore the resolving ability of these two types of markers. The south-western and central mitochondrial DNA (mtDNA) phylogroups were divergent to some extent in sequence-based nuclear data, while mixed together in microsatellites data. The F ST values among clades were about four times lower in microsatellite loci than those in sequence-based nuclear loci. We are of the opinion that size homoplasy may have contributed to the inability of microsatellites to uncover differentiation. Our results suggest that sequence-based nuclear loci outperformed microsatellite loci in detecting population structures, especially those focused on populations with large effective population sizes. There was no significant correlation between F ST values and allelic size variability, which suggested that the efficiency of microsatellite loci in detecting genetic structure may be independent of their polymorphism. F ST is better than R ST in detecting intraspecific divergence due to the high variance of R ST . In agreement with sequence-based nuclear loci, microsatellite loci did resolve the genetic distinctness of the Taiwan Residents phylogroup. The genetic differentiation between the Taiwan Residents and continental clades may involve allopatric divergence without gene flow.展开更多
The Daurian Partridge(Perdix dauuricae) is a kind of hunting bird with high economic value.Genetic diversity and structure in the Daurian Partridge were studied by analyzing eight microsatellite loci in 23 populations...The Daurian Partridge(Perdix dauuricae) is a kind of hunting bird with high economic value.Genetic diversity and structure in the Daurian Partridge were studied by analyzing eight microsatellite loci in 23 populations found throughout the range of the species in China.The objectives were to evaluate the consequences on genetic diversity and differentiation of Daurian Partridge populations and to obtain a profound genetic insight for future management decisions and for effective measures to protect and exploit Daurian Partridges.The results showed that microsatellites were polymorphic in all Daurian Partridge populations,with a high level of genetic diversity over all the loci,especially in the Qaidam Basin populations which have the highest level of diversity.Significant genetic divergence was observed among different groups as well as between populations within the same group;most pairwise FST values were highly significant.Both phylogenetic trees and Bayesian clustering analyses revealed clear differentiation among the 23 populations of the Daurian Partridge,which were classified into two genetically differentiated groups.A bottleneck analysis indicated that Daurian Partridge populations have experienced a recent bottleneck.Our study argues that the Qaidam populations,North China populations,JN population,ZJC population,and Liupan Mountain populations should be paid special attention in order to retain adequate population sizes for maintaining genetic diversity.展开更多
文摘The mussel is one of the main cultivated species in the world.A significant challenge faced by suspension-cultured mussels is the high incidence of mussel fall-off from cultivation ropes,adversely impacting harvest yields,which have been documented at commercial mussel farms in the United Kingdom,the United States of America,Canada,Spain,New Zealand and China.Byssus is an important attachment structure for marine mussels,and weakness in byssal thread attachment is a major factor leading to mussel detachment from ropes.To investigate the relationship between genetic variability and byssal thread phenotypic characteristics in the hard-shelled mussel(Mytilus coruscus),we collected three wild populations of M.coruscus from different latitudes in the East China Sea,including the Shengsi(SS),Jiaojiang(JJ),and Fuding(FD)populations.The genetic diversity and structure of these populations were investigated using 10 microsatellite loci.The mean observed heterozygosity(Ho)in the SS population was 0.44,higher than the mean Ho values of the JJ(0.40)and FD(0.39)populations.The mean inbreeding coefficients(F_(is))in the SS population was 0.20,lower than the mean F_(is)values of the JJ(0.33)and FD populations(0.40).These results revealed that the SS population exhibited higher genetic diversity compared to the other two populations.The different numbers of private alleles(P_(a))in the three populations,ranging from 10 to 17,suggest that these populations have experienced selective pressures from various environments.Moreover,genetic differentiation was observed in the genetic distance between the SS population and the other two populations.We also examined the phenotypic characteristics of their byssal threads.There were significant differences in byssus attachment strength among the three populations,with the SS population located at the highest latitude secreting more byssal threads and exhibiting greater byssal breaking force and plaque adhesion strength,while the Fuding(FD)population located at the lowest latitude had the weakest byssal attachment.The observed differentiation in private alleles and byssus phenotypes might suggest that the three wild populations have experienced different environmental selective pressures.This study provides insight for future genetic enhancement programs aimed at improving byssus attachment in M.coruscus.
基金supported by the Natural Science Foundation of Qinghai Province(No.2022-ZJ-901)the National Breeding Joint Research Project。
文摘Introduction Tibetan sheep,economically important animals on the Qinghai–Tibet Plateau,have diversified into numerous local breeds with unique characteristics through prolonged environmental adaptation and selective breeding.However,most current research focuses on one or two breeds,and lacks a comprehensive representa-tion of the genetic diversity across multiple Tibetan sheep breeds.This study aims to fill this gap by investigating the genetic structure,diversity and high-altitude adaptation of 6 Tibetan sheep breeds using whole-genome rese-quencing data.Results Six Tibetan sheep breeds were investigated in this study,and whole-genome resequencing data were used to investigate their genetic structure and population diversity.The results showed that the 6 Tibetan sheep breeds exhibited distinct separation in the phylogenetic tree;however,the levels of differentiation among the breeds were minimal,with extensive gene flow observed.Population structure analysis broadly categorized the 6 breeds into 3 distinct ecological types:plateau-type,valley-type and Euler-type.Analysis of unique single-nucleotide polymor-phisms(SNPs)and selective sweeps between Argali and Tibetan sheep revealed that Tibetan sheep domestication was associated primarily with sensory and signal transduction,nutrient absorption and metabolism,and growth and reproductive characteristics.Finally,comprehensive analysis of selective sweep and transcriptome data sug-gested that Tibetan sheep breeds inhabiting different altitudes on the Qinghai–Tibet Plateau adapt by enhancing cardiopulmonary function,regulating body fluid balance through renal reabsorption,and modifying nutrient diges-tion and absorption pathways.Conclusion In this study,we investigated the genetic diversity and population structure of 6 Tibetan sheep breeds in Qinghai Province,China.Additionally,we analyzed the domestication traits and investigated the unique adapta-tion mechanisms residing varying altitudes in the plateau region of Tibetan sheep.This study provides valuable insights into the evolutionary processes of Tibetan sheep in extreme environments.These findings will also contribute to the preservation of genetic diversity and offer a foundation for Tibetan sheep diversity preservation and plateau animal environmental adaptation mechanisms.
基金Supported by the National Natural Science Foundation of China(No.31600325)the Self-determined Research Funds of the Central China Normal University(CCNU)from the Colleges’Basic Research and Operation of MOE(No.CCNU20TS022)。
文摘To assess the population development of submerged plant species in disturbed lake ecosystems,we need to better understand the genetic diversity and spatial genetic structure at a fine scale,as well as the impact of disturbances on the populations.Caohai Lake,in southwest China,is a suitable natural sampling lake because of its abundance of submerged plants and the intense human disturbance.Three widely distributed species,Potamogeton lucens,Ceratophyllum demersum,and Myriophyllum spicatum,were sampled;the spatial position of each individual was recorded in two-dimensional coordinates;and the species were analyzed genetically using microsatellite markers.Among the species studied,M.spicatum exhibited the highest genetic and clonal diversities.All P.lucens subpopulations but one showed a significant fine-scale spatial genetic structure(FSGS),which may result from the limited gene dispersal.However,M.spicatum and C.demersum,with a relatively large distance of gene dispersal,had no significant FSGS.The FSGS pattern of P.lucens at the dock site with intense boat disturbance was significantly different from that at other sites.Our results imply that the FSGS of submerged plants is affected by many factors including seed dispersal,vegetative reproduction and disturbance from birds and boats.Most subpopulations of the three species hadσ_(sex)^(2)/σ_(veg)^(2)values greater than one,implying that the sexual dispersal contributes more than vegetative dispersal to total gene dispersal.Therefore,it is worth paying attention to the importance of seed dispersal for population development of submerged plants in lake ecosystems.
文摘The present investigation aims at unveiling the main causes of the recorded disparate phylogeographic patterning among the two highly dispersive coastal crab species Carcinus aestuarii and Pachygrapsus marmoratus in the Mediterranean Sea.For this purpose,available mitochondrial and nuclear data for both species were re-analyzed and investigated for genetic polymorphism and differentiation patterns across three defined geographic scales in their distribution ranges,but also across the same locations in the Mediterranean Sea.The temporal frame of genetic diversification was also determined for both species in order to check whether observed differences in phylogeographic patterns among these coastal decapods could be attributed to different evolutionary histories.The obtained results revealed a more variable and diversified gene pool in the green crab C.aestuarii than the one recorded in the marbled crab P.marmoratus.Lack of significant correlation between pairwise genetic dissimilarities observed among C.aestuarii populations and those detected for P.marmoratus was notably discerned across the same defined Mediterranean locations.This finding indicates that the pattern of pairwise genetic differentiation does not vary in the same way in both examined crab species.Significant outputs of population genetic differentiation,retrieved within both species,were shown to be differently associated with the potential effects of various kinds of isolation processes(related to geography,environment and biogeographic boundary).Evolutionary history reconstruction showed older genetic diversification event in C.aestuarii than the one recorded in P.marmoratus.These recorded temporal frames suggest different modes of genetic diversification in both crab species(glacial vicariance for C.aestuarii and interglacial dispersal for P.marmoratus).They may also provide an explanation for the recorded differences in variation of patterns of population genetic diversity and structure,when integrated with species ecological requirements and life-history traits.
基金This work was supported by Grants from the National Science Foundation of China to Yanwen Zhang(32272757,31972363)Grants from the Liaoning Provincial Department of Education Project to Dandan Wang(JYTMS20230698)Grants from the Liaoning Provincial Science and Technology Fund Project:Comparative Multi-Omics Study of Wild and Cultivated Species of Taxus chinensis.
文摘Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and genetic structure between them by specific length amplified fragment sequencing(SLAF-seq).Finally,470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained.Phylogenetic analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(p<0.001),this suggested that the genetic variation in the T.cuspidata is mainly attributed to within-population factors.In conclusion,the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations,and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations.As evident,the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T.cuspidata species.These developed SNP markers can provide a molecular foundation for T.cuspidata breeding,construction of genetic maps,variety identification,and association analysis of agronomic traits.
基金co-supported by the National Natural Science Foundation of China(Grant No.31470311)the Ph.D.Programs Foundation of the Ministry of Education of China(Grant No.20136101130001).
文摘China is a hotspot of relict plant species that were once widespread throughout the Northern Hemisphere.Recent research has demonstrated that the occurrence of long-term stable refugia in the mountainous regions of central and south-western China allowed their persistence through the late Neogene climate fluctuations.One of these relict lineages is Dipteronia,an oligotypic tree genus with a fossil record extending to the Paleocene.Here,we investigated the genetic variability,demographic dynamics and diversification patterns of the two currently recognized Dipteronia species(Dipteronia sinensis and D.dyeriana).Molecular data were obtained from 45 populations of Dipteronia by genotyping three cpDNA regions,two single copy nuclear genes and 15 simple sequence repeat loci.The genetic study was combined with niche comparison analyses on the environmental space,ecological niche modeling,and landscape connectivity analysis.We found that the two Dipteronia species have highly diverged both in genetic and ecological terms.Despite the incipient speciation processes that can be observed in D.sinensis,the occurrence of long-term stable refugia and,particularly,a dispersal corridor along Daba Shan-west Qinling,likely ensured its genetic and ecological integrity to date.Our study will not only help us to understand how populations of Dipteronia species responded to the tectonic and climatic changes of the Cenozoic,but also provide insight into how Arcto-Tertiary relict plants in East Asia survived,evolved,and diversified.
文摘Understanding the intra-population genetic diversity and population genetic structure is beneficial for plant protection and breeding.Dendrobium huoshanense is an endangered authentic medicinal herb.To analyze the population differentiation and genetic diversity in D.huoshanense,simple sequence repeat(SSR)markers were obtained by high-throughput transcriptome sequencing,and 10 expressed sequence tag(EST)-SSRs were studied in 182 Dendrobium individual samples from 15 populations distributed in Huoshan County,southwest Anhui Province.After deep sequencing of D.huoshanense transcriptome,a total of 58202 unigenes were obtained,and 7781 SSRs with 1~6 base repeats were detected.Among them,dinucleotide SSRs were the dominant repeating motifs(3119,40.085%),and the most common was AG/CT(2666,54.01%).Ten SSR primers were screened out from the designed 120 primer pairs for further polymorphism verification.The results showed that 75 alleles were detected,and the number of alleles at each locus ranged from 4 to 11,with an average of 7.5.The mean expected heterozygosity(H_(e)),observed heterozygosity(H_(o))and polymorphism information content(C_(pi))of the 10 SSR loci were 0.646,0.574,and 0.607,respectively.D.huoshanense populations exhibited a high level of genetic diversity(H_(o)=0.591,H_(e)=0.557)and a moderate level of differentiation(F_(ST)=0.10069),and the genetic variation mainly existed within populations.The results of Structure and neighbour-joining(NJ)analysis based on 10 polymorphic primers showed that D.huoshanense populations were clustered into 2 groups,and the populations KS,HSD,and JXZ had rich genetic diversity and multiple private alleles,suggesting that these populations could be used for genetic improvement of the species.The study revealed frequency distribution of D.huoshanense SSR loci,and successfully developed microsatellite genetic markers,which are expected to expand the repertoire of DNA markers for genetic study of D.huoshanense.
基金the National Natural Science Foundation of China (No. 30471196)the Special Program for Doctorial Site of Universities (No. 200404344011).
文摘One hundred and nine Malus sieversii accessions from four geographical populations located at Kuerdening in Mohe town, Gongliu County, Jiaowutuohai, in Xinyuan County, Daxigou in Houcheng County of Ily State, and Baerluke Mountain in Yumin County of Tacheng State, Xinjiang Uygur Autonomous Region of China were studied by SSR markers. The purpose of the study was to determine the genetic structure and diversity in these eco-geographical populations with eight pair SSR primers of apple. The results indicated that： an average of 16 bands was detected in the four populations. The percentage of polymorphic bands in Gongliu population （89.06%） was the highest in the four populations. The average Nei＇s gene diversity index was 0.257 for all the loci. Totally, 128 polymorphic loci were detected and the percentage of polymorphic loci （P） was 100%, 88.28%, 84.83%, 87.50%, and 87.12%, respectively, at the species level and Gongliu, Xinyuan, Huocheng, and Yumin population levels. The Nei＇s gene diversity index （H = 0.2619） and Shannon＇s information index （1 = 0.4082） in the species level were higher than in the population level. The Nei＇s gene diversity index and Shannon＇s information index in the four populations were Gongliu 〉 Huocheng 〉 Xinyuan 〉 Yumin. Gongliu population and Xinyuan population were the highest in genetic identity and the closest in genetic distance. Gene flow between the populations was 7.265 based on genetic differentiation coefficient （GST = 0.064）. The UPGMA cluster analysis indicated that the genetic relationships between the Gongliu and Xinyuan population were the closest, and the Yumin population were the farthest with the other three populations. The UPGMA cluster analysis indicated that the four geographical populations located in Gongliu, Xinyuan, Huocheng, and Yumin were relatively independent populations. Concurrently, there was also mild gene exchange between the populations. On the basis of the study of population genetic structure and the highest genetic diversity, Gongliu population should be given a high priority consideration in Malus sieversii population＇s in situ germplasm conservation.
基金2006 Shandong Provincial Science and Technology Development Plans (No. 2006GG2209009)Research Funds for Junior Scientist of Shandong Academy of Agricultural Sciences (No. 2005YQ012).
文摘Eighty-five pomegranate （Punica granatum L.） cultivars from six geographical populations located at Shandong, Anhui, Shaanxi, Henan, Yunnan, and Xinjiang Provinces were studied for its population genetic diversity by means of fluorescent-AFLP markers. The results indicated that 135-185 polymorphic loci were amplified by eight pairs of primers at species level. An average of 158.25 polymorphic loci was amplified for each primer combination. The polymorphism percentage ranged from 62.5% to 86.11%, and the average polymorphism percentage was 73.26%. This indicated that there was plentiful genetic diversity in pomegranate cultivars. The genetic diversity at the species level was higher than that at the population level. The order of the genetic diversity was Henan population 〉 Xinjiang population 〉 Shaanxi population 〉 Anhui population 〉 Shandong population 〉 Yunnan population. Variance analysis showed that there was significant difference between populations in genetic diversity. The genetic differentiation coefficient between populations （Gsr） was 0.2018, which indicated that gene differentiation was mainly within the population, and between populations, it accounted for 20.18% of the total variation. Gene flow （Nm） between the populations measured was 1.9027 based on the genetic differentiation coefficient between populations, indicating that there was mild gene flow between populations. The UPGMA cluster analysis showed that most accessions from the same population were clustered together, but there was partly gene exchange. All genetic parameters indicated that there was plentiful genetic diversity in pomegranate cultivars in China, of which Henan population was significantly higher than the other populations, and it had wide application foreground in pomegranate breeding in China.
基金This work was supported by the National Natural Science Foundation (No. 30471196)the Special Program for Doctorial Site of Universities (No. 200404344011).
文摘Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot （Prunus armeniaca L.） cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous Region of China. The purpose of this study was to determine the genetic structure and genotypic diversity among the different eco-geographical populations. Based on the results from this study, 8 pairs of fluorescent-AFLP primers showed clear electrophoregram and high polymorphism amongst the 64 pairs of EcoR Ⅰ/Mse Ⅰ （Mse Ⅰ - a FAM fluorescent marked primer） primers screened. There was a significant polymorphic difference for the same primer pair in different populations and for the same population with different primer pairs. The percentage of polymorphic loci （P） at species level was higher than Kuche, Hetian, Kashi population levels, respectively. The Nei＇s gene diversity index （H） and Shannon＇s information index （I） at species level were higher than those of Kuche, Hetian, and Kashi at population level, respectively. H and I of Kuche population were the highest amongst the three populations. Apricot population genetic diversity was found mainly within the population, Genetic differentiation coefficient between populations （GST） was 0.0882. Gene flow Nm between the populations was 5.1689. Population genetic identity was between 0.9772-0.9811 and genetic distance was between 0.0191-0.0232. These results further indicated that the similarity between populations was higher and the genetic distance between populations was smaller. The UPGMA cluster analysis indicates that the geographical populations at Kuche, Kashi, Hetian were relatively independent Mendelian populations. Concurrently, there was also partial gene exchange between the populations. All the evidences indicated that the genetic diversity in Kuche population was the highest, suggesting that it could be a transition population from wild apricot to cultivated apricot. There were abundant genetic diversities in apricot cultivar populations in southern Xinjiang, China, which provide promising germplasm for further breeding and theoretical basis for biodiversity conservation and utilization for apricot population in this area.
文摘Genetic structure and differentiation of Reaumuria soongorica (Pall.) Maxim population from the desert of Fukang, Xinjiang, were assessed by means of random amplified polymorphic DNA (RAPD) markers. High genetic diversity and differentiation were revealed in the population of R soongorica by 15 random primers. One hundred and thirty-six individuals from seven subpopulations were sampled in the study. Seventy-one loci have been detected, and among them 69 were polymorphic. The mean proportion of polymorphic loci (PPB) was 97.18%. The analyses of Shannon information index (0.307 5), Nei's gene diversity (0.312 7) and G(ST)(0.312 0) indicated that there were more genetic variations within the subpopulations than those among the subpopulations. The results of AMOVA analysis showed that 61.58% of the genetic variations existed within subpopulations, and 38.02% among the subpopulations. The gene flow among the subpopulations of R soongorica (Nm = 1.102 8) was much less than that of the common anemophytes (Nm = 5.24), so genetic differentiation among the subpopulations occurred to some extent. Additionally, through the use of clustering and the correlation analyses, we found that the genetic structure of natural population of R soongorica was related to some ecological factors (soil factors mainly) of the oasis-desert transition zone. The genetic diversity level of R soongorica had negative correlation with the content of total soil P and Cl significantly (P < 0.05). On the contrary, it had significant positive correlation with CO32- (P < 0.05), showing that the distribution of the individuals of R soongorica in the sampled areas correlates with certain soluble salt. Furthermore, the genetic diversity of the natural population of R soongorica increased with the decreasing of the content of soil organic matters, water, total N and total P in soil. The paper concluded that the microenvironment ecological factors played an important role in the adaptive evolution of R soongorica population.
文摘Genetic diversity and population genetic structure in 188 individuals from five natural populations of Castampsis fargesii Franch. were studied by RAPD markers. Three hundred and eighty-five loci were identified with 41 oligonucleotide primers, out of which 157 loci were polymorphic and accounted for 40.78% of total genetic diversity at species level. Shannon's indices of diversity (I) and Nei's gene diversity ( h) were 0.459 7 and 0.296 at the species level, respectively. The result showed that genetic variation of C. fargesii populations mainly existed within populations. Genetic differentiation (Hsp-hpop)/Hsp estimated with Shannon's index of diversity and coefficient of gene differentiation (Gst) were 0.047 6 and 0.042 9 respectively, which were confirmed by the analysis of molecular variance (AMOVA). Therefore, it is apparent that within-population variation accounted for 94.97% and among-populations variation accounted for only 5.03% of the total genetic diversity. AMOVA also indicated that there was significant differentiation among populations as well as among individuals within a population.
基金supported by the National Natural Science Foundation of China (Grant No 31172117)the Anhui Academic and Technical Leaders Fund
文摘The Hooded Crane (Grus monacha) is a waterbird wintering in the wetlands of the middle and lower reaches of the Yangtze River, China. The gradual habitat loss resulting from wetland degradation may have posed negative effects on the structure of our wintering populations. For its effective protection, it is important to conduct an intensive study on the genetic structure of this population. A total of 221 faecal samples, nine feather samples and four muscle samples of Hooded Cranes from four wintering populations, i.e., from Caizi Lake and Shengjin Lake in Anhui, Poyang Lake in Jiangxi and Chongming Dongtan in Shanghai, were collected for this study. Full-length 1103–1104 bp mtDNA D-loop sequences from 72 samples were amplified using PCR. Based on our amplified D-loop sequences and the sequences of two individual birds obtained from GenBank (AB017625 and AB023813), we analyzed the genetic structure of these four wintering Hooded Crane populations. Twenty six variable sites were found among 72 target sequences in the four wintering populations and 23 haplotypes were defined. Genetic diversity analyses showed that the haplotype diversity of Hooded Cranes was 0.823 ± 0.042 with a nucleotide diversity of 0.00157 ± 0.00021. The FST values of the four populations show that there is no significant genetic differentiation among the populations of Hooded Cranes wintering in the middle and lower reaches of the Yangtze River. Tajima’s D and Fu’s tests suggest that the Hooded Crane populations may have experienced population expansion in their evolutionary history.
基金Supported by Agricultural Science and Technology Innovation Fund of Anhui Province(14B1148)Special Fund for Talent Development in Anhui Province(13C1109)Science and Technology Major Project of Anhui Province(15CZZ03132)~~
文摘In order to determine population genetic structure and pathogenicity of Ustilaginoidea virens in the major rice-growing areas of Anhui Province, total 92 U. virens strains were collected from 28 rice-planting counties （cities） of Anhui Province. Their genetic diversity was analyzed by using REP-PCR （repetitive extragenic palindromic sequence PCR）, and pathogenicity was determined with artificial inoculation method. The results showed that U. virens in rice-growing regions of Anhui Province had a rich genetic diversity. At the similarity level of 0.76, the 92 U. virens strains could be classified into 7 groups. Significant differences were found in pathogenicity among the 24 U. virens strains belonging to different groups, which showed no association with territorial source of U. virens strain or cluster method adopted by this study. Strain pathogenicity and rice varieties showed significant specificity.
基金Supported by National Natural Science Foundation of China(30900161)~~
文摘[Objective] This study aimed to analyze the genetic structure of eight populations of Spartina alterniflora in China at the nuclear DNA level.[Method] The EH277045-derived sequences were amplified from 75 samples in 8 populations and directly sequenced.Nucleotide diversity,haplotype diversity,the mean value of Nei＇s genetic distance,genetic differentiation index FST and other genetic parameters were calculated to estimate the genetic diversity and genetic differentiation of S.alterniflora populations in China.[Result] 75 samples were divided into 25 haplotypes by 28 polymorphic sites.Relatively high nucleotide diversity（π=0.011） and haplotype diversity（Hd=0.794） were detected.The mean value of Nei＇s genetic distance and genetic differentiation index FST among eight populations were 0.056 and 0.222,respectively,the Nei＇s genetic distance ranged from 0.000 to 0.189 and FST ranged from 0.000 to 0.444 between each pair of the eight populations.AMOVA result revealed that 79% and 21% of the total genetic variation was partitioned within and among S.alterniflora populations,respectively.[Conclusion] At the nuclear DNA level,there were a relatively high level of genetic diversity and a relatively low level of genetic differentiation among S.alterniflora populations in China,and the genetic diversity existed mainly within rather than among populations.
基金supported by the Central Asia Drug Discovery and Development Centre of Chinese Academy of Sciences(180GJHZ2024036MI)National Natural Science Foundation of China(32070433,32470466,31672270,31872959)+2 种基金Third Xinjiang Scientific Expedition Program(2021xjkk0600)Special Exchange Program of the Chinese Academy of Sciencessponsored by the ANSO Scholarship for Young Talents
文摘Comprehensive phylogeographic insights require the integration of evidence across diverse taxa,ecosystems,and geographical regions.However,our understanding of the arid biota of the vast Asian drylands remains limited.Accordingly,this study combined phylogeographic analyses with ecological niche modeling to investigate patterns of diversification and demography of the Central Asian racerunner(Eremias vermiculata),a widespread lizard inhabiting arid eastern-Central Asia(AECA).Mitochondrial DNA(mtDNA)sequences were obtained from 876 individuals across 113 localities,while three nuclear genes-CGNL1,MAP1A,andβ-fibint7-were sequenced from 204,170,and 138 individuals,respectively.Analyses identified four distinct mtDNA lineages corresponding to specific geographic subregions within the AECA,reflecting the topographic and ecological heterogeneity of the region.The detection of mito-nuclear discordance indicated the presence of complex evolutionary dynamics.Divergence dating placed the initial lineage splits at approximately 1.18 million years ago,coinciding with major tectonic activity and climatic aridification that likely promoted allopatric divergence.In particular,lineage diversification within the Tarim Basin suggests that recent environmental shifts may have contributed to genetic divergence.Demographic reconstructions revealed signatures of population expansion or range shifts across all lineages during the Last Glacial Maximum,signifying the combined influence of the unique topography and climate dynamics of the AECA on diversification and demographic change.These results highlight the need for fine-scale genomic investigations to clarify the mechanisms underlying mito-nuclear discordance and local adaptation.Such efforts are essential for advancing understanding of how genetic diversity in dryland taxa responds to environmental change,providing insights into the evolutionary adaptability of species in dynamic landscapes.
基金National Natural Science Foundation of China(62373187)Forward-looking Layout Special Projects(ILA220591A22)。
文摘In the field of calculating the attack area of air-to-air missiles in modern air combat scenarios,the limitations of existing research,including real-time calculation,accuracy efficiency trade-off,and the absence of the three-dimensional attack area model,restrict their practical applications.To address these issues,an improved backtracking algorithm is proposed to improve calculation efficiency.A significant reduction in solution time and maintenance of accuracy in the three-dimensional attack area are achieved by using the proposed algorithm.Furthermore,the age-layered population structure genetic programming(ALPS-GP)algorithm is introduced to determine an analytical polynomial model of the three-dimensional attack area,considering real-time requirements.The accuracy of the polynomial model is enhanced through the coefficient correction using an improved gradient descent algorithm.The study reveals a remarkable combination of high accuracy and efficient real-time computation,with a mean error of 91.89 m using the analytical polynomial model of the three-dimensional attack area solved in just 10^(-4)s,thus meeting the requirements of real-time combat scenarios.
基金supported by the National Science Fund for Distinguished Young Scientists (No. 30925008)the Major International (Regional) Joint Research Project (No. 31010103901)+1 种基金the CAS-IOZ Innovation Program (KSCX2-EW-J-2) by a grant (No. O529YX5105) from the Key Laboratory of the Zoological Systematics and Evolution of the Chinese Academy of Sciences to F.M. Lei
文摘Although a growing number of both sequence-based and microsatellite nuclear loci have been used to infer genetic structures, their relative efficiencies remain poorly understood. In our study, we used the Green-backed Tit (Parus monticolus) to explore the resolving ability of these two types of markers. The south-western and central mitochondrial DNA (mtDNA) phylogroups were divergent to some extent in sequence-based nuclear data, while mixed together in microsatellites data. The F ST values among clades were about four times lower in microsatellite loci than those in sequence-based nuclear loci. We are of the opinion that size homoplasy may have contributed to the inability of microsatellites to uncover differentiation. Our results suggest that sequence-based nuclear loci outperformed microsatellite loci in detecting population structures, especially those focused on populations with large effective population sizes. There was no significant correlation between F ST values and allelic size variability, which suggested that the efficiency of microsatellite loci in detecting genetic structure may be independent of their polymorphism. F ST is better than R ST in detecting intraspecific divergence due to the high variance of R ST . In agreement with sequence-based nuclear loci, microsatellite loci did resolve the genetic distinctness of the Taiwan Residents phylogroup. The genetic differentiation between the Taiwan Residents and continental clades may involve allopatric divergence without gene flow.
基金supported by the National Natural Science Foundation of China (Grant No. 30530130)
文摘The Daurian Partridge(Perdix dauuricae) is a kind of hunting bird with high economic value.Genetic diversity and structure in the Daurian Partridge were studied by analyzing eight microsatellite loci in 23 populations found throughout the range of the species in China.The objectives were to evaluate the consequences on genetic diversity and differentiation of Daurian Partridge populations and to obtain a profound genetic insight for future management decisions and for effective measures to protect and exploit Daurian Partridges.The results showed that microsatellites were polymorphic in all Daurian Partridge populations,with a high level of genetic diversity over all the loci,especially in the Qaidam Basin populations which have the highest level of diversity.Significant genetic divergence was observed among different groups as well as between populations within the same group;most pairwise FST values were highly significant.Both phylogenetic trees and Bayesian clustering analyses revealed clear differentiation among the 23 populations of the Daurian Partridge,which were classified into two genetically differentiated groups.A bottleneck analysis indicated that Daurian Partridge populations have experienced a recent bottleneck.Our study argues that the Qaidam populations,North China populations,JN population,ZJC population,and Liupan Mountain populations should be paid special attention in order to retain adequate population sizes for maintaining genetic diversity.
