Stichopus chloronotus is a tropical sea cucumber with facultative asexual reproduction in the Indo-Western Pacific,yet its wild populations are decreasing due to extensive harvesting.Understanding the species’genetic...Stichopus chloronotus is a tropical sea cucumber with facultative asexual reproduction in the Indo-Western Pacific,yet its wild populations are decreasing due to extensive harvesting.Understanding the species’genetic characteristics is essential for effective management and conservation.To develop novel microsatellite markers and assess the genetic diversity,clonality,and genetic structure of eight populations of S.chloronotus in the South China Sea,193 individuals from eight populations across Wuzhizhou and Fenjiezhou(Boundary)islands were analyzed using nine newly developed microsatellite markers and five previously established markers.RNA-Seq was employed to obtained 62662 unigenes and identified 16926 microsatellite loci.Fourteen polymorphic microsatellite loci were developed,of which 11 were highly polymorphic(polymorphic information content>0.5).The number of alleles(N_(a))ranged from 3 to 6 per locus,and the average Shannon diversity index(I)was 1.107.All the populations exhibited asexual reproduction,with regional variations in reproductive modes.Asexual reproduction was predominant in the northwestern Wuzhizhou Island population(SY 7)and the Fenjiezhou Island population(LS 8),where four and five predominant clones represented more than 89%of the individuals,which led to reduced genetic diversity.Overall,genetic diversity was moderately low,with significant genetic differentiation among populations(F_(ST)=0.33;P<0.001),suggesting limited gene flow(the number of migrants(N_(m))<1).These findings highlight the role of reproductive strategies in shaping fine-scale genetic differentiation in S.chloronotus.The limited recruitment success of sexually produced larvae and habitat heterogeneity likely constrain clone dispersal,contributing to distinct genetic restructuring.This study provided key insights into the interplay between reproductive strategies and genetic patterns in sea cucumbers,offering a scientific basis for targeted conservation efforts.展开更多
Cynomolgus macaques,a species of Old World primate native to southeastern and eastern Asia and the island of Mauritius,are one of the most important nonhuman primate models for infectious disease.Although the closely ...Cynomolgus macaques,a species of Old World primate native to southeastern and eastern Asia and the island of Mauritius,are one of the most important nonhuman primate models for infectious disease.Although the closely related rhesus macaque is classified into subspecies based on geographic origin,no such subdivision exists for cynomolgus macaques,and they continue to be used interchangeably in infectious disease research,reducing the comparability of data produced from these studies.Research into the population genetics of cynomolgus macaques has found significant differences between macaques native to different areas,including their genetic diversity,with macaques from insular populations such as Mauritius and the Philippines exhibiting highly restricted heterozygosity compared to mainland populations native to Indonesia or Cambodia.In the context of infectious disease studies,research into pathogens,including Ebola virus,Crimean-Congo hemorrhagic fever virus,and Mycobacterium tuberculosis have found differences in study outcomes,survival times,and immune cell responses between different populations of macaques.This review provides an overview of the differences between cynomolgus macaque populations in the context of genetic diversity,and in response to infection,and highlights the need for clear reporting of geographic origin of primates used in research.This will improve data comparison between studies and help to further refine this important animal model.展开更多
Evidence has shown that differential transcriptomic profiles among human populations from diverse ancestries,supporting the role of genetic architecture in regulating gene expression alongside environmental stimuli.Ge...Evidence has shown that differential transcriptomic profiles among human populations from diverse ancestries,supporting the role of genetic architecture in regulating gene expression alongside environmental stimuli.Genetic variants that regulate gene expression,known as expression quantitative trait loci(eQTL),are primarily shaped by human migration history and evolutionary forces,likewise,regulation of gene expression in principle could have been influenced by these events.Therefore,a comprehensive understanding of how human evolution impacts eQTL offers important insights into how phenotypic diversity is shaped.Recent studies,however,suggest that eQTL is enriched in genes that are selectively constrained.Whether eQTL is minimally affected by selective pressures remains an open question and requires comprehensive investigations.In addition,such studies are primarily dominated by the major populations of European ancestry,leaving many marginalized populations underrepresented.These observations indicate there exists a fundamental knowledge gap in the role of genomics variation on phenotypic diversity,which potentially hinders precision medicine.This article aims to revisit the abundance of eQTL across diverse populations and provide an overview of their impact from the population and evolutionary genetics perspective,subsequently discuss their influence on phenomics,as well as challenges and opportunities in the applications to precision medicine.展开更多
The correct understanding of fish population structure plays a positive role in their fishery management.The dotted gizzard shad,Konosirus punctatus,is widely distributed in the coastal waters of the northwestern Paci...The correct understanding of fish population structure plays a positive role in their fishery management.The dotted gizzard shad,Konosirus punctatus,is widely distributed in the coastal waters of the northwestern Pacific.With the over-exploitation of economically important fishes,its importance is increasingly prominent.To further examine the population genetic structure of K.punctatus across the northwestern Pacific,the amplified fragment length polymorphism(AFLP)and the inter-simple sequence repeats(ISSRs)were employed to perform genetic variation analysis.The results showed that the combination of polyacrylamide gel electrophoresis and silver staining can effectively detect genetic variation for K.punctatus populations.The average proportions of polymorphic loci were 46.26%and 87.13%for AFLP and ISSR markers,respectively,and the genetic diversity parameters showed no obvious differences among populations.Both analysis molecular variance(AMOVA)and pairwise F_(st)suggested that there was significant genetic differentiation between Chinese and Japanese populations.All samples also clustered into two clades based on the unweighted pair-group method analysis(UPGMA)tree by two markers,which indicated significant genetic differentiation among populations.Consistent with the previous studies,there are two highly differentiated groups at the nuclear gene level and they were suggested to be treated as two separate genetic management units.The results of the present study could provide the genetic management strategy for this important economic species.展开更多
Starch gel electrophoresis was used to analyze genetic structure of three populations of Oxya chinensis from Shanxi Province,China.Four allozyme polymorphic loci (MDH-1,MDH-2,LDH,ME) were found.The data suggest that t...Starch gel electrophoresis was used to analyze genetic structure of three populations of Oxya chinensis from Shanxi Province,China.Four allozyme polymorphic loci (MDH-1,MDH-2,LDH,ME) were found.The data suggest that two populations of O.chinensis about 41 kilometers apart are genetically similar,but differentiated from the third population with a geographic distance of 357 kilometers.However,the heterozygosity levels of those two genetically similar populations were much different.The Nei's genetic distance between two geographically close populations is 0.068,which is much smaller than those of geographically distant populations (0.23 in average).The observed overlap of geographical distance and genetic distance implies that for O.chinensis population divergence may correlate with geographic isolation.展开更多
For the population genetics analysis of the naturally grown brown seaweed Laminaria japonica （Laminariales,Phaeophyta） sampled from Dalian,Yantai,Weihai,Rongcheng and Qingdao in China,ten primers were employed to pr...For the population genetics analysis of the naturally grown brown seaweed Laminaria japonica （Laminariales,Phaeophyta） sampled from Dalian,Yantai,Weihai,Rongcheng and Qingdao in China,ten primers were employed to produce 88 bands as revealed by randomly amplified polymorphic DNA （RAPD） markers,and all these bands were polymorphic.According to these band patterns,there were 94 distinct phenotypes occurred in 100 samples indicating the high heterozygosity of this kelp.Dalian population samples showed the highest percentage of polymorphism （71.67%）,and also the higher diversity estimated on the basis of the Shannon’s index （8.498）,suggesting that this population could be chosen as the best resource for genetic breeding.The highest diversity of Yantai population possibly resulted from the introduction of L.longissima used for interspecific cross breeding with L.japonica cultivated in China.From Dalian southwards to Qingdao,the genetic variation of the five populations became less with a decrease in latitude,possibly due to the natural selection especially of high temperature.The genetic distance （Φ ST values） of the five populations was a little significantly correlated with the geographical distance （r=0.496） at P =0.05 by Mantel’s test.Weihai,Rongcheng and Yantai populations were closely grouped genetically together by Neighbor-joining cluster analysis probably in that the dispersal of the kelp by propagules more easily occurring in the range of relatively short distance.The analysis of molecular variance （AMOVA） also demonstrated that the relatively higher variation occurred among populations （71.49%） at an extremely significant level （P 0.000 1）.All these evidence showed that there was a relatively distinct genetic differentiation among the sampled kelp populations,and L.japonica grown in China was also rather heterozygous in heredity.展开更多
Helicobacter pylori （H. pylorl） is a Gram-negative bac- terium that infects half of the human population. The infection is associated with chronic inflammation of the gastric mucosa and peptic ulcers. It is also a m...Helicobacter pylori （H. pylorl） is a Gram-negative bac- terium that infects half of the human population. The infection is associated with chronic inflammation of the gastric mucosa and peptic ulcers. It is also a major risk factor for gastric cancer. Phylogenetic analysis of global strains reveals there are seven populations of H. pylori, including hpAfrical, hpAfrica2, hpEastAsia, hpEurope, hpNEAfrica, hpAsia2 and hpSahul. These populations are consistent with their geographical origins, and pos- sibly result from geographical separation of the bac- terium leading to reduced bacterial recombination in some populations. For each population, H. pylori has evolved to possess genomic contents distinguishable from others. The hpEurope population is distinct in that it has the largest genome of 1.65 mbp on average, and the highest number of coding sequences. This confers its competitive advantage over other populations but at the cost of a lower infection rate. The large genomic size could be a cause of the frequent occurrence of the deletion of the cag pathogenicity island in H. pylori strains from hpEurope. The incidence of gastric cancer varies among different geographical regions. This can be attributed in part to different rates of infection of H. pylori. Recent studies found that different popula- tions of H, pylori vary in their carcinogenic potential and contribute to the variation in incidence of gastric cancer among geographical regions. This could be related to the ancestral origin of H, pylori. Further studies are indi- cated to investigate the bacterial factors contributing to differential virulence and their influence on the clinical features in infected individuals.展开更多
Sargassum horneri is a common brown macro-alga that is found in the inter-tidal ecosystems of China. To investigate the current status of seaweed resources and provide basic data for its sustainable development, ISSR ...Sargassum horneri is a common brown macro-alga that is found in the inter-tidal ecosystems of China. To investigate the current status of seaweed resources and provide basic data for its sustainable development, ISSR (inter simple sequence repeat) and SRAP (sequence related amplified polymorphism) markers were used to analyze the population genetics among nine natural populations of S. horneri. The nine studied populations were distributed over 2 000 km from northeast to south China. The percentage of polymorphic loci P% (ISSR, 99.44%; SRAP, 100.00%), Nei's genetic diversity H (ISSR, 0.107-0.199; SRAP, 0.100-0.153), and Shannon's information index I (ISSR, 0.157-0.291; SRAP, 0.148-0.219) indicated a fair amount of genetic variability among the nine populations. Moreover, the high degree of gene differentiation G st (ISSR, 0.654; SRAP, 0.718) and low gene flow N m (ISSR, 0.265; SRAP, 0.196) implied that there was significant among-population differentiation, possibly as a result of habitat fragmentation. The matrices of genetic distances and fixation indices (F st ) among the populations correlated well with their geographical distribution (Mantel test R=0.541 5, 0.541 8; P=0.005 0, 0.002 0 and R=0.728 6, 0.641 2; P=0.001 0, 0.001 0, respectively); the Rongcheng population in the Shandong peninsula was the only exception. Overall, the genetic differentiation agreed with the geographic isolation. The fair amount of genetic diversity that was revealed in the S. horneri populations in China indicated that the seaweed resources had not been seriously affected by external factors.展开更多
The common marmoset(Callithrix jacchus)has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies.Epileptic marmosets have been independ...The common marmoset(Callithrix jacchus)has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies.Epileptic marmosets have been independently reported in two Asian primate research centers.Nevertheless,the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated.Here,we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing.We identified 14558184 single nucleotide polymorphisms(SNPs)from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples.Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers.In addition,SNP and copy number variation(CNV)analyses suggested that the WW domain-containing oxidoreductase(WWOX)and Tyrosine-protein phosphatase nonreceptor type 21(PTPN21)genes may be associated with epilepsy in marmosets.Notably,KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets.This study provides valuable population genomic resources for marmosets in two Asian primate centers.Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers,while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.展开更多
Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock ...Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock enhancement in the Bohai Bay in 2013. A total of 254 and 238 alleles were identified in the spawner and recaptured populations, respectively, and the numbers of alleles（N_a） were 8–63 and 6–60, respectively. The numbers of effective alleles（N_e） were 2.52–21.60 and 2.67–20.72, respectively. The polymorphism information content ranged from 0.529 to 0.952. The observed heterozygosity（H_o） values（0.638–0.910 and 0.712–0.927） were lower than the expected heterozygosity（H_e） values（0.603–0.954 and 0.625–0.952）, which indicated that the two populations possessed a rich genetic diversity. In 16 tests（2 populations×8 loci）, 13 tests deviated from the HardyWeinberg equilibrium. F_（is） values were positive at seven loci and the inbreeding coefficients（F） of the two populations estimated by trio ML were 13.234% and 11.603%, suggesting that there was a relatively high degree of inbreeding. A certain level of inbreeding depression had occurred in the Chinese shrimp population. F_（st） values ranged from 0 to 0.059, with a mean of 0.028, displaying a low level of genetic differentiation in the two populations. Effective population sizes（3 060.2 and 3 842.8） were higher than the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. For enhancement activity in 2014,the ideal number of captured shrimp spawners should have ranged from 7 686 to 19 214 to maintain genetic diversity and effective population size. Further strategies to adjust the balance of economic cost, fishing effort and ideal number of shrimp spawners to maintain a satisfactory effective population size for ensuring the sustainability of Chinese shrimp are proposed.展开更多
Amphioctopus fangsiao(Cephalopoda:Octopodidae)is an important commercial species in the coastal waters of China.In recent years,however,the resource of A.fangsiao have declined because of habitat destruction and overf...Amphioctopus fangsiao(Cephalopoda:Octopodidae)is an important commercial species in the coastal waters of China.In recent years,however,the resource of A.fangsiao have declined because of habitat destruction and overfishing.To analyze the genetic variations of A.fangsiao caused by the fluctuation of resources,the population genetic structure of nine sampling locations collected from the Bohai Sea to the South China Sea were investigated,using mtDNA COI fragments and microsatellite DNA.The results of F-statistics,AMOVA,STRUCTURE and PCA analyses showed three phylogeographic clades(Clades A,B and C),revealing limited genetic exchange between north and south populations.These clades diverged in 2.23(Clades A and B)and 3.67(Clades A,B and C)million years ago,during the dramatic environmental fluctuations,such as sea level and temperature changes,have exerted great influence on the survival distribution pattern of global organisms.Our results for low genetic connectivity among A.fangsiao populations provide insights into the development of management strategies,that is,to manage this species as separate management unit.展开更多
The Liaoning clawed salamander(Onychodactylus zhaoermii)is an endemic and critically endangered amphibian species of China.To study the population genetics of natural populations of this species,32 samples were collec...The Liaoning clawed salamander(Onychodactylus zhaoermii)is an endemic and critically endangered amphibian species of China.To study the population genetics of natural populations of this species,32 samples were collected from six different locations,and the mitochondrial genome was sequenced.Population genetic analyses showed that the Liaoning clawed salamander is composed of only one radialized cluster with ultralow nucleotide diversity.Late Pleistocene climate cooling(-100 to-30 kya)may have reduced the effective population size of the Liaoning clawed salamander,and the subsequent temperature increase(~25 kya to present)provided the opportunity for population expansion.Because of heat sensitivity,the maximum temperature of the prebreeding period,especially from March to May,is very important for the surface environment living in the Liaoning clawed salamander.Three suitable regions were predicted by the MaxEnt model,and the largest suitable region(approximately 899 km2)was at the four-county boundary area and was larger than the present’Natural Conservation Community of the Liaoning Clawed Salamander’.To ensure more effective protection of all Liaoning clawed salamanders,we suggest extending the current’Natural Conservation Community of the Liaoning Clawed Salamander’to include the four-county boundary area.展开更多
Periwinkle Littoraria sinensis is a widely distributed gastropod in rocky intertidal zone of the northwestern Pacifi c.To examine genetic diversity and genetic connectivity among coastal populations of L.sinensis in C...Periwinkle Littoraria sinensis is a widely distributed gastropod in rocky intertidal zone of the northwestern Pacifi c.To examine genetic diversity and genetic connectivity among coastal populations of L.sinensis in China,1636 pairs of primers were successfully designed using whole-genome shotgun sequencing,de novo assembly,and a bioinformatics pipeline QDD.Twelve highly variable polymorphic markers were selected to genotype 351 individuals from 15 populations.Data of nine microsatellite loci were retained for population genetic analysis,and weak genetic differentiation among populations were detected,suggesting high gene flow among populations.The long planktonic larval duration of L.sinensis might have played an important role in the high gene flow among populations.A tendency of genetic differentiation between north and south populations of L.sinensis was detected,which might be resulted from isolation due to lowered sea level in the last glacial maximum.Furthermore,the newly founded populations along the coast of Jiangsu Province were closely related to populations to the south of the Changjiang(Yangtze)River estuary,suggesting that the main source of the newly founded populations is from natural rocky populations south of the estuary.展开更多
Knowledge of population genetic structure plays an important role in fisheries management.In this research,In-ter-Simple-Sequence-Repeat(ISSR)markers were employed to evaluate the genetic structure of Japanese sardine...Knowledge of population genetic structure plays an important role in fisheries management.In this research,In-ter-Simple-Sequence-Repeat(ISSR)markers were employed to evaluate the genetic structure of Japanese sardinella(Sardinella zun-asi)populations in the Northwest Pacific.Eighty seven individuals from 5 locations were screened using 4 highly polymorphic prim-ers.A total of 173 polymorphic loci were detected out of 191 loci amplified.Small but significant genetic differentiation was de-tected between the Chinese and Japanese populations by both AMOVA and pairwise FST analyses,which was further supported by cluster analysis.We consider that climate change during glaciations should be responsible for the genetic differentiation.Isolation by geographic distance among populations was observed,indicating that the distance might also lead to the genetic differentiation.However,no genetic structure was found within the populations off both the Chinese and Japanese coasts,indicating a high-level along-coast gene flow,which might result from ocean current transport and common ground for over-wintering.展开更多
Despite the diversity and ecological importance of cestodes,there is a paucity of studies on their life stages(i.e.,complete lists of intermediate,paratenic,and definitive hosts)and genetic variation.For example,in th...Despite the diversity and ecological importance of cestodes,there is a paucity of studies on their life stages(i.e.,complete lists of intermediate,paratenic,and definitive hosts)and genetic variation.For example,in the Gulf of Mexico(GoM)98 species of cestodes have been reported to date;however,data on their intraspecific genetic variation and population genetic studies are lacking.The trypanorhynch cestode,Oncomegas wageneri,is found(among other places)off the American Western Atlantic Coast,including the GoM,and has been reported as an adult from stingrays and from several teleost species in its larval form(as plerocerci).This study represents the first report of 2 previously unregistered definitive hosts for O.wageneri,namely the Atlantic sharpnose shark Rhizoprionodon terraenovae and the southern stingray Hypanus americanus.In this work,partial sequences of the 28S(region D1-D2)ribosomal DNA were analyzed to include O.wageneri within an eutetrarhynchoid phylogenetic framework.All O.wageneri individuals(which included plerocerci and adults)were recovered as monophyletic and Oncomegas celatus was identified as the sister species of O.wageneri.Furthermore,population genetic analyses of O.wageneri from the southern GoM were carried out using DNA sequences of the mitochondrial cytochrome c oxi-dase subunit 1(COI)gene,which reflected high genetic variation and a lack of genetic structure among the 9 oceanographic sampling sites.Based on these results,O.wageneri is panmictic in the southern GoM.More extensive sampling along the species entire distribution is necessary to make more accurate inferences of population genetics of O.wageneri.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
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
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
The Random Amplified Polymorphism DNA (RAPD) markers were used to stu dy the intra-specific diversity and regional differentiation of the Chinese fore st frogs (Rana chensinensis), which were sampled from the fields o...The Random Amplified Polymorphism DNA (RAPD) markers were used to stu dy the intra-specific diversity and regional differentiation of the Chinese fore st frogs (Rana chensinensis), which were sampled from the fields of 8 regions in Heilongjiang Province. Totally 78 polymorphic DNA loci were amplified by 10 RAP D primers. By genetic distance analysis and phylogenetic tree reconstruction wit h the Neighbor-Joining (NJ) method the results showed that the populations of Ch inese forest frogs distributed in 8 regions existed great differentiation (Avera ge Fst=0.347, SD=0.235) while there was the paradox between geographic distances and genetic distances. Based on geographic and geological data, a hypothesis wa s posed that it is very possible that the hilly lands in the downstream of the S onghua River and the Heilong River were the center of the origin of the Chinese forest frogs in Heilongjiang Province. And mainly through the Songhua River syst em, the Chinese forest frogs dispersed into the Songneng Plain from the Sanjiang Plain whereas the Fangzheng region became a sub-center for the western dispersi on.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 Baerluke ...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
基金Supported by the National Key Research and Development Program of China(Nos.2022YFD2401305,2022YFD2401303)the National Natural Science Foundation of China(Nos.42166005,42076097)。
文摘Stichopus chloronotus is a tropical sea cucumber with facultative asexual reproduction in the Indo-Western Pacific,yet its wild populations are decreasing due to extensive harvesting.Understanding the species’genetic characteristics is essential for effective management and conservation.To develop novel microsatellite markers and assess the genetic diversity,clonality,and genetic structure of eight populations of S.chloronotus in the South China Sea,193 individuals from eight populations across Wuzhizhou and Fenjiezhou(Boundary)islands were analyzed using nine newly developed microsatellite markers and five previously established markers.RNA-Seq was employed to obtained 62662 unigenes and identified 16926 microsatellite loci.Fourteen polymorphic microsatellite loci were developed,of which 11 were highly polymorphic(polymorphic information content>0.5).The number of alleles(N_(a))ranged from 3 to 6 per locus,and the average Shannon diversity index(I)was 1.107.All the populations exhibited asexual reproduction,with regional variations in reproductive modes.Asexual reproduction was predominant in the northwestern Wuzhizhou Island population(SY 7)and the Fenjiezhou Island population(LS 8),where four and five predominant clones represented more than 89%of the individuals,which led to reduced genetic diversity.Overall,genetic diversity was moderately low,with significant genetic differentiation among populations(F_(ST)=0.33;P<0.001),suggesting limited gene flow(the number of migrants(N_(m))<1).These findings highlight the role of reproductive strategies in shaping fine-scale genetic differentiation in S.chloronotus.The limited recruitment success of sexually produced larvae and habitat heterogeneity likely constrain clone dispersal,contributing to distinct genetic restructuring.This study provided key insights into the interplay between reproductive strategies and genetic patterns in sea cucumbers,offering a scientific basis for targeted conservation efforts.
文摘Cynomolgus macaques,a species of Old World primate native to southeastern and eastern Asia and the island of Mauritius,are one of the most important nonhuman primate models for infectious disease.Although the closely related rhesus macaque is classified into subspecies based on geographic origin,no such subdivision exists for cynomolgus macaques,and they continue to be used interchangeably in infectious disease research,reducing the comparability of data produced from these studies.Research into the population genetics of cynomolgus macaques has found significant differences between macaques native to different areas,including their genetic diversity,with macaques from insular populations such as Mauritius and the Philippines exhibiting highly restricted heterozygosity compared to mainland populations native to Indonesia or Cambodia.In the context of infectious disease studies,research into pathogens,including Ebola virus,Crimean-Congo hemorrhagic fever virus,and Mycobacterium tuberculosis have found differences in study outcomes,survival times,and immune cell responses between different populations of macaques.This review provides an overview of the differences between cynomolgus macaque populations in the context of genetic diversity,and in response to infection,and highlights the need for clear reporting of geographic origin of primates used in research.This will improve data comparison between studies and help to further refine this important animal model.
基金supported by the Ministry of Higher Education(MOHE)Malaysia through Fundamental Research Grant Scheme(FRGS)with project code:FRGS/1/2021/STG01/UCSI/01/.SX was funded by the National Natural Science Foundation of China(NSFC)grants 32030020 and 32288101funded by the NSFC grant 32270665.
文摘Evidence has shown that differential transcriptomic profiles among human populations from diverse ancestries,supporting the role of genetic architecture in regulating gene expression alongside environmental stimuli.Genetic variants that regulate gene expression,known as expression quantitative trait loci(eQTL),are primarily shaped by human migration history and evolutionary forces,likewise,regulation of gene expression in principle could have been influenced by these events.Therefore,a comprehensive understanding of how human evolution impacts eQTL offers important insights into how phenotypic diversity is shaped.Recent studies,however,suggest that eQTL is enriched in genes that are selectively constrained.Whether eQTL is minimally affected by selective pressures remains an open question and requires comprehensive investigations.In addition,such studies are primarily dominated by the major populations of European ancestry,leaving many marginalized populations underrepresented.These observations indicate there exists a fundamental knowledge gap in the role of genomics variation on phenotypic diversity,which potentially hinders precision medicine.This article aims to revisit the abundance of eQTL across diverse populations and provide an overview of their impact from the population and evolutionary genetics perspective,subsequently discuss their influence on phenomics,as well as challenges and opportunities in the applications to precision medicine.
基金The National Key Research and Development Program of China under contract No.2023YFD2401903.
文摘The correct understanding of fish population structure plays a positive role in their fishery management.The dotted gizzard shad,Konosirus punctatus,is widely distributed in the coastal waters of the northwestern Pacific.With the over-exploitation of economically important fishes,its importance is increasingly prominent.To further examine the population genetic structure of K.punctatus across the northwestern Pacific,the amplified fragment length polymorphism(AFLP)and the inter-simple sequence repeats(ISSRs)were employed to perform genetic variation analysis.The results showed that the combination of polyacrylamide gel electrophoresis and silver staining can effectively detect genetic variation for K.punctatus populations.The average proportions of polymorphic loci were 46.26%and 87.13%for AFLP and ISSR markers,respectively,and the genetic diversity parameters showed no obvious differences among populations.Both analysis molecular variance(AMOVA)and pairwise F_(st)suggested that there was significant genetic differentiation between Chinese and Japanese populations.All samples also clustered into two clades based on the unweighted pair-group method analysis(UPGMA)tree by two markers,which indicated significant genetic differentiation among populations.Consistent with the previous studies,there are two highly differentiated groups at the nuclear gene level and they were suggested to be treated as two separate genetic management units.The results of the present study could provide the genetic management strategy for this important economic species.
文摘Starch gel electrophoresis was used to analyze genetic structure of three populations of Oxya chinensis from Shanxi Province,China.Four allozyme polymorphic loci (MDH-1,MDH-2,LDH,ME) were found.The data suggest that two populations of O.chinensis about 41 kilometers apart are genetically similar,but differentiated from the third population with a geographic distance of 357 kilometers.However,the heterozygosity levels of those two genetically similar populations were much different.The Nei's genetic distance between two geographically close populations is 0.068,which is much smaller than those of geographically distant populations (0.23 in average).The observed overlap of geographical distance and genetic distance implies that for O.chinensis population divergence may correlate with geographic isolation.
基金The National Natural Science Foundation of China under grant Nos 39800105 and 30471328the Shanghai Development Foundation of Education under grant No. 98-SG-32Key Discipline of Shanghai Municipal Education Commission (J50701)
文摘For the population genetics analysis of the naturally grown brown seaweed Laminaria japonica （Laminariales,Phaeophyta） sampled from Dalian,Yantai,Weihai,Rongcheng and Qingdao in China,ten primers were employed to produce 88 bands as revealed by randomly amplified polymorphic DNA （RAPD） markers,and all these bands were polymorphic.According to these band patterns,there were 94 distinct phenotypes occurred in 100 samples indicating the high heterozygosity of this kelp.Dalian population samples showed the highest percentage of polymorphism （71.67%）,and also the higher diversity estimated on the basis of the Shannon’s index （8.498）,suggesting that this population could be chosen as the best resource for genetic breeding.The highest diversity of Yantai population possibly resulted from the introduction of L.longissima used for interspecific cross breeding with L.japonica cultivated in China.From Dalian southwards to Qingdao,the genetic variation of the five populations became less with a decrease in latitude,possibly due to the natural selection especially of high temperature.The genetic distance （Φ ST values） of the five populations was a little significantly correlated with the geographical distance （r=0.496） at P =0.05 by Mantel’s test.Weihai,Rongcheng and Yantai populations were closely grouped genetically together by Neighbor-joining cluster analysis probably in that the dispersal of the kelp by propagules more easily occurring in the range of relatively short distance.The analysis of molecular variance （AMOVA） also demonstrated that the relatively higher variation occurred among populations （71.49%） at an extremely significant level （P 0.000 1）.All these evidence showed that there was a relatively distinct genetic differentiation among the sampled kelp populations,and L.japonica grown in China was also rather heterozygous in heredity.
文摘Helicobacter pylori （H. pylorl） is a Gram-negative bac- terium that infects half of the human population. The infection is associated with chronic inflammation of the gastric mucosa and peptic ulcers. It is also a major risk factor for gastric cancer. Phylogenetic analysis of global strains reveals there are seven populations of H. pylori, including hpAfrical, hpAfrica2, hpEastAsia, hpEurope, hpNEAfrica, hpAsia2 and hpSahul. These populations are consistent with their geographical origins, and pos- sibly result from geographical separation of the bac- terium leading to reduced bacterial recombination in some populations. For each population, H. pylori has evolved to possess genomic contents distinguishable from others. The hpEurope population is distinct in that it has the largest genome of 1.65 mbp on average, and the highest number of coding sequences. This confers its competitive advantage over other populations but at the cost of a lower infection rate. The large genomic size could be a cause of the frequent occurrence of the deletion of the cag pathogenicity island in H. pylori strains from hpEurope. The incidence of gastric cancer varies among different geographical regions. This can be attributed in part to different rates of infection of H. pylori. Recent studies found that different popula- tions of H, pylori vary in their carcinogenic potential and contribute to the variation in incidence of gastric cancer among geographical regions. This could be related to the ancestral origin of H, pylori. Further studies are indi- cated to investigate the bacterial factors contributing to differential virulence and their influence on the clinical features in infected individuals.
基金Supported by the National Natural Science Foundation of China(Nos.40618001,40976085)the Chinese Academy of Sciences and Guangdong Provincial Joint Projects(No.2009B091300086)Public Science and Technology Research Funds Projects of Ocean
文摘Sargassum horneri is a common brown macro-alga that is found in the inter-tidal ecosystems of China. To investigate the current status of seaweed resources and provide basic data for its sustainable development, ISSR (inter simple sequence repeat) and SRAP (sequence related amplified polymorphism) markers were used to analyze the population genetics among nine natural populations of S. horneri. The nine studied populations were distributed over 2 000 km from northeast to south China. The percentage of polymorphic loci P% (ISSR, 99.44%; SRAP, 100.00%), Nei's genetic diversity H (ISSR, 0.107-0.199; SRAP, 0.100-0.153), and Shannon's information index I (ISSR, 0.157-0.291; SRAP, 0.148-0.219) indicated a fair amount of genetic variability among the nine populations. Moreover, the high degree of gene differentiation G st (ISSR, 0.654; SRAP, 0.718) and low gene flow N m (ISSR, 0.265; SRAP, 0.196) implied that there was significant among-population differentiation, possibly as a result of habitat fragmentation. The matrices of genetic distances and fixation indices (F st ) among the populations correlated well with their geographical distribution (Mantel test R=0.541 5, 0.541 8; P=0.005 0, 0.002 0 and R=0.728 6, 0.641 2; P=0.001 0, 0.001 0, respectively); the Rongcheng population in the Shandong peninsula was the only exception. Overall, the genetic differentiation agreed with the geographic isolation. The fair amount of genetic diversity that was revealed in the S. horneri populations in China indicated that the seaweed resources had not been seriously affected by external factors.
基金supported by the National Natural Science Foundation of China (82001372)National Key Research and Development Program of China (2018YFE0126700)+3 种基金Shanghai Jiao Tong University 2030 Initiative (WH510363001-7)Shanghai Municipal Commission of Science and Technology Program (21dz2210100)Shanghai Education Commission Research and Innovation Program (2019-01-07-00-02-E00037)a National Institutes of Health (NIH)grant (5R01HG002385)to E.E.E。
文摘The common marmoset(Callithrix jacchus)has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies.Epileptic marmosets have been independently reported in two Asian primate research centers.Nevertheless,the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated.Here,we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing.We identified 14558184 single nucleotide polymorphisms(SNPs)from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples.Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers.In addition,SNP and copy number variation(CNV)analyses suggested that the WW domain-containing oxidoreductase(WWOX)and Tyrosine-protein phosphatase nonreceptor type 21(PTPN21)genes may be associated with epilepsy in marmosets.Notably,KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets.This study provides valuable population genomic resources for marmosets in two Asian primate centers.Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers,while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.
基金The National Basic Research Program of China(973 Program)Adaptive Response of Fishery Species to Environmental Changes and Their Effects on Population Dynamics under contract No.2015CB453303the International Science&Technology Cooperation Program of China under contract No.2013DFA31410
文摘Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock enhancement in the Bohai Bay in 2013. A total of 254 and 238 alleles were identified in the spawner and recaptured populations, respectively, and the numbers of alleles（N_a） were 8–63 and 6–60, respectively. The numbers of effective alleles（N_e） were 2.52–21.60 and 2.67–20.72, respectively. The polymorphism information content ranged from 0.529 to 0.952. The observed heterozygosity（H_o） values（0.638–0.910 and 0.712–0.927） were lower than the expected heterozygosity（H_e） values（0.603–0.954 and 0.625–0.952）, which indicated that the two populations possessed a rich genetic diversity. In 16 tests（2 populations×8 loci）, 13 tests deviated from the HardyWeinberg equilibrium. F_（is） values were positive at seven loci and the inbreeding coefficients（F） of the two populations estimated by trio ML were 13.234% and 11.603%, suggesting that there was a relatively high degree of inbreeding. A certain level of inbreeding depression had occurred in the Chinese shrimp population. F_（st） values ranged from 0 to 0.059, with a mean of 0.028, displaying a low level of genetic differentiation in the two populations. Effective population sizes（3 060.2 and 3 842.8） were higher than the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. For enhancement activity in 2014,the ideal number of captured shrimp spawners should have ranged from 7 686 to 19 214 to maintain genetic diversity and effective population size. Further strategies to adjust the balance of economic cost, fishing effort and ideal number of shrimp spawners to maintain a satisfactory effective population size for ensuring the sustainability of Chinese shrimp are proposed.
基金The National Natural Science Foundation of China under contract Nos 32170536 and 31672257。
文摘Amphioctopus fangsiao(Cephalopoda:Octopodidae)is an important commercial species in the coastal waters of China.In recent years,however,the resource of A.fangsiao have declined because of habitat destruction and overfishing.To analyze the genetic variations of A.fangsiao caused by the fluctuation of resources,the population genetic structure of nine sampling locations collected from the Bohai Sea to the South China Sea were investigated,using mtDNA COI fragments and microsatellite DNA.The results of F-statistics,AMOVA,STRUCTURE and PCA analyses showed three phylogeographic clades(Clades A,B and C),revealing limited genetic exchange between north and south populations.These clades diverged in 2.23(Clades A and B)and 3.67(Clades A,B and C)million years ago,during the dramatic environmental fluctuations,such as sea level and temperature changes,have exerted great influence on the survival distribution pattern of global organisms.Our results for low genetic connectivity among A.fangsiao populations provide insights into the development of management strategies,that is,to manage this species as separate management unit.
基金supported financially by the Research Fund for the Educational Commission of Liaoning Province of China(LQN201904 and LJC201901)the Doctoral Program of Shenyang Normal University(Grant No.BS201821)the Natural Science Foundation of Liaoning Province of China(2020-BS-148 and 2021-MS-241)。
文摘The Liaoning clawed salamander(Onychodactylus zhaoermii)is an endemic and critically endangered amphibian species of China.To study the population genetics of natural populations of this species,32 samples were collected from six different locations,and the mitochondrial genome was sequenced.Population genetic analyses showed that the Liaoning clawed salamander is composed of only one radialized cluster with ultralow nucleotide diversity.Late Pleistocene climate cooling(-100 to-30 kya)may have reduced the effective population size of the Liaoning clawed salamander,and the subsequent temperature increase(~25 kya to present)provided the opportunity for population expansion.Because of heat sensitivity,the maximum temperature of the prebreeding period,especially from March to May,is very important for the surface environment living in the Liaoning clawed salamander.Three suitable regions were predicted by the MaxEnt model,and the largest suitable region(approximately 899 km2)was at the four-county boundary area and was larger than the present’Natural Conservation Community of the Liaoning Clawed Salamander’.To ensure more effective protection of all Liaoning clawed salamanders,we suggest extending the current’Natural Conservation Community of the Liaoning Clawed Salamander’to include the four-county boundary area.
基金Supported by the National Natural Science Foundation of China(No.31970488)。
文摘Periwinkle Littoraria sinensis is a widely distributed gastropod in rocky intertidal zone of the northwestern Pacifi c.To examine genetic diversity and genetic connectivity among coastal populations of L.sinensis in China,1636 pairs of primers were successfully designed using whole-genome shotgun sequencing,de novo assembly,and a bioinformatics pipeline QDD.Twelve highly variable polymorphic markers were selected to genotype 351 individuals from 15 populations.Data of nine microsatellite loci were retained for population genetic analysis,and weak genetic differentiation among populations were detected,suggesting high gene flow among populations.The long planktonic larval duration of L.sinensis might have played an important role in the high gene flow among populations.A tendency of genetic differentiation between north and south populations of L.sinensis was detected,which might be resulted from isolation due to lowered sea level in the last glacial maximum.Furthermore,the newly founded populations along the coast of Jiangsu Province were closely related to populations to the south of the Changjiang(Yangtze)River estuary,suggesting that the main source of the newly founded populations is from natural rocky populations south of the estuary.
基金supported by the Special Research Foundation for Public Welfare Marine Program (200905019-2)
文摘Knowledge of population genetic structure plays an important role in fisheries management.In this research,In-ter-Simple-Sequence-Repeat(ISSR)markers were employed to evaluate the genetic structure of Japanese sardinella(Sardinella zun-asi)populations in the Northwest Pacific.Eighty seven individuals from 5 locations were screened using 4 highly polymorphic prim-ers.A total of 173 polymorphic loci were detected out of 191 loci amplified.Small but significant genetic differentiation was de-tected between the Chinese and Japanese populations by both AMOVA and pairwise FST analyses,which was further supported by cluster analysis.We consider that climate change during glaciations should be responsible for the genetic differentiation.Isolation by geographic distance among populations was observed,indicating that the distance might also lead to the genetic differentiation.However,no genetic structure was found within the populations off both the Chinese and Japanese coasts,indicating a high-level along-coast gene flow,which might result from ocean current transport and common ground for over-wintering.
基金Grant No.Al-S-15134 by the Conscjo National de Ciencia y Tecnologia(CONACyT)(to F.S.C.)Research funded by the CONACyT(Mexican Ministry of Energy)Hydrocarbon Trust,project 201441.
文摘Despite the diversity and ecological importance of cestodes,there is a paucity of studies on their life stages(i.e.,complete lists of intermediate,paratenic,and definitive hosts)and genetic variation.For example,in the Gulf of Mexico(GoM)98 species of cestodes have been reported to date;however,data on their intraspecific genetic variation and population genetic studies are lacking.The trypanorhynch cestode,Oncomegas wageneri,is found(among other places)off the American Western Atlantic Coast,including the GoM,and has been reported as an adult from stingrays and from several teleost species in its larval form(as plerocerci).This study represents the first report of 2 previously unregistered definitive hosts for O.wageneri,namely the Atlantic sharpnose shark Rhizoprionodon terraenovae and the southern stingray Hypanus americanus.In this work,partial sequences of the 28S(region D1-D2)ribosomal DNA were analyzed to include O.wageneri within an eutetrarhynchoid phylogenetic framework.All O.wageneri individuals(which included plerocerci and adults)were recovered as monophyletic and Oncomegas celatus was identified as the sister species of O.wageneri.Furthermore,population genetic analyses of O.wageneri from the southern GoM were carried out using DNA sequences of the mitochondrial cytochrome c oxi-dase subunit 1(COI)gene,which reflected high genetic variation and a lack of genetic structure among the 9 oceanographic sampling sites.Based on these results,O.wageneri is panmictic in the southern GoM.More extensive sampling along the species entire distribution is necessary to make more accurate inferences of population genetics of O.wageneri.
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the Natural Science Foundation of Heilongjiang Province (C9726).
文摘The Random Amplified Polymorphism DNA (RAPD) markers were used to stu dy the intra-specific diversity and regional differentiation of the Chinese fore st frogs (Rana chensinensis), which were sampled from the fields of 8 regions in Heilongjiang Province. Totally 78 polymorphic DNA loci were amplified by 10 RAP D primers. By genetic distance analysis and phylogenetic tree reconstruction wit h the Neighbor-Joining (NJ) method the results showed that the populations of Ch inese forest frogs distributed in 8 regions existed great differentiation (Avera ge Fst=0.347, SD=0.235) while there was the paradox between geographic distances and genetic distances. Based on geographic and geological data, a hypothesis wa s posed that it is very possible that the hilly lands in the downstream of the S onghua River and the Heilong River were the center of the origin of the Chinese forest frogs in Heilongjiang Province. And mainly through the Songhua River syst em, the Chinese forest frogs dispersed into the Songneng Plain from the Sanjiang Plain whereas the Fangzheng region became a sub-center for the western dispersi on.
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.
