In evolutionary games,most studies on finite populations have focused on a single updating mechanism.However,given the differences in individual cognition,individuals may change their strategies according to different...In evolutionary games,most studies on finite populations have focused on a single updating mechanism.However,given the differences in individual cognition,individuals may change their strategies according to different updating mechanisms.For this reason,we consider two different aspiration-driven updating mechanisms in structured populations:satisfied-stay unsatisfied shift(SSUS)and satisfied-cooperate unsatisfied defect(SCUD).To simulate the game player’s learning process,this paper improves the particle swarm optimization algorithm,which will be used to simulate the game player’s strategy selection,i.e.,population particle swarm optimization(PPSO)algorithms.We find that in the prisoner’s dilemma,the conditions that SSUS facilitates the evolution of cooperation do not enable cooperation to emerge.In contrast,SCUD conditions that promote the evolution of cooperation enable cooperation to emerge.In addition,the invasion of SCUD individuals helps promote cooperation among SSUS individuals.Simulated by the PPSO algorithm,the theoretical approximation results are found to be consistent with the trend of change in the simulation results.展开更多
Simulation was used to investigate the effects of population structure and migration on metrics of pairwise shared ancestry. Random and hierarchical structures, or migration geometries, were examined. Compared to panm...Simulation was used to investigate the effects of population structure and migration on metrics of pairwise shared ancestry. Random and hierarchical structures, or migration geometries, were examined. Compared to panmictic populations, progress to all qualitative metrics of pairwise ancestry is delayed in structured populations. However, unless migration is very low, the time required is generally less than triple and often less than twice that required in a panmictic population of the same total size. Population structure also increases, to a similar degree, the time required for a population-wide most recent common ancestor (MRCA). As a result, the relationships between various qualitative metrics of pairwise shared ancestry and MRCA time are relatively unaffected by population structure. For example, the mean time to most recent shared ancestor (MRSA) with global sampling of pairs is 40% - 50% of the MRCA time for almost all simulated structures and migration levels. Quantitative pairwise genealogical overlap is strongly affected by population structure. With global sampling, pairwise quantitative overlap never approaches 1.0, as it does in panmictic populations;and instead eventually becomes stationary at much lower values. Possible implications of the present results for human pairwise shared ancestry are discussed. For globally sampled pairs, the longest time to most recent shared ancestor (MRSA) for humans is suggested to be approximately 2100 years before the present. If generation time is 30 years, then all humans are 69th, or closer, cousins. For people with recent European ancestry, the MRSA time may be only half as long, about 1000 years.展开更多
The growth of filamentous microorganism is contributed by tip extension and branching. The microscopic growth of filamentous microorganism means the growth process from one or a few spores. In order to describe the mi...The growth of filamentous microorganism is contributed by tip extension and branching. The microscopic growth of filamentous microorganism means the growth process from one or a few spores. In order to describe the microscopic process, a population morphologically structured model is proposed, in which three morphological compartment and their interactions were considered, and the heterogeneity of hyphal growth was included. The model was applied to describe the microscopic growth of Streptomyces tendae and Geotrichum candidum with good agreement. From model prediction, it is concluded that if the number of hyphae is large enough (macroscopic growth), the specific growth rate of filamentous microorganism and the ratio of morphological forms in hyphae will become constant.展开更多
Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformat...Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis.The total length was612.91 Mb,and 25755 genes were detected in the chayote genome.The contig N50 was more than 20.01 Mb,and the scaffold N50 was over47.11 Mb.Of the genome,60.35%were composed of repetitive sequences,and 31.18%of genome sequences belonged to long-terminal repeats.A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference.Based on this genome-wide and global alignment map,researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species.Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree,population structure analysis,and principal component analysis using genome re-sequencing data.The chayote genome,re-sequencing dataset,and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.展开更多
Understanding how species diverge and adapt is fundamental to unraveling biodiversity.While environmental impacts on species evolution are well-documented,the roles of intrinsic life-history traits remain underexplore...Understanding how species diverge and adapt is fundamental to unraveling biodiversity.While environmental impacts on species evolution are well-documented,the roles of intrinsic life-history traits remain underexplored.The Qinghai-Xizang Plateau,with its harsh conditions and unique biodiversity,offers a natural laboratory for such investigations.Here,we examine two sympatric small mammals—the solitary,low-dispersal plateau zokor(Eospalax baileyi)and the social,high-dispersal plateau pika(Ochotona curzoniae)—to elucidate how life-history traits shape population structures and adaptive strategies.Through whole-genome sequencing and cardiac-blood phenotype analyses,we reveal striking differences in their evolutionary trajectories.Despite enduring similar environmental pressures,plateau zokor populations exhibit pronounced genetic subdivisions,high inbreeding,and distinct local adaptations.In contrast,plateau pika populations display genetic panmixia,widespread diversity,and adaptive uniformity.Demographic inference highlights that plateau zokors experienced severe population bottlenecks and restricted gene flow during glacial periods,underscoring the impact of dispersal capacity on evolutionary outcomes.Our findings demonstrate that intrinsic biological traits,particularly dispersal ability,fundamentally influence genetic architecture,population connectivity,and local adaptation.This study not only provides empirical evidence of how life-history traits shape evolutionary dynamics but also offers a framework for integrating intrinsic and extrinsic factors in understanding biodiversity formation.展开更多
Microsatellite markers with polymorphic advantages are widely used in the exploration and utilization of marine fishery resources.In this study,16 polymorphic microsatellite markers were used to evaluate the diversity...Microsatellite markers with polymorphic advantages are widely used in the exploration and utilization of marine fishery resources.In this study,16 polymorphic microsatellite markers were used to evaluate the diversity and population structure of Setipinna tenuifilis,a nearshore fish of economic and ecological value in the western Pacific Ocean and Indian Ocean.The genetic diversity of S.tenuifilis showed a high level[mean Na(number of alleles)is 23.25,mean Ho(observed heterozygosity)is 0.639,mean R_(a)(allelic richness)is 11.625,and the polymorphic information content(PIC)is 0.844]similar to other Clupeiformes fish species.The nine wild S.tenuifilis populations showed significant differentiation(F_(ST)ranging from 0.00384 to 0.19346)and were generally divided into southern and northern populations based on genetic structure,except for the Zhoushan population,which exhibited genetic mixture.Our results provide fundamental but significant genetic insights for the management and conservation of S.tenuifilis fishery resources.展开更多
Background As an important genetic resource of chickens,gamecock has unique morphological and behavioral characteristics such as large size,muscular development and strong aggression,making it a good model for studyin...Background As an important genetic resource of chickens,gamecock has unique morphological and behavioral characteristics such as large size,muscular development and strong aggression,making it a good model for studying muscle development and behavior patterns,as well as an excellent breeding material.Gamecocks are distributed worldwide,forming different breeds and strains.However,the single or multiple origin of global gamecocks has not been fully established and much remains unknown about genetic introgression events between gamecocks and other chickens.Therefore,in this study,based on whole genome data of gamecocks,Chinese indigenous chickens,commercial chickens and wild jungle fowls,we performed population structure analysis,selection signal analysis,and genomic introgression analysis of gamecocks.Results The population structure analysis revealed that gamecocks have multiple origins.In addition,we used Fst,π-Ratio and XP-EHH methods to explore the candidate signatures of positive selection in gamecocks.A total number of fifteen shared candidate genes were identified using the three different detection strategies.Among these candidate genes,ETV1,DGKB,AGMO,MEOX2,ISPD and PLCB4 are related to the growth and muscle development,fighting performance and neurodevelopment of gamecocks.Furthermore,we detected the introgression event at the MYBPHL region from the Gallus sonneratii into Euramerican gamecocks and at the CPZ gene region from the Gallus gallus gallus into multiple gamecock populations,respectively,indicating the introgression from the wild junglefowl may impact the skeletal and muscle development as well as aggressive behavior of gamecocks.Conclusions In summary,we conducted a genome-wide exploration of gamecocks from multiple regions worldwide.Our analysis confirmed multiple origins of gamecocks and detected several candidate genes that are possibly related to important traits and characteristics in gamecocks.More importantly,this is the first study that has detected introgression events and genes from wild jungle fowls to gamecocks,which provides evidence of the wild jungle fowls contributing to the genetic diversity of gamecocks.Our findings offer new perspectives on the impact of introgression on gamecocks,and provide a basis for further resource conservation and utilization of gamecock,as well as provide excellent material for the genetic improvement of domestic chickens.展开更多
This paper was based on data collected during the 38th and 39th Chinese National Antarctic Research Expeditions in the Amundsen Sea. The spatiotemporal distribution patterns of length(total length, AT) and sexual matu...This paper was based on data collected during the 38th and 39th Chinese National Antarctic Research Expeditions in the Amundsen Sea. The spatiotemporal distribution patterns of length(total length, AT) and sexual maturity stages of Antarctic krill(Euphausia superba) were examined. The age structure and geographic distribution of cluster groups also were studied. The results reveal significant diurnal variations in the length and maturity stages of Antarctic krill during the morning(MRN) to morning twilight(MTW) period, with mean lengths ranging from 28.92 to 45.87 mm. Two cyclical patterns were observed.Regarding maturity stages, the krill were composed of juveniles, adult males, and adult females in increasing order of proportion,with a notably higher proportion of non-gravid females compared to gravid females, and mainly distributed in evening twilight(ETW) to dawn(DWN), MTW to day(DAY), MRN to MTW, MRN to MTW and night(NIT) to DAY periods, respectively.Significant spatial variations in krill length and maturity stages occur, with a marked regional boundary around 130°W. K-means clustering analysis of krill length identified Group Ⅰ, Group Ⅱ, and Group Ⅲ, with dominant age classes of 3+, 0 and 3+, and 3+to 4+, respectively. Group Ⅱ was widely distributed in the surveyed waters, whereas Group Ⅰ and Group Ⅲ were distributed only in waters west of 130°W. The study area features a significant continental slope, where adults and gravid females were primarily distributed on its slopes and to the south. This spatial pattern also profoundly influenced the distribution of different cluster groups.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
In order to determine an appropriate sampling strategy for the effective conservation of wild soybean (Glycine soja Sieb. et Zucc.) in China, a natural population from Jiangwan Airport in Shanghai was studied for its ...In order to determine an appropriate sampling strategy for the effective conservation of wild soybean (Glycine soja Sieb. et Zucc.) in China, a natural population from Jiangwan Airport in Shanghai was studied for its genetic diversity through the inter-simple sequence repeat (ISSR) marker analysis of a sample set consisting of 100 randomly collected individuals. A relatively large genetic diversity was detected among the samples based on estimation of DNA products amplified from 15 selected ISSR primers, with the similarity coefficient varying from 0.17 to 0.89. The mean expected heterozygosity (He) was 0.171 4 per locus, and Shannon index (1) was 0.271 4. The Principal Coordinate Analysis (PCA) further indicated that genetic diversity of the Jiangwan wild soybean population was not evenly distributed, instead, was presented by a mosaic or clustered distribution pattern. Correlation study between genetic diversity and number of samples demonstrated that genetic diversity increased dramatically with the increase of number of samples within 40 individuals, but the increase became slow and rapidly reached a plateau when more than 40 individuals were included in the analysis. It is concluded that (i) a sample set of approximately 35-45 individuals should be included to represent possibly high genetic diversity when conservation of a wild soybean population ex situ is undertaken; and (ii) collection of wild soybean samples should be spread out as wide as possible within a population, and a certain distance should be kept as intervals among individuals for sampling.展开更多
The spatial distribution and population dynamics of Quercus liaotungensis Koidz., Fraxinus rhynchophylla Hance and Acer mono Maxim. were studied in three warm temperate deciduous forests in Dongling Mountain, Beijing....The spatial distribution and population dynamics of Quercus liaotungensis Koidz., Fraxinus rhynchophylla Hance and Acer mono Maxim. were studied in three warm temperate deciduous forests in Dongling Mountain, Beijing. Clumped distributions appeared in most seedlings (≤0.4 m), short saplings (0.4-1 m) and tall saplings (1-2 m). Random distributions appeared in adults of Q. liaotungensis in Plot 1, F. rhynchophylla in Plot 3. The LSD method was used to discern the differences of different aged population. The class distribution of Q. liaotungensis was nearly a reverse-J shape for Plot 1 and Plot 3, suggesting that the population regenerates continuously. The age-structures of F. rhynchophylla and A. mono in Plot 1 and the test results indicated that they would increase continuously. In Plot 2, the class distribution and the test results showed that all populations would not regenerate continuously.展开更多
We used sequences of mitochondrial control region （807bp） in 75 samples from three breeding colonies and one wintering population to investigate the genetic diversity and population structure of Marsh Grassbird （Lo...We used sequences of mitochondrial control region （807bp） in 75 samples from three breeding colonies and one wintering population to investigate the genetic diversity and population structure of Marsh Grassbird （Locustella pryeri sinensis） in different regions of China. Marsh Grassbird retained a moderate amount of haplotype （0.759 ± 0.056） and nucleotide diversity （0.002）. The results of FST among 3 phy-logeographic units and ФST between breeding and wintering sites revealed little evidence of genetic distinction between different colonies. Neither UPGMA tree structure analysis nor Network picture analysis showed obvious divergence between populations at different locations. Analysis of molecular variance also showed a lack of regional subdivision within Locustella pryeri sinesis, 98.5% of source of variation within populations and only 1.5% among populations. The neutrality test showed negative Fu’s FS value, which, in combination with detection of the mismatch distribution, suggested that population expansion occurred in the evolu-tionary history of this species. This hypothesis was further supported by Tajima’s D test and Fu’s test （D = -1.80, p = 0.02; Fs = -22.11, p = 0.001）, this expansion was estimated to occur about 28,700 years ago.展开更多
Objective The aim was to elucidate the effects of N rates on rice canopy microclimate and community health so as to provide a sci- entific basis for studying the production potential in irrigated rice with healthy can...Objective The aim was to elucidate the effects of N rates on rice canopy microclimate and community health so as to provide a sci- entific basis for studying the production potential in irrigated rice with healthy canopy. Method The effects of rice population structure traits under different N rates on rice canopy temperature, relative humidity （ RH）, light transmittance and sheath blight were studied by using Sunscan canopy analysis system and HOBO（ Pro Temp/RH IS logger）. Result The results showed that leaf area index, plant height and tiller number had significant effects on canopy cooling, RH enhancing and light reducing. Extremely significant multiple linear regression relationships existed among canopy day temperature, day RH, LAI and tiller number, and among light transmittance, tiller number and plant height. At flowering stage, per unit LAI could result in a day-maximum-temperature （Tmax） deceasing of 0.87℃ and a day-minimum-RH （RHmin） enhancing of 2.5% within canopy. Similarly, 100 plants per ms could respectively cause a Tmax deceasing of 1.23℃ and an RHmin enhancing of 3.3% in rice canopy. And per 10 cm plant height and 100 plants per m^2 could respectively reduce 9.3% and 7.8% of light in canopy. Conclusion Sheath blight disease index was significantly enhanced as the canopy day temperature decreased, day RH increased and light transmittance reduced. Bigger canopy from higher nitrogen level treatment leads to a more stable canopy microclimate with little changes in temperature and RH during day and night, which has the risk of worsening canopy health. Thus, moderately controlling the space development of canopy is the basis of constructing healthy canopy in rice.展开更多
In this study, 34 molecular markers of starch synthesis-related genes were used to evaluate the genetic variation and population structure of 87 indica rice cultivars from different countries and regions. The results ...In this study, 34 molecular markers of starch synthesis-related genes were used to evaluate the genetic variation and population structure of 87 indica rice cultivars from different countries and regions. The results showed that a total of 80 alleles were amplified using 34 primer pairs, with an average of 2.5 alleles per locus. The allele number varied from 2 to 6 among various cultivars. Shannon＇s diversity index of molecular markers varied from 0.303 to 0.796, with an average of 0.539. Polymorphism information content （PIC） varied from 0.084 to 0.658, with an average of 0.295. The genetic similarity coefficients of 87 indica rice cultivars ranged from 0.265 to 0.990, indicating significant genetic differences of starch synthesis-related genes among different cultivars, but the variation frequency of alleles varied among different cultivars. Population structure analysis showed that these 87 indica rice cultivars were divided into three categories. Genetic differences were small within the same category but great among different categories. Moreover, indica rice cultivars with simple genetic components accounted for 39.1% and those with complex genetic background accounted for 60.9%. This study may not only provide theoretical basis for genetic improvement of rice starch quality, but also lay a solid foundation for subsequent association analysis of rice quality-related traits.展开更多
This paper discussed the stability of model of an age structured population systems,proved that the equilibrium solution systems is globally asymptotically stable.
Age, maturation and population structure of the Humboldt squid Dosidicus gigas were studied based on random sampling of the Chinese jigging fishery off the Peruvian Exclusive Economic Zones （EEZ） during 2008-2010. E...Age, maturation and population structure of the Humboldt squid Dosidicus gigas were studied based on random sampling of the Chinese jigging fishery off the Peruvian Exclusive Economic Zones （EEZ） during 2008-2010. Estimated ages ranged from 144 to 633 days, confirming that the squid is a short-lived species with longevity no longer than 2 years. Occurrence of mature females and hatching in each month indicated that Humboldt squid spawned year-round. Back-calculated hatching dates for the samples were from January 22^nd, 2008 to April 22nd, 2010 with a peak between January and March. Two size-based and two hatching date-based populations could be defined from mantle length （ML） at maturity and back-calculated hatching dates, respectively. Females matured at a larger size than males, and there was a significant difference in ML at maturity between the two hatching groups （P〈0.05）. The waters adjacent to 1 l^S off the Peruvian EEZ may be a potential spawning ground. This study shows the complexity of the population structure and large variability in key life history parameters in the Humboldt squid off the Peruvian EEZ, which should be considered in the assessment and management of this important resource.展开更多
Chinese mitten crab （Eriocheir sinensis） has higher commercial value as food source than any other species of Eriocheir in China. To evaluate the germplasm resources and characterize the genetic diversity and popula...Chinese mitten crab （Eriocheir sinensis） has higher commercial value as food source than any other species of Eriocheir in China. To evaluate the germplasm resources and characterize the genetic diversity and population structure of the crabs in different water systems, two stocks and two farming populations were assessed with 25 polymorphic microsallite loci available in public GenBank. Basic statistics showed that the average observed heterozygosity （Ho） amongst populations ranged from 0.5789 to 0.6824. However, a remarkable presence of inbreeding and heterozygote deficiencies were observed. To analyze population structure, pairwise FST coefficients explained only -10.3% variability from the subdivision of mitten crab populations, the remaining variability stems from the subdivision within subpopulations. Although the four populations had slight differentiation, different allelic frequencies resulted in distinct population structures. Two stocks and one farming population were clustered together to the phylogenetic branch of Yangtze crab, with an approximate membership of 95%. Whereas, another farming population was clustered singly to the phylogenetic branch of the Liaohe crab, with a membership of 97.1%. The tests for individual admixture showed that Yangtze crab had probably been contaminated with individuals from other water systems. Genetic relationships between populations also supported the conclusion that Yangtze crab and Liaohe crab had different gene pools in spite of the origins of the same species.展开更多
Nine Chinese yak breeds （Maiwa, Tianzhu White, Qinghai Plateau, Sibu, Zhongdian, Pali, Tibetan High Mountain, Jiulong, and Xinjiang） and Gayal were analyzed by means of 16 microsatellite markers to determine the lev...Nine Chinese yak breeds （Maiwa, Tianzhu White, Qinghai Plateau, Sibu, Zhongdian, Pali, Tibetan High Mountain, Jiulong, and Xinjiang） and Gayal were analyzed by means of 16 microsatellite markers to determine the level of genetic variation within populations, genetic relationship between populations, and population structure for each breed. A total of 206 microsatellite alleles were observed. Mean F-statistics （0.056） for 9 yak breeds indicated that 94.4% of the genetic variation was observed within yak breeds and 5.6% of the genetic variation existed amongst breeds. The Neighbor-Joining phylogenetic tree was constructed based on Nei＇s standard genetic distances and two clusters were obtained. The Gayal separated from the yaks far away and formed one cluster and 9 yak breeds were grouped together. The analysis of population structure for 9 yak breeds and the Gayal showed that they resulted in four clusters; one cluster includes yaks from Tibet Autonomous Region and Qinghai Province, one cluster combines Zhongdian, Maiwa, and Tianzhu White, and Jiulong and Xinjiang come into the third cluster. Pali was mainly in the first cluster （90%）, Jiulong was mainly in the second cluster （87.1%）, Zhongdian was primarily in the third cluster （83%）, and the other yak breeds were distributed in two to three clusters. The Gayal was positively left in the fourth cluster （99.3%）.展开更多
基金Project supported by the Doctoral Foundation Project of Guizhou University(Grant No.(2019)49)the National Natural Science Foundation of China(Grant No.71961003)the Science and Technology Program of Guizhou Province(Grant No.7223)。
文摘In evolutionary games,most studies on finite populations have focused on a single updating mechanism.However,given the differences in individual cognition,individuals may change their strategies according to different updating mechanisms.For this reason,we consider two different aspiration-driven updating mechanisms in structured populations:satisfied-stay unsatisfied shift(SSUS)and satisfied-cooperate unsatisfied defect(SCUD).To simulate the game player’s learning process,this paper improves the particle swarm optimization algorithm,which will be used to simulate the game player’s strategy selection,i.e.,population particle swarm optimization(PPSO)algorithms.We find that in the prisoner’s dilemma,the conditions that SSUS facilitates the evolution of cooperation do not enable cooperation to emerge.In contrast,SCUD conditions that promote the evolution of cooperation enable cooperation to emerge.In addition,the invasion of SCUD individuals helps promote cooperation among SSUS individuals.Simulated by the PPSO algorithm,the theoretical approximation results are found to be consistent with the trend of change in the simulation results.
文摘Simulation was used to investigate the effects of population structure and migration on metrics of pairwise shared ancestry. Random and hierarchical structures, or migration geometries, were examined. Compared to panmictic populations, progress to all qualitative metrics of pairwise ancestry is delayed in structured populations. However, unless migration is very low, the time required is generally less than triple and often less than twice that required in a panmictic population of the same total size. Population structure also increases, to a similar degree, the time required for a population-wide most recent common ancestor (MRCA). As a result, the relationships between various qualitative metrics of pairwise shared ancestry and MRCA time are relatively unaffected by population structure. For example, the mean time to most recent shared ancestor (MRSA) with global sampling of pairs is 40% - 50% of the MRCA time for almost all simulated structures and migration levels. Quantitative pairwise genealogical overlap is strongly affected by population structure. With global sampling, pairwise quantitative overlap never approaches 1.0, as it does in panmictic populations;and instead eventually becomes stationary at much lower values. Possible implications of the present results for human pairwise shared ancestry are discussed. For globally sampled pairs, the longest time to most recent shared ancestor (MRSA) for humans is suggested to be approximately 2100 years before the present. If generation time is 30 years, then all humans are 69th, or closer, cousins. For people with recent European ancestry, the MRSA time may be only half as long, about 1000 years.
文摘The growth of filamentous microorganism is contributed by tip extension and branching. The microscopic growth of filamentous microorganism means the growth process from one or a few spores. In order to describe the microscopic process, a population morphologically structured model is proposed, in which three morphological compartment and their interactions were considered, and the heterogeneity of hyphal growth was included. The model was applied to describe the microscopic growth of Streptomyces tendae and Geotrichum candidum with good agreement. From model prediction, it is concluded that if the number of hyphae is large enough (macroscopic growth), the specific growth rate of filamentous microorganism and the ratio of morphological forms in hyphae will become constant.
基金supported by the National Natural Science Foundation of China Project(Grant No.32260097)the National Guidance Foundation for Local Science and Technology Development of China(Grant No.[2023]009)the Natural Science Foundation for Distinguished Young Scholars of Hebei(Grant No.C2022209010)。
文摘Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis.The total length was612.91 Mb,and 25755 genes were detected in the chayote genome.The contig N50 was more than 20.01 Mb,and the scaffold N50 was over47.11 Mb.Of the genome,60.35%were composed of repetitive sequences,and 31.18%of genome sequences belonged to long-terminal repeats.A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference.Based on this genome-wide and global alignment map,researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species.Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree,population structure analysis,and principal component analysis using genome re-sequencing data.The chayote genome,re-sequencing dataset,and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research(STEP)Program(2019QZKK05010900 and 2019QZKK05010405)the National Natural Science Foundation of China(32100339 and 32200350)+3 种基金Yunnan Revitalization Talent Support Program Top team(202405AS350022)supported by the Youth Innovation Promotion Association,Chinese Academy of Sciencessupported by Yunnan Fundamental Research Projects(202201AU070208)supported by Yunnan Revitalization Talent Support Program Yunling Scholar Project(XML)。
文摘Understanding how species diverge and adapt is fundamental to unraveling biodiversity.While environmental impacts on species evolution are well-documented,the roles of intrinsic life-history traits remain underexplored.The Qinghai-Xizang Plateau,with its harsh conditions and unique biodiversity,offers a natural laboratory for such investigations.Here,we examine two sympatric small mammals—the solitary,low-dispersal plateau zokor(Eospalax baileyi)and the social,high-dispersal plateau pika(Ochotona curzoniae)—to elucidate how life-history traits shape population structures and adaptive strategies.Through whole-genome sequencing and cardiac-blood phenotype analyses,we reveal striking differences in their evolutionary trajectories.Despite enduring similar environmental pressures,plateau zokor populations exhibit pronounced genetic subdivisions,high inbreeding,and distinct local adaptations.In contrast,plateau pika populations display genetic panmixia,widespread diversity,and adaptive uniformity.Demographic inference highlights that plateau zokors experienced severe population bottlenecks and restricted gene flow during glacial periods,underscoring the impact of dispersal capacity on evolutionary outcomes.Our findings demonstrate that intrinsic biological traits,particularly dispersal ability,fundamentally influence genetic architecture,population connectivity,and local adaptation.This study not only provides empirical evidence of how life-history traits shape evolutionary dynamics but also offers a framework for integrating intrinsic and extrinsic factors in understanding biodiversity formation.
基金The Zhejiang Provincial Natural Science Foundation of China under contract Nos LY22D060001 and LY20C190008the National Natural Science Foundation of China(NSFC)under contract No.41806156the Key Research and Development Projects in Xizang under contract No.XZ202301ZY0012N.
文摘Microsatellite markers with polymorphic advantages are widely used in the exploration and utilization of marine fishery resources.In this study,16 polymorphic microsatellite markers were used to evaluate the diversity and population structure of Setipinna tenuifilis,a nearshore fish of economic and ecological value in the western Pacific Ocean and Indian Ocean.The genetic diversity of S.tenuifilis showed a high level[mean Na(number of alleles)is 23.25,mean Ho(observed heterozygosity)is 0.639,mean R_(a)(allelic richness)is 11.625,and the polymorphic information content(PIC)is 0.844]similar to other Clupeiformes fish species.The nine wild S.tenuifilis populations showed significant differentiation(F_(ST)ranging from 0.00384 to 0.19346)and were generally divided into southern and northern populations based on genetic structure,except for the Zhoushan population,which exhibited genetic mixture.Our results provide fundamental but significant genetic insights for the management and conservation of S.tenuifilis fishery resources.
基金supported by the National Key Research and Development Program of China(2024YFF1001400)the Open Project of State Key Laboratory of Animal Biotech Breeding(2024SKLAB6-106)Fundamental Research Funds for Central University(7110100870).
文摘Background As an important genetic resource of chickens,gamecock has unique morphological and behavioral characteristics such as large size,muscular development and strong aggression,making it a good model for studying muscle development and behavior patterns,as well as an excellent breeding material.Gamecocks are distributed worldwide,forming different breeds and strains.However,the single or multiple origin of global gamecocks has not been fully established and much remains unknown about genetic introgression events between gamecocks and other chickens.Therefore,in this study,based on whole genome data of gamecocks,Chinese indigenous chickens,commercial chickens and wild jungle fowls,we performed population structure analysis,selection signal analysis,and genomic introgression analysis of gamecocks.Results The population structure analysis revealed that gamecocks have multiple origins.In addition,we used Fst,π-Ratio and XP-EHH methods to explore the candidate signatures of positive selection in gamecocks.A total number of fifteen shared candidate genes were identified using the three different detection strategies.Among these candidate genes,ETV1,DGKB,AGMO,MEOX2,ISPD and PLCB4 are related to the growth and muscle development,fighting performance and neurodevelopment of gamecocks.Furthermore,we detected the introgression event at the MYBPHL region from the Gallus sonneratii into Euramerican gamecocks and at the CPZ gene region from the Gallus gallus gallus into multiple gamecock populations,respectively,indicating the introgression from the wild junglefowl may impact the skeletal and muscle development as well as aggressive behavior of gamecocks.Conclusions In summary,we conducted a genome-wide exploration of gamecocks from multiple regions worldwide.Our analysis confirmed multiple origins of gamecocks and detected several candidate genes that are possibly related to important traits and characteristics in gamecocks.More importantly,this is the first study that has detected introgression events and genes from wild jungle fowls to gamecocks,which provides evidence of the wild jungle fowls contributing to the genetic diversity of gamecocks.Our findings offer new perspectives on the impact of introgression on gamecocks,and provide a basis for further resource conservation and utilization of gamecock,as well as provide excellent material for the genetic improvement of domestic chickens.
基金supported by the 38th and 39th CHINAREs and all members of the two Antarctic cruisessupported by Ministry of Natural Resources of the People’s Republic of China and the Chinese Arctic and Antarctic Administration。
文摘This paper was based on data collected during the 38th and 39th Chinese National Antarctic Research Expeditions in the Amundsen Sea. The spatiotemporal distribution patterns of length(total length, AT) and sexual maturity stages of Antarctic krill(Euphausia superba) were examined. The age structure and geographic distribution of cluster groups also were studied. The results reveal significant diurnal variations in the length and maturity stages of Antarctic krill during the morning(MRN) to morning twilight(MTW) period, with mean lengths ranging from 28.92 to 45.87 mm. Two cyclical patterns were observed.Regarding maturity stages, the krill were composed of juveniles, adult males, and adult females in increasing order of proportion,with a notably higher proportion of non-gravid females compared to gravid females, and mainly distributed in evening twilight(ETW) to dawn(DWN), MTW to day(DAY), MRN to MTW, MRN to MTW and night(NIT) to DAY periods, respectively.Significant spatial variations in krill length and maturity stages occur, with a marked regional boundary around 130°W. K-means clustering analysis of krill length identified Group Ⅰ, Group Ⅱ, and Group Ⅲ, with dominant age classes of 3+, 0 and 3+, and 3+to 4+, respectively. Group Ⅱ was widely distributed in the surveyed waters, whereas Group Ⅰ and Group Ⅲ were distributed only in waters west of 130°W. The study area features a significant continental slope, where adults and gravid females were primarily distributed on its slopes and to the south. This spatial pattern also profoundly influenced the distribution of different cluster groups.
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.
文摘In order to determine an appropriate sampling strategy for the effective conservation of wild soybean (Glycine soja Sieb. et Zucc.) in China, a natural population from Jiangwan Airport in Shanghai was studied for its genetic diversity through the inter-simple sequence repeat (ISSR) marker analysis of a sample set consisting of 100 randomly collected individuals. A relatively large genetic diversity was detected among the samples based on estimation of DNA products amplified from 15 selected ISSR primers, with the similarity coefficient varying from 0.17 to 0.89. The mean expected heterozygosity (He) was 0.171 4 per locus, and Shannon index (1) was 0.271 4. The Principal Coordinate Analysis (PCA) further indicated that genetic diversity of the Jiangwan wild soybean population was not evenly distributed, instead, was presented by a mosaic or clustered distribution pattern. Correlation study between genetic diversity and number of samples demonstrated that genetic diversity increased dramatically with the increase of number of samples within 40 individuals, but the increase became slow and rapidly reached a plateau when more than 40 individuals were included in the analysis. It is concluded that (i) a sample set of approximately 35-45 individuals should be included to represent possibly high genetic diversity when conservation of a wild soybean population ex situ is undertaken; and (ii) collection of wild soybean samples should be spread out as wide as possible within a population, and a certain distance should be kept as intervals among individuals for sampling.
文摘The spatial distribution and population dynamics of Quercus liaotungensis Koidz., Fraxinus rhynchophylla Hance and Acer mono Maxim. were studied in three warm temperate deciduous forests in Dongling Mountain, Beijing. Clumped distributions appeared in most seedlings (≤0.4 m), short saplings (0.4-1 m) and tall saplings (1-2 m). Random distributions appeared in adults of Q. liaotungensis in Plot 1, F. rhynchophylla in Plot 3. The LSD method was used to discern the differences of different aged population. The class distribution of Q. liaotungensis was nearly a reverse-J shape for Plot 1 and Plot 3, suggesting that the population regenerates continuously. The age-structures of F. rhynchophylla and A. mono in Plot 1 and the test results indicated that they would increase continuously. In Plot 2, the class distribution and the test results showed that all populations would not regenerate continuously.
基金supported by National Natural Science Foundation of China (No. 130370221 and No. 30770309)
文摘We used sequences of mitochondrial control region （807bp） in 75 samples from three breeding colonies and one wintering population to investigate the genetic diversity and population structure of Marsh Grassbird （Locustella pryeri sinensis） in different regions of China. Marsh Grassbird retained a moderate amount of haplotype （0.759 ± 0.056） and nucleotide diversity （0.002）. The results of FST among 3 phy-logeographic units and ФST between breeding and wintering sites revealed little evidence of genetic distinction between different colonies. Neither UPGMA tree structure analysis nor Network picture analysis showed obvious divergence between populations at different locations. Analysis of molecular variance also showed a lack of regional subdivision within Locustella pryeri sinesis, 98.5% of source of variation within populations and only 1.5% among populations. The neutrality test showed negative Fu’s FS value, which, in combination with detection of the mismatch distribution, suggested that population expansion occurred in the evolu-tionary history of this species. This hypothesis was further supported by Tajima’s D test and Fu’s test （D = -1.80, p = 0.02; Fs = -22.11, p = 0.001）, this expansion was estimated to occur about 28,700 years ago.
基金Supported by Oversea Project of National Natural and Science Foundationof China(30528005)RTOP Project of International RiceResearch Institute(IRRI)+1 种基金Grain High-yield Project of China(2004BA520A12)And 948 Introduction Project of the Ministry ofAgriculture(2003-Z53)~~
文摘Objective The aim was to elucidate the effects of N rates on rice canopy microclimate and community health so as to provide a sci- entific basis for studying the production potential in irrigated rice with healthy canopy. Method The effects of rice population structure traits under different N rates on rice canopy temperature, relative humidity （ RH）, light transmittance and sheath blight were studied by using Sunscan canopy analysis system and HOBO（ Pro Temp/RH IS logger）. Result The results showed that leaf area index, plant height and tiller number had significant effects on canopy cooling, RH enhancing and light reducing. Extremely significant multiple linear regression relationships existed among canopy day temperature, day RH, LAI and tiller number, and among light transmittance, tiller number and plant height. At flowering stage, per unit LAI could result in a day-maximum-temperature （Tmax） deceasing of 0.87℃ and a day-minimum-RH （RHmin） enhancing of 2.5% within canopy. Similarly, 100 plants per ms could respectively cause a Tmax deceasing of 1.23℃ and an RHmin enhancing of 3.3% in rice canopy. And per 10 cm plant height and 100 plants per m^2 could respectively reduce 9.3% and 7.8% of light in canopy. Conclusion Sheath blight disease index was significantly enhanced as the canopy day temperature decreased, day RH increased and light transmittance reduced. Bigger canopy from higher nitrogen level treatment leads to a more stable canopy microclimate with little changes in temperature and RH during day and night, which has the risk of worsening canopy health. Thus, moderately controlling the space development of canopy is the basis of constructing healthy canopy in rice.
基金Supported by Agricultural Science and Technology Independent Innovation Fund of Jiangsu Province[CX(14)5107]Science and Technology Support Program of Jiangsu Province(BE2015355)Special Fund for Construction of Modern Agricultural Industry Technology System(CARS-01-47)~~
文摘In this study, 34 molecular markers of starch synthesis-related genes were used to evaluate the genetic variation and population structure of 87 indica rice cultivars from different countries and regions. The results showed that a total of 80 alleles were amplified using 34 primer pairs, with an average of 2.5 alleles per locus. The allele number varied from 2 to 6 among various cultivars. Shannon＇s diversity index of molecular markers varied from 0.303 to 0.796, with an average of 0.539. Polymorphism information content （PIC） varied from 0.084 to 0.658, with an average of 0.295. The genetic similarity coefficients of 87 indica rice cultivars ranged from 0.265 to 0.990, indicating significant genetic differences of starch synthesis-related genes among different cultivars, but the variation frequency of alleles varied among different cultivars. Population structure analysis showed that these 87 indica rice cultivars were divided into three categories. Genetic differences were small within the same category but great among different categories. Moreover, indica rice cultivars with simple genetic components accounted for 39.1% and those with complex genetic background accounted for 60.9%. This study may not only provide theoretical basis for genetic improvement of rice starch quality, but also lay a solid foundation for subsequent association analysis of rice quality-related traits.
文摘This paper discussed the stability of model of an age structured population systems,proved that the equilibrium solution systems is globally asymptotically stable.
基金Supported by the National Natural Science Foundation of China (No.41276156)the National High Technology Research and Development Program of China (863 Program) (No. 2012AA092303)+3 种基金the Innovation Program of Shanghai Municipal Education Commission (No. 13YZ091)Shanghai Leading Academic Disciplin Projectsupported by National Distant-Water Fisheries Engineering Research Center, and Scientific Observing and Experimental Station of Oceanic Fishery Resources, Ministry of AgricultureYong Chen’s involvement in the project was supported by the Shanghai Dongfang Scholar Program
文摘Age, maturation and population structure of the Humboldt squid Dosidicus gigas were studied based on random sampling of the Chinese jigging fishery off the Peruvian Exclusive Economic Zones （EEZ） during 2008-2010. Estimated ages ranged from 144 to 633 days, confirming that the squid is a short-lived species with longevity no longer than 2 years. Occurrence of mature females and hatching in each month indicated that Humboldt squid spawned year-round. Back-calculated hatching dates for the samples were from January 22^nd, 2008 to April 22nd, 2010 with a peak between January and March. Two size-based and two hatching date-based populations could be defined from mantle length （ML） at maturity and back-calculated hatching dates, respectively. Females matured at a larger size than males, and there was a significant difference in ML at maturity between the two hatching groups （P〈0.05）. The waters adjacent to 1 l^S off the Peruvian EEZ may be a potential spawning ground. This study shows the complexity of the population structure and large variability in key life history parameters in the Humboldt squid off the Peruvian EEZ, which should be considered in the assessment and management of this important resource.
文摘Chinese mitten crab （Eriocheir sinensis） has higher commercial value as food source than any other species of Eriocheir in China. To evaluate the germplasm resources and characterize the genetic diversity and population structure of the crabs in different water systems, two stocks and two farming populations were assessed with 25 polymorphic microsallite loci available in public GenBank. Basic statistics showed that the average observed heterozygosity （Ho） amongst populations ranged from 0.5789 to 0.6824. However, a remarkable presence of inbreeding and heterozygote deficiencies were observed. To analyze population structure, pairwise FST coefficients explained only -10.3% variability from the subdivision of mitten crab populations, the remaining variability stems from the subdivision within subpopulations. Although the four populations had slight differentiation, different allelic frequencies resulted in distinct population structures. Two stocks and one farming population were clustered together to the phylogenetic branch of Yangtze crab, with an approximate membership of 95%. Whereas, another farming population was clustered singly to the phylogenetic branch of the Liaohe crab, with a membership of 97.1%. The tests for individual admixture showed that Yangtze crab had probably been contaminated with individuals from other water systems. Genetic relationships between populations also supported the conclusion that Yangtze crab and Liaohe crab had different gene pools in spite of the origins of the same species.
文摘Nine Chinese yak breeds （Maiwa, Tianzhu White, Qinghai Plateau, Sibu, Zhongdian, Pali, Tibetan High Mountain, Jiulong, and Xinjiang） and Gayal were analyzed by means of 16 microsatellite markers to determine the level of genetic variation within populations, genetic relationship between populations, and population structure for each breed. A total of 206 microsatellite alleles were observed. Mean F-statistics （0.056） for 9 yak breeds indicated that 94.4% of the genetic variation was observed within yak breeds and 5.6% of the genetic variation existed amongst breeds. The Neighbor-Joining phylogenetic tree was constructed based on Nei＇s standard genetic distances and two clusters were obtained. The Gayal separated from the yaks far away and formed one cluster and 9 yak breeds were grouped together. The analysis of population structure for 9 yak breeds and the Gayal showed that they resulted in four clusters; one cluster includes yaks from Tibet Autonomous Region and Qinghai Province, one cluster combines Zhongdian, Maiwa, and Tianzhu White, and Jiulong and Xinjiang come into the third cluster. Pali was mainly in the first cluster （90%）, Jiulong was mainly in the second cluster （87.1%）, Zhongdian was primarily in the third cluster （83%）, and the other yak breeds were distributed in two to three clusters. The Gayal was positively left in the fourth cluster （99.3%）.
