In this paper,we establish and study a single-species logistic model with impulsive age-selective harvesting.First,we prove the ultimate boundedness of the solutions of the system.Then,we obtain conditions for the asy...In this paper,we establish and study a single-species logistic model with impulsive age-selective harvesting.First,we prove the ultimate boundedness of the solutions of the system.Then,we obtain conditions for the asymptotic stability of the trivial solution and the positive periodic solution.Finally,numerical simulations are presented to validate our results.Our results show that age-selective harvesting is more conducive to sustainable population survival than non-age-selective harvesting.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
In this study,families of selected population for growth(SP_BWT),selected population for white spot syndrome virus(WSSV)resistance(SP_RW),Bohai wild population(WP_BH)and Huanghai wild population(WP_HH)of F.chinensis w...In this study,families of selected population for growth(SP_BWT),selected population for white spot syndrome virus(WSSV)resistance(SP_RW),Bohai wild population(WP_BH)and Huanghai wild population(WP_HH)of F.chinensis were constructed through artificial insemination and with the standardized procedure of larvae rearing.Growth and survival performance were studied among four populations after a 70 days common test.The results showed that the maximum least square mean of body weight was 17.50 g in SP_BWT while the minimum was 13.03 g in WP_HH.Compared with WP_BH,body weight of SP_BWT increased by 23.41%(P<0.01)and that of SP_RW by 12.20%(P>0.05).Body weights of SP_BWT and SP_RW were significantly higher than that of WP_HH,which increased by 34.31%(P<0.01)and 22.10%(P<0.05),respectively.The mean AGR of four populations was 0.19,0.18,0.17 and 0.16 g d^(-1),respectively.Coefficient of variation of body weight among four populations was high,which ranged from 32.67% to 35.25%.Such a range showed that there was the potentiality for further improvement in selected populations.Coefficient of variation of survival rate among four populations was low,varying between 3.20% and 5.90%.The difference of survival was highly significant(P<0.01)between SP_BWT and WP_BH,and significant(P<0.05)between SP_RW and WP_BH.However,no significant difference among other populations(P>0.05)was observed.Different growth performances were also observed among different families in each population.The body weight of 798F family was the highest.The absolute growth rate(AGR)was 0.25 g d^(-1),150%higher than that of the lowest one,0.1 g d^(-1) in 807F family.Survival rate of families among four populations was different.The highest was 94.74%,and the lowest was 71.88%.展开更多
To assess the genetic diversity between randomly and selectively bred populations,we sequenced 438 bp of the mitochondrial DNA control region from 102 pigs.These samples represented four native pig breeds,one nucleus ...To assess the genetic diversity between randomly and selectively bred populations,we sequenced 438 bp of the mitochondrial DNA control region from 102 pigs.These samples represented four native pig breeds,one nucleus and one conservation herd from Yunnan,China.Twenty haplotypes with sixteen polymorphic sites were identified.The number of haplotypes in the nucleus herd of Saba pig and the conservation herd of Banna miniature pig were restricted to three and one,respectively,while the randomly bred pig populations exhibited over six haplotypes.Notably,haplotype diversity in randomly bred populations was significantly greater than the selectively bred populations（h=0.732 vs.0.425 and 0,exact test,P≤0.0036）.These findings demonstrate that selective breeding generated low genetic diversity compared to randomly bred pig breeds.A timely intervention and well programmed breeding approach would stop further genetic diversity reduction in the nucleus and conservation herds of native pig breeds.Otherwise,selective breeding would dramatically reduce genetic diversity in only several years,indicating that sharp contradictions exist between breeding,conservation and genetic diversity.Genetic relationships are discussed based on net genetic distances among pig populations.展开更多
ln this study, 12 maize populations were improved with the improved S1 selection method, aiming to increase the improvement efficiency of maize popula-tions. The results showed that number of rows per spike, number of...ln this study, 12 maize populations were improved with the improved S1 selection method, aiming to increase the improvement efficiency of maize popula-tions. The results showed that number of rows per spike, number of grains per row and 100-grain weight were the three important component traits of maize yield. The highest genetic increment was found in Mengqun 2, fol owed by Mengqun 4, Mengqun 1 and other 7 maize populations. Negative genetic increment was shown in Mengqun 3 and 3 introduced foreign maize populations. Some changes were shown in spikes, plant traits and genetic diversity of maize populations. Based on our results, we concluded that Mengqun 2, Mengqun 4, Zhongzong 7, Mengqun C and Mengqun A could be directly used for the line breeding by selfing for their higher genetic increment of yield and better improvement effects of other agricultural traits. Compared with these 5 populations, the improvement potential of other maize populations was limited for their lower genetic increment.展开更多
Reid, Lancaster, Tuxpeno and Suwan are the most common maize (Zea mays L.) germplasms. Reid × Lancaster and Suwan × Tuxpeno are very important heterotic patterns in temperate areas and tropical areas, respec...Reid, Lancaster, Tuxpeno and Suwan are the most common maize (Zea mays L.) germplasms. Reid × Lancaster and Suwan × Tuxpeno are very important heterotic patterns in temperate areas and tropical areas, respectively. Broadening the genetic basis of maize has usually been conducted in inter-populations formed by crossing temperate and tropical germplasms. Reciprocal recurrent selection (RRS) is a breeding procedure to improve the inter-populational cross of two base populations. The objective of this study was to evaluate the direct and indirect effects of reciprocal recurrent selection on grain yield in the TR (Tuxpeno-Reid) and SL (Suwan-Lancaster) maize populations. The populations and the inter-populational crosses of each selection cycle, as well as two commercial hybrids, were evaluated in four environments. The effect of mean grain yield on TR × SL inter-population crosses was 4.63% (or 0.365 Mg·ha-1) cycle-1. The grain yield of SL increased by 2.78% (or 0.20 Mg·ha-1) cycle-1, but the grain yield of TR essentially did not change. Most changes in other agronomic traits occurred in the desired direction. After 3 selection cycles, the ear tip-barrenness length decreased in TR × SL, TR and SL by 39.70%, 37.50% and 24.57%, respectively, which indicates that the increase in grain yield may be largely due to a decreasing ear tip-barrenness length. The mid-parent heterosis of grain yield of the inter-populational cross increased from 15.49% to 25.96% from C0 to C3. The mean grain yields of TRC3 × SLC3 were 100.01% and 103.88% of the mean grain yields of the commercial single-crosses GD8 and QD16, respectively. The results suggest that Tuxpeno-Reid × Suwan-Lancaster may be possible new heterotic patterns in the southern region of China.展开更多
To solve the problem that soybean has narrow genetic base, we constructed a series of male sterile recurrent selection populations, and studied the effects of quality improvement and practical value. An LD-base popula...To solve the problem that soybean has narrow genetic base, we constructed a series of male sterile recurrent selection populations, and studied the effects of quality improvement and practical value. An LD-base population, which fits to our ecology type was constructed by 6 years＇ gene enrichment through the introduction of new genes from 23 local varieties and recurrent selection. The LD-base populations were then improved by making crosses with high protein and high oil genotypes. As a result we obtained a high protein sub-population （db） and a high oil sub-population （gy）, For the db sub-population, the protein content is 1.18% higher than the base population, 22.38% of the individuals contain 45% or more of protein, which is 10.99% higher than the base population. For the gy sub-population, oil content is 0.24% higher than the base population. Individuals with oil content of 20% or more are 11.05% higher than the base population. The quantitative characters such as flowering date, mature date, pod habit, and hilum color, etc., all showed wide range of separation, and the segregation ratio approached balance. The c.v. of branch number of ms1 recurrent population （72.8%） is higher than general cross-population （57.3%）, and the c.v. of 100 seed weight of ms1 （18.1%） is higher than general cross population （16.5%）, the coefficient of variation of plant height, pods per plant, and seeds per pod were not significantly different. It was demonstrated in this paper that the quality character of ms 1 male sterile recurrent selection population was improved by adding new genes. And the segregation of other characters widened, making the populations suitable for the objective of soybean breeding. In this paper, we also discussed the breeding method, key technology, and selection effect of soybean ms 1 population.展开更多
Genomic selection(GS)has been widely used in livestock,which greatly accelerated the genetic progress of complex traits.The population size was one of the significant factors affecting the prediction accuracy,while it...Genomic selection(GS)has been widely used in livestock,which greatly accelerated the genetic progress of complex traits.The population size was one of the significant factors affecting the prediction accuracy,while it was limited by the purebred population.Compared to directly combining two uncorrelated purebred populations to extend the reference population size,it might be more meaningful to incorporate the correlated crossbreds into reference population for genomic prediction.In this study,we simulated purebred offspring(PAS and PBS)and crossbred offspring(CAB)base on real genotype data of two base purebred populations(PA and PB),to evaluate the performance of genomic selection on purebred while incorporating crossbred information.The results showed that selecting key crossbred individuals via maximizing the expected genetic relationship(REL)was better than the other methods(individuals closet or farthest to the purebred population,CP/FP)in term of the prediction accuracy.Furthermore,the prediction accuracy of reference populations combining PA and CAB was significantly better only based on PA,which was similar to combine PA and PAS.Moreover,the rank correlation between the multiple of the increased relationship(MIR)and reliability improvement was 0.60-0.70.But for individuals with low correlation(Cor(Pi,PA or B),the reliability improvement was significantly lower than other individuals.Our findings suggested that incorporating crossbred into purebred population could improve the performance of genetic prediction compared with using the purebred population only.The genetic relationship between purebred and crossbred population is a key factor determining the increased reliability while incorporating crossbred population in the genomic prediction on pure bred individuals.展开更多
The maize population Csyn 4 was improved for three cycles with three recurrent selection methods MS1, MS1-HS, and MHSRRS in northern China. A total of 40 NC Ⅱ testcrosses were made by four testers with Csyn 4 and 10 ...The maize population Csyn 4 was improved for three cycles with three recurrent selection methods MS1, MS1-HS, and MHSRRS in northern China. A total of 40 NC Ⅱ testcrosses were made by four testers with Csyn 4 and 10 improved populations, which were evaluated in four environments in the cropping season of 2005. Analysis of variance indicated a significant progress （P〈 0.05） in yield and other chief agronomic traits in the improved populations and testcrosses, demonstrating that the three recurrent selection methods were effective for increasing grain yield of testcrosses and improvement of general combining ability in maize population. The average grain yield increase of population Csyn 4 in MS1, MS1-HS, and MHSRRS recurrent selections was 266.7 kg ha^-1 （5.3%）, 288.0 kg ha^-1 （5.7%）, and 231.3 kg ha^-1 （4.6%） per cycle, while the grain yield of S 1 progeny of population for Csyn 4 was increased by 420.0 kg ha^-1 （10.9%）, 376.0 kg ha^-1 （9.8%）, and 414.7 kg ha^-1 （10.8%） per cycle in MS1, MS1-HS, and MHSRRS recurrent selections, respectively. Linear responses （b） in the MS1, MS1-HS, and MHSRRS recurrent selections were the same as the realized responses of the selection （G） for grain yield increase of Csyn 4 and S1 progeny of the populations. The grain yield of testcrosses increased by 3.3-5.2% on average per cycle. The value of heterosis did not display any differences amongst the different cycles of selections. The GCA for yield component traits of population Csyn 4 was improved significantly by means of three selection methods, whereas the GCA for plant height, ear height, days to silking, and days to pollen did not show significant increase in the recurrent selections. GCA for the number of tassel branches were decreased in the selections, while GCA for the number of plant leaves were increased, but the difference was not significant.展开更多
Trawl is a main fishing gear in Chinese fishery,capturing large fish and letting small ones at large.However,long-term use of trawl would result in changes of phenotypic traits of the fish stocks,such as smaller size-...Trawl is a main fishing gear in Chinese fishery,capturing large fish and letting small ones at large.However,long-term use of trawl would result in changes of phenotypic traits of the fish stocks,such as smaller size-at-age and earlier age-at-maturation.In this study,we simulated a fish population with size characteristics of trawl fishing and the population produces one generation of offspring and lives for one year,used trawl to exploit the simulated fish population,and captured individuals by body size.We evaluated the impact of the changes on selectivity parameters,such as selective range and the length at 50% retention.Under fishing pressure,we specified the selectivity parameters,and determined that smaller selection rates and greater length at 50% retention were associated with an increased tendency towards miniaturization.展开更多
In many fields such as signal processing,machine learning,pattern recognition and data mining,it is common practice to process datasets containing huge numbers of features.In such cases,Feature Selection(FS)is often i...In many fields such as signal processing,machine learning,pattern recognition and data mining,it is common practice to process datasets containing huge numbers of features.In such cases,Feature Selection(FS)is often involved.Meanwhile,owing to their excellent global search ability,evolutionary computation techniques have been widely employed to the FS.So,as a powerful global search method and calculation fast than other EC algorithms,PSO can solve features selection problems well.However,when facing a large number of feature selection,the efficiency of PSO drops significantly.Therefore,plenty of works have been done to improve this situation.Besides,many studies have shown that an appropriate population initialization can effectively help to improve this problem.So,basing on PSO,this paper introduces a new feature selection method with filter-based population.The proposed algorithm uses Principal Component Analysis(PCA)to measure the importance of features first,then based on the sorted feature information,a population initialization method using the threshold selection and the mixed initialization is proposed.The experiments were performed on several datasets and compared to several other related algorithms.Experimental results show that the accuracy of PSO to solve feature selection problems is significantly improved after using proposed method.展开更多
In this paper, we explore a novel ensemble method for spectral clustering. In contrast to the traditional clustering ensemble methods that combine all the obtained clustering results, we propose the adaptive spectral ...In this paper, we explore a novel ensemble method for spectral clustering. In contrast to the traditional clustering ensemble methods that combine all the obtained clustering results, we propose the adaptive spectral clustering ensemble method to achieve a better clustering solution. This method can adaptively assess the number of the component members, which is not owned by many other algorithms. The component clusterings of the ensemble system are generated by spectral clustering （SC） which bears some good characteristics to engender the diverse committees. The selection process works by evaluating the generated component spectral clustering through resampling technique and population-based incremental learning algorithm （PBIL）. Experimental results on UCI datasets demonstrate that the proposed algorithm can achieve better results compared with traditional clustering ensemble methods, especially when the number of component clusterings is large.展开更多
The level of genetic variation within a breeding population affects the effectiveness of selection strategies for genetic improvement.The relationship between genetic variation level within Pinus tabuliformis breeding...The level of genetic variation within a breeding population affects the effectiveness of selection strategies for genetic improvement.The relationship between genetic variation level within Pinus tabuliformis breeding populations and selection strategies or selection effectiveness is not fully investigated.Here,we compared the selection effectiveness of combined and individual direct selection strategies using half-and full-sib families produced from advanced-generation P.tabuliformis seed orchard as our test populations.Our results revealed that,within half-sib families,average diameter at breast height(DBH),tree height,and volume growth of superior individuals selected by the direct selection strategy were higher by 7.72%,18.56%,and 31.01%,respectively,than those selected by the combined selection strategy.Furthermore,significant differences(P<0.01)were observed between the two strategies in terms of the expected genetic gains for average tree height and volume.In contrast,within full-sib families,the differences in tree average DBH,height,and volume between the two selection strategies were relatively minor with increase of 0.17%,2.73%,and 2.21%,respectively,and no significant differences were found in the average expected genetic gains for the studied traits.Half-sib families exhibited greater phenotypic and genetic variation,resulting in improved selection efficiency with the direct selection strategy but also introduced a level of inbreeding risk.Based on genetic distance estimates using molecular markers,our comparative seed orchard design analysis showed that the Improved Adaptive Genetic Programming Algorithm(IAPGA)reduced the average inbreeding coefficient by 14.36% and 14.73% compared to sequential and random designs,respectively.In conclusion,the combination of the direct selection strategy with IAPGA seed orchard design aimed at minimizing inbreeding offered an efficient approach for establishing advanced-generation P.tabuliformis seed orchards.展开更多
A nonresonant two-photon absorption process can be manipulated by tailoring the ultra-short laser pulse. In this paper, we theoretically demonstrate a highly selective population of two excited states in the nonresona...A nonresonant two-photon absorption process can be manipulated by tailoring the ultra-short laser pulse. In this paper, we theoretically demonstrate a highly selective population of two excited states in the nonresonant two- photon absorption process by rationally designing a spectral phase distribution. Our results show that one excited state is maximally populated while the other state population is widely tunable from zero to the maximum value. We believe that the theoretical results may play an important role in the selective population of a more complex nonlinear process comprising nonresonant two-photon absorption, such as resonance-mediated （2-~l）-three-photon absorption and （2q-1）-resonant multiphoton ionization.展开更多
[Objectives]This study was conducted to rationally and effectively use natural genetic resources of white birch(Betula platyphylla Suk.),and improve the scientific and technological content of improved varieties.[Meth...[Objectives]This study was conducted to rationally and effectively use natural genetic resources of white birch(Betula platyphylla Suk.),and improve the scientific and technological content of improved varieties.[Methods]With the progeny of the white birch populations naturally distributed in northern China as objects,based on genetic effect analysis and comprehensive evaluation,the genetic variation,heritability and genetic gain of the growth characters in the progeny forest were systematically analyzed,by which populations or individuals with good growth vigor and strong stress resistance and adaptability were finally selected.[Results]There were extremely significant differences in the growth characters between the natural populations of white birch in northern China.The variation was the smallest in tree height,followed by crown width,and largest in DBH,and the average coefficients of variation were 20.56%,32.25%and 33.00%,respectively.The differences in characters between progeny of the same population were also extremely significant.The growth characters of white birch were more controlled by genes,and the genetic gains were larger.The heritability of tree height,DBH and crown width was 0.971,0.816 and 0.576,respectively,and the genetic gains were 15.97%,21.54%and 13.87%,respectively.[Conclusions]With the growth characters as the main evaluation indexes,taking various influencing factors into account,the Shanxi[SX]population,Hebei[HB]population and Liaoning[LN]population were selected to be excellent populations,and LN305,SX516 and HB403 were excellent individuals,which are advised to be widely used in multi-generation genetic improvement breeding.展开更多
Small and isolated populations face several intrinsic risks,such as genetic drift,inbreeding depression,and reduced gene fow.Thus,patterns of genetic diversity and differentiation have become an important focus of con...Small and isolated populations face several intrinsic risks,such as genetic drift,inbreeding depression,and reduced gene fow.Thus,patterns of genetic diversity and differentiation have become an important focus of conservation genetics research.The golden snub-nosed monkey Rhinopithecus roxellana,an endangered species endemic to China,has experienced rapid reduction in population size and severe population fragmentation over the past few decades.We measured the patterns of genetic diversity and population differentiation using both neutral microsatellites and adaptive major histocompatibility complex(MHC)genes in 2 R.roxellana populations(DPY and GNG)distributed on the northern and southern slopes of the Qinling Mountains,respectively.Eight MHC-linked haplotypes formed by 5 DQA1 alleles,5 DQB1 alleles,5 DRB1 alleles,and 4 DRB2 alleles were detected in the 2 populations.The larger GNG population showed higher genetic variation for both MHC and microsatellites than the smaller DPY population,suggesting an effect of genetic drift on genetic variation.Genetic differentiation index(FST)outlier analyses,principal coordinate analysis(PCoA),and inferred population genetic structure showed lower genetic differentiation in the MHC variations than microsatellites,suggesting that pathogen-mediated balancing selection,rather than local adaptation,homogenized the MHC genes of both populations.This study indicates that both balancing selection and genetic drift may shape genetic variation and differentiation in small and fragmented populations.展开更多
It is one of the key problems for application ofanther culture in hybrid breeding, geneticanalysis, and molecular mapping whether thedoubled haploid (DH) population derived fromanther culture of rice crosses represent...It is one of the key problems for application ofanther culture in hybrid breeding, geneticanalysis, and molecular mapping whether thedoubled haploid (DH) population derived fromanther culture of rice crosses represents a ran-dom array of the microspore population, i.e.whether gametic selection occurs in androgene-sis. A DH population including 132 lines de-展开更多
Population differentiation is a fundamental process of evolution, and many evolutionary studies, such as population genetics, phylogeography and conservation biology, all require the inference of population differenti...Population differentiation is a fundamental process of evolution, and many evolutionary studies, such as population genetics, phylogeography and conservation biology, all require the inference of population differentiation. Recently, there has been a lot of debate over the validity of FST （and its analogue Gsr） as a measure for population genetic differentiation, notably since the proposal of the new index D in 2008. Although several papers reviewed or explored specific features of these statistical measures, a succinct account of this bewildering issue with an overall update appears to be desirable. This is the purpose of the present review. The available statistics generally fall into two categories, represented by Fsv and D, respectively. None of them is perfect in measuring population genetic differentiation. Nevertheless, they each have advantages and are valuable for current re- search. In practice, both indices should be calculated and a comparison of them can generate useful insights into the evolutionary processes that influence population differentiation. FsT （GsT） has some unique irreplaceable characteristics assuring its standing as the default measure for the foreseeable near future. Also, it will continue to serve as the standard for any alternative measures to contrast with. Instead of being anxious about making choice between these indices, one should pay due attention to the equili-brium status and the level of diversity （especially Hs） of the populations, since they largely sway the power of a given statistic to address a specific question. We provide a multi-faceted comparative summary of the various statistics, which can serve as a basic reference for readers to guide their applications [Current Zoology 61 （5）： 886-897, 2015].展开更多
On the basis of Hardy-Weinberg law the distinction in the philosophy of the description of a family tree and a population is considered. With the help of introduction of the equivalent constant mutagen factor both in ...On the basis of Hardy-Weinberg law the distinction in the philosophy of the description of a family tree and a population is considered. With the help of introduction of the equivalent constant mutagen factor both in a family tree and in a population, the analysis of hemophilia is led. Influence of selection at presence of hemophilia is considered. On the basis of idea of Danforth and Haldane about the balance mutagenesis and selection at presence of hemophilia, the inter-relation of selection parameter and the equivalent constant mutagen factor is found. It is shown, that dynamics of development of hemophilia in a family tree and in population are similar.展开更多
When hybridization results in reduced fitness, natural selection is expected to favor the evolution of traits that minimize the likelihood of hybridizing in the first place. This process, termed reinforcement （or, mo...When hybridization results in reduced fitness, natural selection is expected to favor the evolution of traits that minimize the likelihood of hybridizing in the first place. This process, termed reinforcement （or, more generally, reproductive character displacement）, thereby contributes to the evolution of enhanced reproductive isolation between hybridizing groups. By enhancing reproductive isolation in this way, reinforcement plays an important role in the final stages of speciation. However, reinforcement can also contribute to the early stages of speciation. Specifically, because selection to avoid hybridization occurs only in sympatric populations, the unfolding of reinforcement can lead to the evolution of traits in sympatric populations that reduce reproduction between conspecifics in sympatry versus those in allopatry. Thus, reinforcement between species can lead to reproductive isolation--and possibly speciation-between populations in sympatry versus those in allopatry or among different sympatric populations. Here, I describe how this process can occur, the conditions under which it is most likely to occur, and the empirical data needed to evaluate the hypothesis that reinforcement can initiate speciation.展开更多
基金Supported by the National Natural Science Foundation of China(12261018)Universities Key Laboratory of Mathematical Modeling and Data Mining in Guizhou Province(2023013)。
文摘In this paper,we establish and study a single-species logistic model with impulsive age-selective harvesting.First,we prove the ultimate boundedness of the solutions of the system.Then,we obtain conditions for the asymptotic stability of the trivial solution and the positive periodic solution.Finally,numerical simulations are presented to validate our results.Our results show that age-selective harvesting is more conducive to sustainable population survival than non-age-selective harvesting.
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 National Natural Science Foundation of China (Nos.31372523 and 31302180)the Scientific and Technological Innovation Project Financially Supported by Qingdao National Laboratory for Marine Science and Technology (No.2015ASKJ02)+4 种基金the Taishan Scholar Program for Seed Industrythe Shandong Provincial Natural Science Foundation (No.ZR2014CQ001)the Special Fund for Postdoctoral Innovative Project of Shandong ProvinceCentral Public-Interest Scientific Institution Basal Research Fund of the Yellow Sea Fisheries Research Institute (No.20603022015013)the China Agriculture Research System (CARS-48)
文摘In this study,families of selected population for growth(SP_BWT),selected population for white spot syndrome virus(WSSV)resistance(SP_RW),Bohai wild population(WP_BH)and Huanghai wild population(WP_HH)of F.chinensis were constructed through artificial insemination and with the standardized procedure of larvae rearing.Growth and survival performance were studied among four populations after a 70 days common test.The results showed that the maximum least square mean of body weight was 17.50 g in SP_BWT while the minimum was 13.03 g in WP_HH.Compared with WP_BH,body weight of SP_BWT increased by 23.41%(P<0.01)and that of SP_RW by 12.20%(P>0.05).Body weights of SP_BWT and SP_RW were significantly higher than that of WP_HH,which increased by 34.31%(P<0.01)and 22.10%(P<0.05),respectively.The mean AGR of four populations was 0.19,0.18,0.17 and 0.16 g d^(-1),respectively.Coefficient of variation of body weight among four populations was high,which ranged from 32.67% to 35.25%.Such a range showed that there was the potentiality for further improvement in selected populations.Coefficient of variation of survival rate among four populations was low,varying between 3.20% and 5.90%.The difference of survival was highly significant(P<0.01)between SP_BWT and WP_BH,and significant(P<0.05)between SP_RW and WP_BH.However,no significant difference among other populations(P>0.05)was observed.Different growth performances were also observed among different families in each population.The body weight of 798F family was the highest.The absolute growth rate(AGR)was 0.25 g d^(-1),150%higher than that of the lowest one,0.1 g d^(-1) in 807F family.Survival rate of families among four populations was different.The highest was 94.74%,and the lowest was 71.88%.
基金supported by research grants of the National Basic Research Program of China (2007CB815700 2006CB102100)Bureau of Science and Technology of Yunnan Province, and Natural Science Foundation of China (30621092)
文摘To assess the genetic diversity between randomly and selectively bred populations,we sequenced 438 bp of the mitochondrial DNA control region from 102 pigs.These samples represented four native pig breeds,one nucleus and one conservation herd from Yunnan,China.Twenty haplotypes with sixteen polymorphic sites were identified.The number of haplotypes in the nucleus herd of Saba pig and the conservation herd of Banna miniature pig were restricted to three and one,respectively,while the randomly bred pig populations exhibited over six haplotypes.Notably,haplotype diversity in randomly bred populations was significantly greater than the selectively bred populations（h=0.732 vs.0.425 and 0,exact test,P≤0.0036）.These findings demonstrate that selective breeding generated low genetic diversity compared to randomly bred pig breeds.A timely intervention and well programmed breeding approach would stop further genetic diversity reduction in the nucleus and conservation herds of native pig breeds.Otherwise,selective breeding would dramatically reduce genetic diversity in only several years,indicating that sharp contradictions exist between breeding,conservation and genetic diversity.Genetic relationships are discussed based on net genetic distances among pig populations.
基金Supported by Science and Technology Innovation Guiding and Incentive Fund of Inner Mongolia Autonomous Region(20111705)~~
文摘ln this study, 12 maize populations were improved with the improved S1 selection method, aiming to increase the improvement efficiency of maize popula-tions. The results showed that number of rows per spike, number of grains per row and 100-grain weight were the three important component traits of maize yield. The highest genetic increment was found in Mengqun 2, fol owed by Mengqun 4, Mengqun 1 and other 7 maize populations. Negative genetic increment was shown in Mengqun 3 and 3 introduced foreign maize populations. Some changes were shown in spikes, plant traits and genetic diversity of maize populations. Based on our results, we concluded that Mengqun 2, Mengqun 4, Zhongzong 7, Mengqun C and Mengqun A could be directly used for the line breeding by selfing for their higher genetic increment of yield and better improvement effects of other agricultural traits. Compared with these 5 populations, the improvement potential of other maize populations was limited for their lower genetic increment.
文摘Reid, Lancaster, Tuxpeno and Suwan are the most common maize (Zea mays L.) germplasms. Reid × Lancaster and Suwan × Tuxpeno are very important heterotic patterns in temperate areas and tropical areas, respectively. Broadening the genetic basis of maize has usually been conducted in inter-populations formed by crossing temperate and tropical germplasms. Reciprocal recurrent selection (RRS) is a breeding procedure to improve the inter-populational cross of two base populations. The objective of this study was to evaluate the direct and indirect effects of reciprocal recurrent selection on grain yield in the TR (Tuxpeno-Reid) and SL (Suwan-Lancaster) maize populations. The populations and the inter-populational crosses of each selection cycle, as well as two commercial hybrids, were evaluated in four environments. The effect of mean grain yield on TR × SL inter-population crosses was 4.63% (or 0.365 Mg·ha-1) cycle-1. The grain yield of SL increased by 2.78% (or 0.20 Mg·ha-1) cycle-1, but the grain yield of TR essentially did not change. Most changes in other agronomic traits occurred in the desired direction. After 3 selection cycles, the ear tip-barrenness length decreased in TR × SL, TR and SL by 39.70%, 37.50% and 24.57%, respectively, which indicates that the increase in grain yield may be largely due to a decreasing ear tip-barrenness length. The mid-parent heterosis of grain yield of the inter-populational cross increased from 15.49% to 25.96% from C0 to C3. The mean grain yields of TRC3 × SLC3 were 100.01% and 103.88% of the mean grain yields of the commercial single-crosses GD8 and QD16, respectively. The results suggest that Tuxpeno-Reid × Suwan-Lancaster may be possible new heterotic patterns in the southern region of China.
文摘To solve the problem that soybean has narrow genetic base, we constructed a series of male sterile recurrent selection populations, and studied the effects of quality improvement and practical value. An LD-base population, which fits to our ecology type was constructed by 6 years＇ gene enrichment through the introduction of new genes from 23 local varieties and recurrent selection. The LD-base populations were then improved by making crosses with high protein and high oil genotypes. As a result we obtained a high protein sub-population （db） and a high oil sub-population （gy）, For the db sub-population, the protein content is 1.18% higher than the base population, 22.38% of the individuals contain 45% or more of protein, which is 10.99% higher than the base population. For the gy sub-population, oil content is 0.24% higher than the base population. Individuals with oil content of 20% or more are 11.05% higher than the base population. The quantitative characters such as flowering date, mature date, pod habit, and hilum color, etc., all showed wide range of separation, and the segregation ratio approached balance. The c.v. of branch number of ms1 recurrent population （72.8%） is higher than general cross-population （57.3%）, and the c.v. of 100 seed weight of ms1 （18.1%） is higher than general cross population （16.5%）, the coefficient of variation of plant height, pods per plant, and seeds per pod were not significantly different. It was demonstrated in this paper that the quality character of ms 1 male sterile recurrent selection population was improved by adding new genes. And the segregation of other characters widened, making the populations suitable for the objective of soybean breeding. In this paper, we also discussed the breeding method, key technology, and selection effect of soybean ms 1 population.
基金supported by the earmarked fund for China Agriculture Research System(CARS-35)the National Natural Science Foundation of China(32022078)supported by the National Supercomputer Centre in Guangzhou。
文摘Genomic selection(GS)has been widely used in livestock,which greatly accelerated the genetic progress of complex traits.The population size was one of the significant factors affecting the prediction accuracy,while it was limited by the purebred population.Compared to directly combining two uncorrelated purebred populations to extend the reference population size,it might be more meaningful to incorporate the correlated crossbreds into reference population for genomic prediction.In this study,we simulated purebred offspring(PAS and PBS)and crossbred offspring(CAB)base on real genotype data of two base purebred populations(PA and PB),to evaluate the performance of genomic selection on purebred while incorporating crossbred information.The results showed that selecting key crossbred individuals via maximizing the expected genetic relationship(REL)was better than the other methods(individuals closet or farthest to the purebred population,CP/FP)in term of the prediction accuracy.Furthermore,the prediction accuracy of reference populations combining PA and CAB was significantly better only based on PA,which was similar to combine PA and PAS.Moreover,the rank correlation between the multiple of the increased relationship(MIR)and reliability improvement was 0.60-0.70.But for individuals with low correlation(Cor(Pi,PA or B),the reliability improvement was significantly lower than other individuals.Our findings suggested that incorporating crossbred into purebred population could improve the performance of genetic prediction compared with using the purebred population only.The genetic relationship between purebred and crossbred population is a key factor determining the increased reliability while incorporating crossbred population in the genomic prediction on pure bred individuals.
文摘The maize population Csyn 4 was improved for three cycles with three recurrent selection methods MS1, MS1-HS, and MHSRRS in northern China. A total of 40 NC Ⅱ testcrosses were made by four testers with Csyn 4 and 10 improved populations, which were evaluated in four environments in the cropping season of 2005. Analysis of variance indicated a significant progress （P〈 0.05） in yield and other chief agronomic traits in the improved populations and testcrosses, demonstrating that the three recurrent selection methods were effective for increasing grain yield of testcrosses and improvement of general combining ability in maize population. The average grain yield increase of population Csyn 4 in MS1, MS1-HS, and MHSRRS recurrent selections was 266.7 kg ha^-1 （5.3%）, 288.0 kg ha^-1 （5.7%）, and 231.3 kg ha^-1 （4.6%） per cycle, while the grain yield of S 1 progeny of population for Csyn 4 was increased by 420.0 kg ha^-1 （10.9%）, 376.0 kg ha^-1 （9.8%）, and 414.7 kg ha^-1 （10.8%） per cycle in MS1, MS1-HS, and MHSRRS recurrent selections, respectively. Linear responses （b） in the MS1, MS1-HS, and MHSRRS recurrent selections were the same as the realized responses of the selection （G） for grain yield increase of Csyn 4 and S1 progeny of the populations. The grain yield of testcrosses increased by 3.3-5.2% on average per cycle. The value of heterosis did not display any differences amongst the different cycles of selections. The GCA for yield component traits of population Csyn 4 was improved significantly by means of three selection methods, whereas the GCA for plant height, ear height, days to silking, and days to pollen did not show significant increase in the recurrent selections. GCA for the number of tassel branches were decreased in the selections, while GCA for the number of plant leaves were increased, but the difference was not significant.
基金Supported by the Special Fund for Agro-scientific Research in the Public Interest of China(No.201203018)the National Key Technology Research and Development Program of China(No.2006BAD09A05)
文摘Trawl is a main fishing gear in Chinese fishery,capturing large fish and letting small ones at large.However,long-term use of trawl would result in changes of phenotypic traits of the fish stocks,such as smaller size-at-age and earlier age-at-maturation.In this study,we simulated a fish population with size characteristics of trawl fishing and the population produces one generation of offspring and lives for one year,used trawl to exploit the simulated fish population,and captured individuals by body size.We evaluated the impact of the changes on selectivity parameters,such as selective range and the length at 50% retention.Under fishing pressure,we specified the selectivity parameters,and determined that smaller selection rates and greater length at 50% retention were associated with an increased tendency towards miniaturization.
基金This work is supported by National Natural Science Foundation of China(Grant Nos.61876089,61403206)by Science and Technology Program of Ministry of Housing and Urban-Rural Development(2019-K-141)+1 种基金by Entrepreneurial Team of Sponge City(2017R02002)by Innovation and entrepreneurship training program for College Students。
文摘In many fields such as signal processing,machine learning,pattern recognition and data mining,it is common practice to process datasets containing huge numbers of features.In such cases,Feature Selection(FS)is often involved.Meanwhile,owing to their excellent global search ability,evolutionary computation techniques have been widely employed to the FS.So,as a powerful global search method and calculation fast than other EC algorithms,PSO can solve features selection problems well.However,when facing a large number of feature selection,the efficiency of PSO drops significantly.Therefore,plenty of works have been done to improve this situation.Besides,many studies have shown that an appropriate population initialization can effectively help to improve this problem.So,basing on PSO,this paper introduces a new feature selection method with filter-based population.The proposed algorithm uses Principal Component Analysis(PCA)to measure the importance of features first,then based on the sorted feature information,a population initialization method using the threshold selection and the mixed initialization is proposed.The experiments were performed on several datasets and compared to several other related algorithms.Experimental results show that the accuracy of PSO to solve feature selection problems is significantly improved after using proposed method.
基金Supported by the National Natural Science Foundation of China (60661003)the Research Project Department of Education of Jiangxi Province (GJJ10566)
文摘In this paper, we explore a novel ensemble method for spectral clustering. In contrast to the traditional clustering ensemble methods that combine all the obtained clustering results, we propose the adaptive spectral clustering ensemble method to achieve a better clustering solution. This method can adaptively assess the number of the component members, which is not owned by many other algorithms. The component clusterings of the ensemble system are generated by spectral clustering （SC） which bears some good characteristics to engender the diverse committees. The selection process works by evaluating the generated component spectral clustering through resampling technique and population-based incremental learning algorithm （PBIL）. Experimental results on UCI datasets demonstrate that the proposed algorithm can achieve better results compared with traditional clustering ensemble methods, especially when the number of component clusterings is large.
基金financially supported by the Biological BreedingNational Science and Technology Major Project(2023ZD0405806)the National Key R&D Program for the 14th Five-Year Plan in China(2022YFD2200304).
文摘The level of genetic variation within a breeding population affects the effectiveness of selection strategies for genetic improvement.The relationship between genetic variation level within Pinus tabuliformis breeding populations and selection strategies or selection effectiveness is not fully investigated.Here,we compared the selection effectiveness of combined and individual direct selection strategies using half-and full-sib families produced from advanced-generation P.tabuliformis seed orchard as our test populations.Our results revealed that,within half-sib families,average diameter at breast height(DBH),tree height,and volume growth of superior individuals selected by the direct selection strategy were higher by 7.72%,18.56%,and 31.01%,respectively,than those selected by the combined selection strategy.Furthermore,significant differences(P<0.01)were observed between the two strategies in terms of the expected genetic gains for average tree height and volume.In contrast,within full-sib families,the differences in tree average DBH,height,and volume between the two selection strategies were relatively minor with increase of 0.17%,2.73%,and 2.21%,respectively,and no significant differences were found in the average expected genetic gains for the studied traits.Half-sib families exhibited greater phenotypic and genetic variation,resulting in improved selection efficiency with the direct selection strategy but also introduced a level of inbreeding risk.Based on genetic distance estimates using molecular markers,our comparative seed orchard design analysis showed that the Improved Adaptive Genetic Programming Algorithm(IAPGA)reduced the average inbreeding coefficient by 14.36% and 14.73% compared to sequential and random designs,respectively.In conclusion,the combination of the direct selection strategy with IAPGA seed orchard design aimed at minimizing inbreeding offered an efficient approach for establishing advanced-generation P.tabuliformis seed orchards.
基金Project partly supported by the Shanghai Leading Academic Discipline Project (Grant No.B408)the Science Foundation of the Ministry of Education of China (Grant No.30800)+1 种基金the National Natural Science Fundation of China (Grant No.11004060)the Shanghai Municipal Science and Technology Commission (Grant Nos.10XD1401800,09142200501,09ZR1409300,09JC1404700,and 10JC1404500)
文摘A nonresonant two-photon absorption process can be manipulated by tailoring the ultra-short laser pulse. In this paper, we theoretically demonstrate a highly selective population of two excited states in the nonresonant two- photon absorption process by rationally designing a spectral phase distribution. Our results show that one excited state is maximally populated while the other state population is widely tunable from zero to the maximum value. We believe that the theoretical results may play an important role in the selective population of a more complex nonlinear process comprising nonresonant two-photon absorption, such as resonance-mediated （2-~l）-three-photon absorption and （2q-1）-resonant multiphoton ionization.
基金Supported by Heilongjiang Provincial Science and Technology Department Project(GC04B116)National Forest Tree Germplasm Resource Platform Running Service Project(2011DKA21003-02)National Forestry Public Welfare Industry Research Project(201204307-07)
文摘[Objectives]This study was conducted to rationally and effectively use natural genetic resources of white birch(Betula platyphylla Suk.),and improve the scientific and technological content of improved varieties.[Methods]With the progeny of the white birch populations naturally distributed in northern China as objects,based on genetic effect analysis and comprehensive evaluation,the genetic variation,heritability and genetic gain of the growth characters in the progeny forest were systematically analyzed,by which populations or individuals with good growth vigor and strong stress resistance and adaptability were finally selected.[Results]There were extremely significant differences in the growth characters between the natural populations of white birch in northern China.The variation was the smallest in tree height,followed by crown width,and largest in DBH,and the average coefficients of variation were 20.56%,32.25%and 33.00%,respectively.The differences in characters between progeny of the same population were also extremely significant.The growth characters of white birch were more controlled by genes,and the genetic gains were larger.The heritability of tree height,DBH and crown width was 0.971,0.816 and 0.576,respectively,and the genetic gains were 15.97%,21.54%and 13.87%,respectively.[Conclusions]With the growth characters as the main evaluation indexes,taking various influencing factors into account,the Shanxi[SX]population,Hebei[HB]population and Liaoning[LN]population were selected to be excellent populations,and LN305,SX516 and HB403 were excellent individuals,which are advised to be widely used in multi-generation genetic improvement breeding.
基金funded by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31020302)the National Natural Science Foundation of China(31730104,31770425,32071495,32170515,32070453,and 32000317)Derek W.Dunn was supported by a Shaanxi Province Talents 100 Fellowships.
文摘Small and isolated populations face several intrinsic risks,such as genetic drift,inbreeding depression,and reduced gene fow.Thus,patterns of genetic diversity and differentiation have become an important focus of conservation genetics research.The golden snub-nosed monkey Rhinopithecus roxellana,an endangered species endemic to China,has experienced rapid reduction in population size and severe population fragmentation over the past few decades.We measured the patterns of genetic diversity and population differentiation using both neutral microsatellites and adaptive major histocompatibility complex(MHC)genes in 2 R.roxellana populations(DPY and GNG)distributed on the northern and southern slopes of the Qinling Mountains,respectively.Eight MHC-linked haplotypes formed by 5 DQA1 alleles,5 DQB1 alleles,5 DRB1 alleles,and 4 DRB2 alleles were detected in the 2 populations.The larger GNG population showed higher genetic variation for both MHC and microsatellites than the smaller DPY population,suggesting an effect of genetic drift on genetic variation.Genetic differentiation index(FST)outlier analyses,principal coordinate analysis(PCoA),and inferred population genetic structure showed lower genetic differentiation in the MHC variations than microsatellites,suggesting that pathogen-mediated balancing selection,rather than local adaptation,homogenized the MHC genes of both populations.This study indicates that both balancing selection and genetic drift may shape genetic variation and differentiation in small and fragmented populations.
文摘It is one of the key problems for application ofanther culture in hybrid breeding, geneticanalysis, and molecular mapping whether thedoubled haploid (DH) population derived fromanther culture of rice crosses represents a ran-dom array of the microspore population, i.e.whether gametic selection occurs in androgene-sis. A DH population including 132 lines de-
文摘Population differentiation is a fundamental process of evolution, and many evolutionary studies, such as population genetics, phylogeography and conservation biology, all require the inference of population differentiation. Recently, there has been a lot of debate over the validity of FST （and its analogue Gsr） as a measure for population genetic differentiation, notably since the proposal of the new index D in 2008. Although several papers reviewed or explored specific features of these statistical measures, a succinct account of this bewildering issue with an overall update appears to be desirable. This is the purpose of the present review. The available statistics generally fall into two categories, represented by Fsv and D, respectively. None of them is perfect in measuring population genetic differentiation. Nevertheless, they each have advantages and are valuable for current re- search. In practice, both indices should be calculated and a comparison of them can generate useful insights into the evolutionary processes that influence population differentiation. FsT （GsT） has some unique irreplaceable characteristics assuring its standing as the default measure for the foreseeable near future. Also, it will continue to serve as the standard for any alternative measures to contrast with. Instead of being anxious about making choice between these indices, one should pay due attention to the equili-brium status and the level of diversity （especially Hs） of the populations, since they largely sway the power of a given statistic to address a specific question. We provide a multi-faceted comparative summary of the various statistics, which can serve as a basic reference for readers to guide their applications [Current Zoology 61 （5）： 886-897, 2015].
文摘On the basis of Hardy-Weinberg law the distinction in the philosophy of the description of a family tree and a population is considered. With the help of introduction of the equivalent constant mutagen factor both in a family tree and in a population, the analysis of hemophilia is led. Influence of selection at presence of hemophilia is considered. On the basis of idea of Danforth and Haldane about the balance mutagenesis and selection at presence of hemophilia, the inter-relation of selection parameter and the equivalent constant mutagen factor is found. It is shown, that dynamics of development of hemophilia in a family tree and in population are similar.
文摘When hybridization results in reduced fitness, natural selection is expected to favor the evolution of traits that minimize the likelihood of hybridizing in the first place. This process, termed reinforcement （or, more generally, reproductive character displacement）, thereby contributes to the evolution of enhanced reproductive isolation between hybridizing groups. By enhancing reproductive isolation in this way, reinforcement plays an important role in the final stages of speciation. However, reinforcement can also contribute to the early stages of speciation. Specifically, because selection to avoid hybridization occurs only in sympatric populations, the unfolding of reinforcement can lead to the evolution of traits in sympatric populations that reduce reproduction between conspecifics in sympatry versus those in allopatry. Thus, reinforcement between species can lead to reproductive isolation--and possibly speciation-between populations in sympatry versus those in allopatry or among different sympatric populations. Here, I describe how this process can occur, the conditions under which it is most likely to occur, and the empirical data needed to evaluate the hypothesis that reinforcement can initiate speciation.
