In this paper,we propose genetic programming(GP) using dynamic population variation(DPV) with four innovations for reducing computational efforts.A new stagnation phase definition and characteristic measure are define...In this paper,we propose genetic programming(GP) using dynamic population variation(DPV) with four innovations for reducing computational efforts.A new stagnation phase definition and characteristic measure are defined for our DPV.The exponential pivot function is proposed to our DPV method in conjunction with the new stagnation phase definition.An appropriate population variation formula is suggested to accelerate convergence.The efficacy of these innovations in our DPV is examined using six benchmark problems.Comparison among the difierent characteristic measures has been conducted for regression problems and the new proposed measure outperformed other measures.It is proved that our DPV has the capacity to provide solutions at a lower computational effort compared with previously proposed DPV methods and standard genetic programming in most cases.Meanwhile,our DPV approach introduced in GP could also rapidly find an excellent solution as well as standard GP in system modeling problems.展开更多
To investigate the genetic diversity of an edible fungus Pleurotus ferulae, a total of 89 wild samples collected from six geographical locations in the Xinjiang Uygur Autonomous Region of China and two geographical lo...To investigate the genetic diversity of an edible fungus Pleurotus ferulae, a total of 89 wild samples collected from six geographical locations in the Xinjiang Uygur Autonomous Region of China and two geographical locations in Italy, were analyzed using three DNA fragments including the translation elongation factor（EF1α）, the second largest subunit of t he RNA polymerase II（RPB2） and the largest subunit of the RNA polymerase II（RPB1）. The results indicated relatively abundant genetic variability in the wild resources of P. ferulae. The analysis of molecular variance（AMOVA） showed that the vast majority of the genetic variation was found within geographical populations. Both the Chinese populations and the Italian populations of P. ferulae displayed a limited genetic differentiation. The degree of differentiation between the Chinese populations and the Italian populations was obviously higher than that between the populations from the same region, and moreover the genetic differentiation among all the tested populations was correlated to the geographical distance. T he phylogeny analyses confirmed that samples from China and Italy belonged to another genetic group separated from Pleurotus eryngii. They were closely related to each other but were clustered according to their geographical origins, which implied the Chinese populations were highly differentiated from the Italian populations because of distance isolation, and the two populations from different regions might be still in the process of allopatric divergence.展开更多
In order to study morphological diversity of codling moth, Cydia pomonella （L.） using thin-plate spline analysis, nine geographical populations from four north western provinces of Iran namely East Azarbayjan, West ...In order to study morphological diversity of codling moth, Cydia pomonella （L.） using thin-plate spline analysis, nine geographical populations from four north western provinces of Iran namely East Azarbayjan, West Azarbayjan, Ardebil and Zandjan were collected during 2003 and 2004. 575 and 564 images were prepared from fore and hind wings, respectively. Then 15 and 11 landmarks were determined from fore and hind wings, respectively. With transforming of landmark＇s two dimensional coordinate data into partial warp scores, 26 and 18 scores were generated for fore and hind wings, respectively. Cluster analysis based on wing shape variables using Ward＇s algorithm assigned nine geographical populations into two groups. The pattern of grouping based on fore and hind wings was different in both sexes. Principal component analysis revealed discrimination between geographic populations and confirmed the result of cluster analysis. Among environmental parameters, wind speed showed the highest correlation with wing shape variables. Non significant correlation was observed between geographic and morphological distance matrices as revealed by Mantel test.展开更多
We studied the waterbird population at Lashihai Lake, Yunnan Province, China, which is a Ramsar Site(Wetland of International Importance), to determine seasonal variation in the species composition and size of the wat...We studied the waterbird population at Lashihai Lake, Yunnan Province, China, which is a Ramsar Site(Wetland of International Importance), to determine seasonal variation in the species composition and size of the waterbird population. The study was conducted at five selected spots along Lashihai Lake at the same time each week from August 2011 to September 2013. In total, 62 waterbird species were recorded, of which 38.71%, 35.48%, 16.13%, and 9.68% were winter migrants, passage visitors, residents, and summer migrants, respectively. We found important seasonal changes in waterbird species composition and population size. Waterbird species richness was highest from September to the following April, with the total species numbers peaking in December. Total individual numbers peaked twice from late November to early December and mid-to-late February. However, waterbird species and individual numbers were comparatively lower from May to August. The change in species composition was determined by the arrival and departure dynamics of winter migrants and passage visitors. Winter migrants primarily caused the periodic changes in population size. Of concern,species and overall waterbird numbers seemed to be lower than the numbers in historical records. The decline of waterbird numbers implies that environmental changes caused by the implementation of the dam upstream of Lashihai Lake may have had adverse effects on this waterbird population. This study confirms the existence of major seasonal changes in species composition and size of the waterbird population at Lashihai Lake. Furthermore, the findings demonstrate that this wetland is of high conservation importance for waterbirds using the Central Asian–Indian and Asian–Pacific migratory routes.展开更多
Objective:The population density and diversity of Sinomenium acutum(Menispermaceae)have been greatly reduced recently by overharvesting for medicinal purposes in China.Therefore,it is urgent that the remaining populat...Objective:The population density and diversity of Sinomenium acutum(Menispermaceae)have been greatly reduced recently by overharvesting for medicinal purposes in China.Therefore,it is urgent that the remaining populations are investigated,and that strategies for the utilization and conservation of this species are developed.This study aimed to find the possible glacial refugia and define the genetic diversity of S.acutum for its proper utilization and conservation.Methods:A total of 77 S.acutum samples were collected from four locations,Qinling Mountains,Daba Mountains,Dalou Mountains,and Xuefeng Mountains,in subtropical China.Genetic diversity among and between these populations were phylogenetically analyzed using four chloroplast DNA molecular markers(atpI-atpH,trnQ-50 rps16,trnH-psbA and trnL-trnF).Results:A total of 14 haplotypes(C1 to C14)were found in collected samples.Haplotypes C1 and C3 were shared among all populations,with C3 as the ancestral haplotype.Haplotypes C11 and C12 diverged the most from C3 and other haplotypes.No obvious phylogeographic structure was found in four locations using the GST/NST test.There is no evidence of rapid demographic expansion in S.acutum based on the mismatch distribution,and the results of Tajima’s D test,and Fu’s FS test.Our analyses of molecular variance revealed a high level of genetic variation within populations.In contrast,the genetic differentiation among S.acutum populations was low,indicating frequent gene flow.Conclusion:Xuefeng,Dalou,and Daba Mountains were possible glacial refugia for the populations of S.acutum.C1,C3,C11 and C12 haplotypes of S.acutum should be carefully preserved and managed for their genetic value.展开更多
Human genetic variants have long been known to play an important role in both Mendelian disorders and common diseases. Notably, pathogenic variants are not limited to single-nucleotide variants. It has become apparent...Human genetic variants have long been known to play an important role in both Mendelian disorders and common diseases. Notably, pathogenic variants are not limited to single-nucleotide variants. It has become apparent that human diseases can also be caused by copy number variations （CNVs）, especially patient- specific novel CNVs （lafrate et al., 2004; Sebat et al., 2004; Redon et al., 2006; LuDski, 2007; Zhan~ et al.. 2009： Wu et al.. 2015）.展开更多
While it is widely accepted that genetic diversity determines the potential of adaptation,the role that gene expression variation plays in adaptation remains poorly known.Here we show that gene expression diversity co...While it is widely accepted that genetic diversity determines the potential of adaptation,the role that gene expression variation plays in adaptation remains poorly known.Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius.RNA-seq was conducted for 80 individuals of the species,with half planted in the energy crop domestication site and the other half planted in the control site near native habitats.A leaf reference transcriptome consisting of 18,503 high-quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA-seq data.The population structure and genetic diversity of M.lutarioriparius were estimated based on 30,609 genic single nucleotide polymorphisms.Population expression（Ep） and expression diversity（Ed）were defined to measure the average level and the magnitude of variation of a gene expression in the population,respectively.It was found that expression diversity increased while genetic Resediversity decreased after the species was transplanted from the native habitats to the harsh domestication site,especially for genes involved in abiotic stress resistance,histone methylation,and biomass synthesis under water limitation.The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.展开更多
Random amplification polymorphicDNA(RAPD)markers were used to assess the genetic variations and the evolutionary relationships among all 14 individuals of a critically endangered Euryodendron excelsum(Theaceae)populat...Random amplification polymorphicDNA(RAPD)markers were used to assess the genetic variations and the evolutionary relationships among all 14 individuals of a critically endangered Euryodendron excelsum(Theaceae)population distributed in Ba Jia Zhen,Yangchun,Guangdong,China.Twenty-three random primers detected 156 sites,out of which 95(60.26%)were polymorphic loci.The number of the observed alleles was 1.6090,and the number of the effective alleles was 1.3471.Nei’s gene diversity was 0.1993,and Shannon index was 0.1534.A relatively high level of genetic variation was identified in E.excelsum.An unweighted pair group method with arithmetic mean(UPGMA)tree established from Jaccard similarity coefficients suggested that 14 individuals were clustered into two subgroups and that the No.2 plant was genetically distant from the rest of the individuals.The UPGMA clustering was also supported by a principle components analysis of RAPD phenotypic data.The management and conservation strategy of E.excelsum was proposed based on our results.展开更多
基金Ministry of Major Science & Technology of Shanghai(No.10DZ1200204)
文摘In this paper,we propose genetic programming(GP) using dynamic population variation(DPV) with four innovations for reducing computational efforts.A new stagnation phase definition and characteristic measure are defined for our DPV.The exponential pivot function is proposed to our DPV method in conjunction with the new stagnation phase definition.An appropriate population variation formula is suggested to accelerate convergence.The efficacy of these innovations in our DPV is examined using six benchmark problems.Comparison among the difierent characteristic measures has been conducted for regression problems and the new proposed measure outperformed other measures.It is proved that our DPV has the capacity to provide solutions at a lower computational effort compared with previously proposed DPV methods and standard genetic programming in most cases.Meanwhile,our DPV approach introduced in GP could also rapidly find an excellent solution as well as standard GP in system modeling problems.
基金funded by the National Basic Research Program of China (2014CB138305)the China Agriculture Research System (CARS24)
文摘To investigate the genetic diversity of an edible fungus Pleurotus ferulae, a total of 89 wild samples collected from six geographical locations in the Xinjiang Uygur Autonomous Region of China and two geographical locations in Italy, were analyzed using three DNA fragments including the translation elongation factor（EF1α）, the second largest subunit of t he RNA polymerase II（RPB2） and the largest subunit of the RNA polymerase II（RPB1）. The results indicated relatively abundant genetic variability in the wild resources of P. ferulae. The analysis of molecular variance（AMOVA） showed that the vast majority of the genetic variation was found within geographical populations. Both the Chinese populations and the Italian populations of P. ferulae displayed a limited genetic differentiation. The degree of differentiation between the Chinese populations and the Italian populations was obviously higher than that between the populations from the same region, and moreover the genetic differentiation among all the tested populations was correlated to the geographical distance. T he phylogeny analyses confirmed that samples from China and Italy belonged to another genetic group separated from Pleurotus eryngii. They were closely related to each other but were clustered according to their geographical origins, which implied the Chinese populations were highly differentiated from the Italian populations because of distance isolation, and the two populations from different regions might be still in the process of allopatric divergence.
文摘In order to study morphological diversity of codling moth, Cydia pomonella （L.） using thin-plate spline analysis, nine geographical populations from four north western provinces of Iran namely East Azarbayjan, West Azarbayjan, Ardebil and Zandjan were collected during 2003 and 2004. 575 and 564 images were prepared from fore and hind wings, respectively. Then 15 and 11 landmarks were determined from fore and hind wings, respectively. With transforming of landmark＇s two dimensional coordinate data into partial warp scores, 26 and 18 scores were generated for fore and hind wings, respectively. Cluster analysis based on wing shape variables using Ward＇s algorithm assigned nine geographical populations into two groups. The pattern of grouping based on fore and hind wings was different in both sexes. Principal component analysis revealed discrimination between geographic populations and confirmed the result of cluster analysis. Among environmental parameters, wind speed showed the highest correlation with wing shape variables. Non significant correlation was observed between geographic and morphological distance matrices as revealed by Mantel test.
基金funded by the“Technology Supporting Programme” of the “State Wetland Conservation Project for Lashihai Wetland”
文摘We studied the waterbird population at Lashihai Lake, Yunnan Province, China, which is a Ramsar Site(Wetland of International Importance), to determine seasonal variation in the species composition and size of the waterbird population. The study was conducted at five selected spots along Lashihai Lake at the same time each week from August 2011 to September 2013. In total, 62 waterbird species were recorded, of which 38.71%, 35.48%, 16.13%, and 9.68% were winter migrants, passage visitors, residents, and summer migrants, respectively. We found important seasonal changes in waterbird species composition and population size. Waterbird species richness was highest from September to the following April, with the total species numbers peaking in December. Total individual numbers peaked twice from late November to early December and mid-to-late February. However, waterbird species and individual numbers were comparatively lower from May to August. The change in species composition was determined by the arrival and departure dynamics of winter migrants and passage visitors. Winter migrants primarily caused the periodic changes in population size. Of concern,species and overall waterbird numbers seemed to be lower than the numbers in historical records. The decline of waterbird numbers implies that environmental changes caused by the implementation of the dam upstream of Lashihai Lake may have had adverse effects on this waterbird population. This study confirms the existence of major seasonal changes in species composition and size of the waterbird population at Lashihai Lake. Furthermore, the findings demonstrate that this wetland is of high conservation importance for waterbirds using the Central Asian–Indian and Asian–Pacific migratory routes.
基金supported by the Hunan Provincial Major Science and Technology Project(2015SK1001)Changsha Science and Technology Plan(kq1801015)+1 种基金Project of Hunan Administration of Traditional Chinese Medicine(2021212)Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine(HCSW2020-01).
文摘Objective:The population density and diversity of Sinomenium acutum(Menispermaceae)have been greatly reduced recently by overharvesting for medicinal purposes in China.Therefore,it is urgent that the remaining populations are investigated,and that strategies for the utilization and conservation of this species are developed.This study aimed to find the possible glacial refugia and define the genetic diversity of S.acutum for its proper utilization and conservation.Methods:A total of 77 S.acutum samples were collected from four locations,Qinling Mountains,Daba Mountains,Dalou Mountains,and Xuefeng Mountains,in subtropical China.Genetic diversity among and between these populations were phylogenetically analyzed using four chloroplast DNA molecular markers(atpI-atpH,trnQ-50 rps16,trnH-psbA and trnL-trnF).Results:A total of 14 haplotypes(C1 to C14)were found in collected samples.Haplotypes C1 and C3 were shared among all populations,with C3 as the ancestral haplotype.Haplotypes C11 and C12 diverged the most from C3 and other haplotypes.No obvious phylogeographic structure was found in four locations using the GST/NST test.There is no evidence of rapid demographic expansion in S.acutum based on the mismatch distribution,and the results of Tajima’s D test,and Fu’s FS test.Our analyses of molecular variance revealed a high level of genetic variation within populations.In contrast,the genetic differentiation among S.acutum populations was low,indicating frequent gene flow.Conclusion:Xuefeng,Dalou,and Daba Mountains were possible glacial refugia for the populations of S.acutum.C1,C3,C11 and C12 haplotypes of S.acutum should be carefully preserved and managed for their genetic value.
基金supported by the National Basic Research Program of China(No.2012CB944600)the National Key Research and Development Program of China(No.2016YFC0905100)+1 种基金the National Natural Science Foundation of China(Nos.31521003,31625015,31571297,31601046,31525014 and 91331204)the Science and Technology Commission of Shanghai Municipality(No.16YF1413900)
文摘Human genetic variants have long been known to play an important role in both Mendelian disorders and common diseases. Notably, pathogenic variants are not limited to single-nucleotide variants. It has become apparent that human diseases can also be caused by copy number variations （CNVs）, especially patient- specific novel CNVs （lafrate et al., 2004; Sebat et al., 2004; Redon et al., 2006; LuDski, 2007; Zhan~ et al.. 2009： Wu et al.. 2015）.
基金supported by grants from the Key Program of the National Natural Science Foundation of China (No.91131902)the Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EX-QR-1)
文摘While it is widely accepted that genetic diversity determines the potential of adaptation,the role that gene expression variation plays in adaptation remains poorly known.Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius.RNA-seq was conducted for 80 individuals of the species,with half planted in the energy crop domestication site and the other half planted in the control site near native habitats.A leaf reference transcriptome consisting of 18,503 high-quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA-seq data.The population structure and genetic diversity of M.lutarioriparius were estimated based on 30,609 genic single nucleotide polymorphisms.Population expression（Ep） and expression diversity（Ed）were defined to measure the average level and the magnitude of variation of a gene expression in the population,respectively.It was found that expression diversity increased while genetic Resediversity decreased after the species was transplanted from the native habitats to the harsh domestication site,especially for genes involved in abiotic stress resistance,histone methylation,and biomass synthesis under water limitation.The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.
基金supported by National Natural Science Foundation of China (No.30271094)the Scientific Research Foundation for the Returned Overseas Chinese Scholars,State Education Ministry (No.[2003]406)the“100 Talent Project”,the Chinese Academy of Sciences (No.05052903).
文摘Random amplification polymorphicDNA(RAPD)markers were used to assess the genetic variations and the evolutionary relationships among all 14 individuals of a critically endangered Euryodendron excelsum(Theaceae)population distributed in Ba Jia Zhen,Yangchun,Guangdong,China.Twenty-three random primers detected 156 sites,out of which 95(60.26%)were polymorphic loci.The number of the observed alleles was 1.6090,and the number of the effective alleles was 1.3471.Nei’s gene diversity was 0.1993,and Shannon index was 0.1534.A relatively high level of genetic variation was identified in E.excelsum.An unweighted pair group method with arithmetic mean(UPGMA)tree established from Jaccard similarity coefficients suggested that 14 individuals were clustered into two subgroups and that the No.2 plant was genetically distant from the rest of the individuals.The UPGMA clustering was also supported by a principle components analysis of RAPD phenotypic data.The management and conservation strategy of E.excelsum was proposed based on our results.
