On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps u...On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps under a climate with freezing winter cold. These findings lead us to-examine the past ideas about domestication and differentiation of rice. Historically, in 1930s two sub-species, indica and japonica, were proposed on the basis of sterility in F1 hybrids between them. Soon after that, the two types were classified by the associations of a number of genetically independent traits. The characteristic associations of traits have been explained by the hybrid sterility or reproductive barriers which were assumed to comprise a set of duplicate recessive lethal genes and to be an inner genetic mechanism to lead to the varietal differentiations In 1980s, the hybrid sterility between Indica and Japonica types was analyzed, and Indica, Japonica, and wide-compatibility type which gives fertile hybrids when cross to Indica and Japonica types, are proved to contain an allele, S5＇, S5＇ and S5^n, respectively at a locus on chromosome 6. And those gametes having Sj allele are found to be partially aborted in the hybrid genotypes of S5＇/S5＇ while no gamete abortion occurs in S5＇/S5^n and S5＇/S5^n genotypes. Since then, the gene S5^n has been used in hybrid rice breeding to obtain fertile and vigorous hybrids between subspecies, and the long-disputed problem of hybrid sterility has been solved. Also in such studies the characteristic association of traits found in each of vadetal groups is better explained by founder effects. On the other hand, a large number of native cultivars of rice were surveyed with enzyme polymorphism in 1980s and later with molecular markers. As a result, profound genetic diversity is found in cultivated rice as well as in wild rice. These findings seem to lead us to the idea of multiple independent domestications of rice. However, before reaching such a conclusion, at least two factors, i.e., long-distance-dissemination of some genotypes and the possibilities of introgression by local wild rice to primitive cultivars need to be examined. Taking the two factors as well as the historical events into consideration, it is considered here that the perennial japonica cultivars which are close to wild rice in the Changjiang River basin were disseminated to East India through Assam or along the Bengal Bay, where they were transformed under the introgressions of local wild rice and formed a secondary center, from which some genotypes seem to be disseminated to colonies in Southeast Asia under the influence of Hinduism. Later some of the genotypes were introduced into China and constituted so called Indica type. This may be a reasonable picture for the varietal differentiation.展开更多
青藏高原是气候变迁的敏感区。但第四纪以来全球气候的反复变化对该地区植物分布格局的影响至今未进行过仔细研究。线粒体DNA在松科植物中是母系遗传,其变异被广泛用于研究该科植物历史上由于气候变迁造成的瓶颈作用以及冰期后扩张中形...青藏高原是气候变迁的敏感区。但第四纪以来全球气候的反复变化对该地区植物分布格局的影响至今未进行过仔细研究。线粒体DNA在松科植物中是母系遗传,其变异被广泛用于研究该科植物历史上由于气候变迁造成的瓶颈作用以及冰期后扩张中形成的奠基者效应。对青海云杉位于青藏高原核心、其边缘甘肃和宁夏地区共12个种群155个个体的线粒体nad 1片段的全序列进行测序,研究该序列在各种群中的变异状况。通过测序发现该片段在青海云杉中十分保守,在所有个体中仅发现由于重复序列造成的5种单倍型(H ap A,H ap B,H ap C,H ap D和H ap E)。高原核心的所有种群均只有H ap A,而所有的4种单倍型都在高原边缘的甘肃地区存在,但这一地区仍然是H ap A占优势;但是在远离高原的宁夏地区则存在5种单倍性;多样性的变异趋势是宁夏地区高于高原边缘的甘肃地区,而甘肃地区又显著高于高原核心地区。这一结果表明,在过去气候变迁过程中,不同地区的青海云杉种群经历了不同的气候影响,这种影响造成的奠基者效应或者瓶颈作用是造成目前这种遗传多样性分布格局的主要原因。现有的单倍型分布格局,特别是高原上所有间断分布种群拥有相同的单倍型表明,森林回迁中的奠基者效应应是更为重要的因素。展开更多
Considering the severe impacts of genetic bottlenecks and small numbers of founders in populations of reintroduced animals, it is necessary to study inbreeding and its effect on fitness in species of conservation conc...Considering the severe impacts of genetic bottlenecks and small numbers of founders in populations of reintroduced animals, it is necessary to study inbreeding and its effect on fitness in species of conservation concern. Pere David＇s deer is one of few large mammal species extinct in the wild but safely preserved in captivity. Its specific background gives us the opportunity to study the relationships between heterozygosity and neonatal fitness in relocated populations. We employed five microsatellite loci to explore heterozygosity-fitness correlations in a population of Pere David＇s deer at the Beijing Milu Ecological Research Center. We observed associations between microsatellite-based variables sMLH, IR, MD^2 and HL, and two components of fitness ex- pressed early in life （birth weight and the neonatal mortality of 123 Pere David＇s deer calves born over six consecutive years）. We found that neonatal mortality was 19.1% - 7.6%, not higher than the 19% or 18% reported in other ungulates. The heterozygosity of calves was not associated with neonatal mortality, nor birth weight. Our study implies that low genetic variability of microsa- l：ellite loci has no overt effect on birth weight and neonatal mortality in reintroduced populations of P^re David＇s deer [Current Zoology 59 （2）： 249-256, 2013].展开更多
Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations. However, compared with spatial genetic structure, few studies ...Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations. However, compared with spatial genetic structure, few studies have been conducted on genetic changes over time. In this study, we used six polymorphic microsatellite loci to assess genetic variation of six size-classes of the population of Liushan, Cryptomeriajaponica var. sinensis, in the Tianmushan National Nature Reserve, whose origin was debatable. The mean number of alleles per locus and expected heterozygosity were 4.583 and 0.5999 respectively, lower than other conifers with the same life history characteristics. FST was 0.0024-0.003, and the pairwise test revealed no significant differentiation in any pair of size classes. Significant heterozygosity excesses were detected in five size classes except the oldest one, indicating bottleneck event（s）. The above results support the hypothesis that Tianmushan population was introduced and followed by natural regeneration.展开更多
Recent empirical and theoretical studies suggest that personality and locomotory performance traits linked to dispersal abilities are crucial components of the dispersal syndromes,and that they can evolve during range...Recent empirical and theoretical studies suggest that personality and locomotory performance traits linked to dispersal abilities are crucial components of the dispersal syndromes,and that they can evolve during range expansions and colonization processes.Island colonization is one of the best characterized processes in dispersal biogeography,and its implication in the evolution of phenotypic traits has been investigated over a wide range of temporal scales.However,the effect of island colonization on personality and performance traits of natural populations,and how these traits could drive island colonization,has been little explored.Noteworthy,no studies have addressed these processes in the context of late Pleistocene range expansions.Here,we investigated the contribution of island colonization triggered by postglacial range expansions to intraspecific variation in personality and locomotory performance traits.We compared boldness,exploration,jumping performance,and stickiness abilities in populations from 3 equidistant areas of the Tyrrhenian tree frog Hyla sarda,2 from the main island(Corsica Island),and 1 from the recently colonized island of Elba.Individuals from Elba were significantly bolder than individuals from Corsica,as they emerged sooner from a shelter(P=0.028),while individuals from Corsica showed markedly higher jumping and stickiness performance(both P<0.001),resulting as more performing than those of Elba.We discuss these results in the context of the major microevolutionary processes at play during range expansion,including selection,spatial sorting,founder effects,and their possible interaction with local adaptation processes.展开更多
Background:Familial hypomagnesemia with hypercalciuria and nephrocalcinosis(FHHNC)is an autosomal recessive tubular disease caused by mutations in the CLDN16 or CLDN19 gene.Previous studies using microsatellite marker...Background:Familial hypomagnesemia with hypercalciuria and nephrocalcinosis(FHHNC)is an autosomal recessive tubular disease caused by mutations in the CLDN16 or CLDN19 gene.Previous studies using microsatellite markers flanking the CLDN19 locus estimated that p.G20D(c.59G>A),a recurrent mutation in Spanish families,is a founder mutation.In the present study,we assessed the haplotype of Spanish patients using single nucleotide polymorphisms(SNPs).Methods:Twenty-seven FHHNC patients were included in this study.We analyzed four SNPs located in CLDN19 introns 3 and 4 by polymerase chain reaction amplification and DNA sequencing.Results:Three new patients with homozygous p.G20D were identified.The SNP genotyping analysis showed that alleles carrying this mutation shared a common SNP haplotype.Conclusions:Our findings suggest the existence of a founder effect responsible for FHHNC in our cohort.Testing for the presence of mutation p.G20D should be the first genetic screening in Spanish patients.展开更多
Since late 2011,outbreaks of pseudorabies virus(PRV)have occurred in southern China causing major economic losses to the pig industry.We previously reported that variant PRV forms and recombination in China could be t...Since late 2011,outbreaks of pseudorabies virus(PRV)have occurred in southern China causing major economic losses to the pig industry.We previously reported that variant PRV forms and recombination in China could be the source of continued epidemics.Here,we analyzed samples from intensive pig farms in eastern China between 2017 and 2019,and sequenced the main glycoproteins(gB,gC,gD,and gE)to study the evolution characteristics of PRV.Based on the gC gene,we found that PRV variants belong to clade 2 and detected a founder effect during by the PRV epidemic.In addition,we detected inter-and intra-clade recombination;in particular,inter-clade recombination in the gB genes of strains FJ-ZXF and FJ-W2,which were recombinant with clade 1 strains.We also found specific amino-acid changes and positively selected sites,possibly associated with functional changes.This analysis of the emergence of PRV in China illustrates the need for continuous monitoring and the development of vaccines against specific variants of PRV.展开更多
Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular...Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular change within populations and the evolution of species diversity. More than 98% of terrestrial fungi belong to the phyla Ascomycota or Basidiomycota. The former is considerably richer in number of species than the latter. We obtained DNA sequences of 21 protein-coding genes from the lichenized fungus Rhizoplaca chrysoleuca and used them together with sequences from GenBank for subsequent analyses. Three datasets were used to test rate discrepancies between Ascomycota and Basidiomycota and that within Ascomycota: (i) 13 taxa including 105 protein-coding genes, (ii) nine taxa including 21 protein-coding genes, and (iii) nuclear LSU rDNA of 299 fungal species. Based on analyses of the 105 protein-coding genes and nuclear LSU rDNA datasets, we found that the evolutionary rate was higher in Ascomycota than in Basidiomycota. The differences in substitution rates between Ascomycota and Basidiomycota were significant. Within Ascomycota, the species-rich Sordariomycetes has the fastest evolutionary rate, while Leotiomycetes has the slowest. Our results indicate that the main contribution to the higher substitution rates in Ascomycota does not come from mutualism, ecological conditions, sterility, metabolic rate or shorter generation time, but is possibly caused by the founder effect. This is another example of the correlation between species number and evolutionary rates, which is consistent with the hypothesis that the founder effect is responsible for accelerated substitution rates in diverse clades.展开更多
文摘On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps under a climate with freezing winter cold. These findings lead us to-examine the past ideas about domestication and differentiation of rice. Historically, in 1930s two sub-species, indica and japonica, were proposed on the basis of sterility in F1 hybrids between them. Soon after that, the two types were classified by the associations of a number of genetically independent traits. The characteristic associations of traits have been explained by the hybrid sterility or reproductive barriers which were assumed to comprise a set of duplicate recessive lethal genes and to be an inner genetic mechanism to lead to the varietal differentiations In 1980s, the hybrid sterility between Indica and Japonica types was analyzed, and Indica, Japonica, and wide-compatibility type which gives fertile hybrids when cross to Indica and Japonica types, are proved to contain an allele, S5＇, S5＇ and S5^n, respectively at a locus on chromosome 6. And those gametes having Sj allele are found to be partially aborted in the hybrid genotypes of S5＇/S5＇ while no gamete abortion occurs in S5＇/S5^n and S5＇/S5^n genotypes. Since then, the gene S5^n has been used in hybrid rice breeding to obtain fertile and vigorous hybrids between subspecies, and the long-disputed problem of hybrid sterility has been solved. Also in such studies the characteristic association of traits found in each of vadetal groups is better explained by founder effects. On the other hand, a large number of native cultivars of rice were surveyed with enzyme polymorphism in 1980s and later with molecular markers. As a result, profound genetic diversity is found in cultivated rice as well as in wild rice. These findings seem to lead us to the idea of multiple independent domestications of rice. However, before reaching such a conclusion, at least two factors, i.e., long-distance-dissemination of some genotypes and the possibilities of introgression by local wild rice to primitive cultivars need to be examined. Taking the two factors as well as the historical events into consideration, it is considered here that the perennial japonica cultivars which are close to wild rice in the Changjiang River basin were disseminated to East India through Assam or along the Bengal Bay, where they were transformed under the introgressions of local wild rice and formed a secondary center, from which some genotypes seem to be disseminated to colonies in Southeast Asia under the influence of Hinduism. Later some of the genotypes were introduced into China and constituted so called Indica type. This may be a reasonable picture for the varietal differentiation.
文摘青藏高原是气候变迁的敏感区。但第四纪以来全球气候的反复变化对该地区植物分布格局的影响至今未进行过仔细研究。线粒体DNA在松科植物中是母系遗传,其变异被广泛用于研究该科植物历史上由于气候变迁造成的瓶颈作用以及冰期后扩张中形成的奠基者效应。对青海云杉位于青藏高原核心、其边缘甘肃和宁夏地区共12个种群155个个体的线粒体nad 1片段的全序列进行测序,研究该序列在各种群中的变异状况。通过测序发现该片段在青海云杉中十分保守,在所有个体中仅发现由于重复序列造成的5种单倍型(H ap A,H ap B,H ap C,H ap D和H ap E)。高原核心的所有种群均只有H ap A,而所有的4种单倍型都在高原边缘的甘肃地区存在,但这一地区仍然是H ap A占优势;但是在远离高原的宁夏地区则存在5种单倍性;多样性的变异趋势是宁夏地区高于高原边缘的甘肃地区,而甘肃地区又显著高于高原核心地区。这一结果表明,在过去气候变迁过程中,不同地区的青海云杉种群经历了不同的气候影响,这种影响造成的奠基者效应或者瓶颈作用是造成目前这种遗传多样性分布格局的主要原因。现有的单倍型分布格局,特别是高原上所有间断分布种群拥有相同的单倍型表明,森林回迁中的奠基者效应应是更为重要的因素。
文摘Considering the severe impacts of genetic bottlenecks and small numbers of founders in populations of reintroduced animals, it is necessary to study inbreeding and its effect on fitness in species of conservation concern. Pere David＇s deer is one of few large mammal species extinct in the wild but safely preserved in captivity. Its specific background gives us the opportunity to study the relationships between heterozygosity and neonatal fitness in relocated populations. We employed five microsatellite loci to explore heterozygosity-fitness correlations in a population of Pere David＇s deer at the Beijing Milu Ecological Research Center. We observed associations between microsatellite-based variables sMLH, IR, MD^2 and HL, and two components of fitness ex- pressed early in life （birth weight and the neonatal mortality of 123 Pere David＇s deer calves born over six consecutive years）. We found that neonatal mortality was 19.1% - 7.6%, not higher than the 19% or 18% reported in other ungulates. The heterozygosity of calves was not associated with neonatal mortality, nor birth weight. Our study implies that low genetic variability of microsa- l：ellite loci has no overt effect on birth weight and neonatal mortality in reintroduced populations of P^re David＇s deer [Current Zoology 59 （2）： 249-256, 2013].
基金the Program for New Century Excellent Talents in University (NCET-05-0431)funding from the Commission of Science and Technol-ogy of Lin'an City to XY Chen
文摘Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations. However, compared with spatial genetic structure, few studies have been conducted on genetic changes over time. In this study, we used six polymorphic microsatellite loci to assess genetic variation of six size-classes of the population of Liushan, Cryptomeriajaponica var. sinensis, in the Tianmushan National Nature Reserve, whose origin was debatable. The mean number of alleles per locus and expected heterozygosity were 4.583 and 0.5999 respectively, lower than other conifers with the same life history characteristics. FST was 0.0024-0.003, and the pairwise test revealed no significant differentiation in any pair of size classes. Significant heterozygosity excesses were detected in five size classes except the oldest one, indicating bottleneck event（s）. The above results support the hypothesis that Tianmushan population was introduced and followed by natural regeneration.
基金supported by a grant from the Italian Ministry of Education,University and Research(PRIN project 2017KLZ3MA).
文摘Recent empirical and theoretical studies suggest that personality and locomotory performance traits linked to dispersal abilities are crucial components of the dispersal syndromes,and that they can evolve during range expansions and colonization processes.Island colonization is one of the best characterized processes in dispersal biogeography,and its implication in the evolution of phenotypic traits has been investigated over a wide range of temporal scales.However,the effect of island colonization on personality and performance traits of natural populations,and how these traits could drive island colonization,has been little explored.Noteworthy,no studies have addressed these processes in the context of late Pleistocene range expansions.Here,we investigated the contribution of island colonization triggered by postglacial range expansions to intraspecific variation in personality and locomotory performance traits.We compared boldness,exploration,jumping performance,and stickiness abilities in populations from 3 equidistant areas of the Tyrrhenian tree frog Hyla sarda,2 from the main island(Corsica Island),and 1 from the recently colonized island of Elba.Individuals from Elba were significantly bolder than individuals from Corsica,as they emerged sooner from a shelter(P=0.028),while individuals from Corsica showed markedly higher jumping and stickiness performance(both P<0.001),resulting as more performing than those of Elba.We discuss these results in the context of the major microevolutionary processes at play during range expansion,including selection,spatial sorting,founder effects,and their possible interaction with local adaptation processes.
基金supported by a research grant(PI11/00342)from Fondo de Investigacion Sanitaria(co-funded by the European Regional Development Fund,"A way to build Europe")to F.C.M.This funding was granted as coordinated project Renaltube
文摘Background:Familial hypomagnesemia with hypercalciuria and nephrocalcinosis(FHHNC)is an autosomal recessive tubular disease caused by mutations in the CLDN16 or CLDN19 gene.Previous studies using microsatellite markers flanking the CLDN19 locus estimated that p.G20D(c.59G>A),a recurrent mutation in Spanish families,is a founder mutation.In the present study,we assessed the haplotype of Spanish patients using single nucleotide polymorphisms(SNPs).Methods:Twenty-seven FHHNC patients were included in this study.We analyzed four SNPs located in CLDN19 introns 3 and 4 by polymerase chain reaction amplification and DNA sequencing.Results:Three new patients with homozygous p.G20D were identified.The SNP genotyping analysis showed that alleles carrying this mutation shared a common SNP haplotype.Conclusions:Our findings suggest the existence of a founder effect responsible for FHHNC in our cohort.Testing for the presence of mutation p.G20D should be the first genetic screening in Spanish patients.
基金financially supported by the National Key Research and Development Program of China (2017YFD0500101)the Natural Science Foundation of Jiangsu Province (BK20170721)the China Association for Science and Technology Youth Talent Lift Project (2017-2019)
文摘Since late 2011,outbreaks of pseudorabies virus(PRV)have occurred in southern China causing major economic losses to the pig industry.We previously reported that variant PRV forms and recombination in China could be the source of continued epidemics.Here,we analyzed samples from intensive pig farms in eastern China between 2017 and 2019,and sequenced the main glycoproteins(gB,gC,gD,and gE)to study the evolution characteristics of PRV.Based on the gC gene,we found that PRV variants belong to clade 2 and detected a founder effect during by the PRV epidemic.In addition,we detected inter-and intra-clade recombination;in particular,inter-clade recombination in the gB genes of strains FJ-ZXF and FJ-W2,which were recombinant with clade 1 strains.We also found specific amino-acid changes and positively selected sites,possibly associated with functional changes.This analysis of the emergence of PRV in China illustrates the need for continuous monitoring and the development of vaccines against specific variants of PRV.
基金supported by the National Natural Science Foundation of China (Grant Nos. 30570008 and 30770012) the Chinese Academy of Sciences (Grant No. KSCX2-YW-Z-041)
文摘Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular change within populations and the evolution of species diversity. More than 98% of terrestrial fungi belong to the phyla Ascomycota or Basidiomycota. The former is considerably richer in number of species than the latter. We obtained DNA sequences of 21 protein-coding genes from the lichenized fungus Rhizoplaca chrysoleuca and used them together with sequences from GenBank for subsequent analyses. Three datasets were used to test rate discrepancies between Ascomycota and Basidiomycota and that within Ascomycota: (i) 13 taxa including 105 protein-coding genes, (ii) nine taxa including 21 protein-coding genes, and (iii) nuclear LSU rDNA of 299 fungal species. Based on analyses of the 105 protein-coding genes and nuclear LSU rDNA datasets, we found that the evolutionary rate was higher in Ascomycota than in Basidiomycota. The differences in substitution rates between Ascomycota and Basidiomycota were significant. Within Ascomycota, the species-rich Sordariomycetes has the fastest evolutionary rate, while Leotiomycetes has the slowest. Our results indicate that the main contribution to the higher substitution rates in Ascomycota does not come from mutualism, ecological conditions, sterility, metabolic rate or shorter generation time, but is possibly caused by the founder effect. This is another example of the correlation between species number and evolutionary rates, which is consistent with the hypothesis that the founder effect is responsible for accelerated substitution rates in diverse clades.
