基于线粒体控制区序列和核基因微卫星标记的杂色山雀遗传多样性研究
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摘要
杂色山雀(Parus varius)属雀形目,山雀科,山雀属,是一种分布区域狭窄、雌雄同色同型的小型森林洞巢鸟类。指名亚种P.v.varius在中国大陆的分布范围很狭窄,主要分布于辽宁的中、东、南部山区和毗邻辽东山区的吉林省部分山区。因为这种分布地的局限性,导致国内对杂色山雀的研究很少,而基于多基因标记的遗传多样性研究更是未见报道。遗传多样性是非常重要的生物资源。开展杂色山雀遗传多样性的研究和分析是我们进一步对其物种发展和种群延续进行保护的基础。
本研究通过使用线粒体DNA控制区序列和核基因微卫星标记对大陆杂色山雀种群的遗传多样性进行了分析,主要得到以下结果:
1)线粒体DNA控制区:在68个样本中得到长度529 bp的控制区序列,其中有14个变异位点,包括11个单变异位点和3个简约信息位点;核苷酸多样性π、单倍型多样性h和平均核苷酸差异数K分别为0.0017、0.5328、0.8917。结果显示基于线粒体DNA控制区序列的杂色山雀遗传多样性较低。中性检验和错配分布图说明大陆杂色山雀种群没有经历过种群扩张。基于邻接法和最小进化法构建的系统发生树显示大陆杂色山雀种群分化不明显,没有形成与采样地相对应的地理格局,说明大陆杂色山雀属于一个地理种群。
2)核基因微卫星标记:9个微卫星位点的等位基因为6~16个,平均为11.78个;观测杂合度、期望杂合度和多态信息含量分别为0.651、0.779和0.755。9个核基因微卫星标记所显示的遗传多样性较高。其中4个位点没有偏离Hard-Weinberg平衡,另外5个位点显著偏离了Hard-Weinberg平衡。不论是等位基因频率的图形检查法,还是等位基因频率分布的缺口分析法,都显示出大陆杂色山雀种群近期很可能没有发生过瓶颈效应。
综上所述,从长期的发展历史来看,中国大陆杂色山雀种群一直处于分布范围狭窄,种群数量有限的状态,其遗传多样性较低;但近期其种群数量稳定,没有经历瓶颈效应等打击,遗传多样性保持较好。
Parus varius (Passeriformes, Paridae, Parus), is a kind of small cavity-nest forest birds and monomorphic with obviously narrow distribution. P.v.varius distributes narrowly in Chinese mainland, such as the middle, eastern, southern mountains of Liaoning province and partial mountains of Jilin province, which is contiguous to eastern mountains of Liaoning province. The limited distribution leads to rarely researches on P.v.varius in China. Furthermore, analysis of genetic diversity based on multi-gene markers has never been reported. Genetic diversity, one kind of important biological resources, is the foundation of protecting species development and continuation of population.
Here, I report the results of genetic diversity of P.v.varius in Chinese mainland based on the analysis of mitochondrial DNA control region and nuclear microsatellite markers:
1) 529 bp in length were sequenced in mitochondrial DNA control region of 68 individuals. Fourteen variations in all were detected, including 11 singleton variable sites and 3 parsimony informative sites. Genetic diversity was low based on mt DNA control region of P.v.varius, with 0.0017 for nucleotide diversity (π) and 0.5328 for haplotype diversity (h). I attribute the low genetic diversity of this bird to its narrow distribution and small population in the long-term history. There were no population expansion events or bottleneck effect in P.v.varius as indicated by the results from neutrality test and mismatch distribution. Both of the phylotypes trees revealed that P.v.varius in Chinese mainland belongs to one population without obvious differentiation.
2) The number of allele was 6~16 with a mean value of 11.78. The average observed heterozyosity, the average expected heterozyosity, and polymorphic information content (PIC) across the nine loci was 0.651, 0.779 and 0.755 respectively. Genetic diversity is high based on nine nuclear microsatellite markers of P.v.varius. The observed genotype frequencies at four loci were consistent with Hardy-Weinberg Equilbrium (HWE) and the remaining five loci were significantly deviated from HWE. The results may be resulted from null allele and genetic drift. Both graphical assessment of allele frequency distributions and allele frequency distribution for gaps showed that there was no bottleneck in the recent history of P.v.varius.
In conclusion, results from the present work indicate that genetic diversity of mitochondrial DNA control region was lower in P.v.varius than in other related birds, which may be accounted for by its narrow distribution and small population in the history. However, the population remains stable and shows no bottleneck effect in recent decades.
本研究通过使用线粒体DNA控制区序列和核基因微卫星标记对大陆杂色山雀种群的遗传多样性进行了分析,主要得到以下结果:
1)线粒体DNA控制区:在68个样本中得到长度529 bp的控制区序列,其中有14个变异位点,包括11个单变异位点和3个简约信息位点;核苷酸多样性π、单倍型多样性h和平均核苷酸差异数K分别为0.0017、0.5328、0.8917。结果显示基于线粒体DNA控制区序列的杂色山雀遗传多样性较低。中性检验和错配分布图说明大陆杂色山雀种群没有经历过种群扩张。基于邻接法和最小进化法构建的系统发生树显示大陆杂色山雀种群分化不明显,没有形成与采样地相对应的地理格局,说明大陆杂色山雀属于一个地理种群。
2)核基因微卫星标记:9个微卫星位点的等位基因为6~16个,平均为11.78个;观测杂合度、期望杂合度和多态信息含量分别为0.651、0.779和0.755。9个核基因微卫星标记所显示的遗传多样性较高。其中4个位点没有偏离Hard-Weinberg平衡,另外5个位点显著偏离了Hard-Weinberg平衡。不论是等位基因频率的图形检查法,还是等位基因频率分布的缺口分析法,都显示出大陆杂色山雀种群近期很可能没有发生过瓶颈效应。
综上所述,从长期的发展历史来看,中国大陆杂色山雀种群一直处于分布范围狭窄,种群数量有限的状态,其遗传多样性较低;但近期其种群数量稳定,没有经历瓶颈效应等打击,遗传多样性保持较好。
Parus varius (Passeriformes, Paridae, Parus), is a kind of small cavity-nest forest birds and monomorphic with obviously narrow distribution. P.v.varius distributes narrowly in Chinese mainland, such as the middle, eastern, southern mountains of Liaoning province and partial mountains of Jilin province, which is contiguous to eastern mountains of Liaoning province. The limited distribution leads to rarely researches on P.v.varius in China. Furthermore, analysis of genetic diversity based on multi-gene markers has never been reported. Genetic diversity, one kind of important biological resources, is the foundation of protecting species development and continuation of population.
Here, I report the results of genetic diversity of P.v.varius in Chinese mainland based on the analysis of mitochondrial DNA control region and nuclear microsatellite markers:
1) 529 bp in length were sequenced in mitochondrial DNA control region of 68 individuals. Fourteen variations in all were detected, including 11 singleton variable sites and 3 parsimony informative sites. Genetic diversity was low based on mt DNA control region of P.v.varius, with 0.0017 for nucleotide diversity (π) and 0.5328 for haplotype diversity (h). I attribute the low genetic diversity of this bird to its narrow distribution and small population in the long-term history. There were no population expansion events or bottleneck effect in P.v.varius as indicated by the results from neutrality test and mismatch distribution. Both of the phylotypes trees revealed that P.v.varius in Chinese mainland belongs to one population without obvious differentiation.
2) The number of allele was 6~16 with a mean value of 11.78. The average observed heterozyosity, the average expected heterozyosity, and polymorphic information content (PIC) across the nine loci was 0.651, 0.779 and 0.755 respectively. Genetic diversity is high based on nine nuclear microsatellite markers of P.v.varius. The observed genotype frequencies at four loci were consistent with Hardy-Weinberg Equilbrium (HWE) and the remaining five loci were significantly deviated from HWE. The results may be resulted from null allele and genetic drift. Both graphical assessment of allele frequency distributions and allele frequency distribution for gaps showed that there was no bottleneck in the recent history of P.v.varius.
In conclusion, results from the present work indicate that genetic diversity of mitochondrial DNA control region was lower in P.v.varius than in other related birds, which may be accounted for by its narrow distribution and small population in the history. However, the population remains stable and shows no bottleneck effect in recent decades.
引文
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