基于微卫星分子标记的中国疫区内苹果蠹蛾Cydia pomonella（L.）种群遗传多样性和遗传结构研究
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摘要
苹果蠹蛾Cydiapomonella（L.）属鳞翅目Lepidoptera，卷蛾科Tortricidae，是果园中的重要害虫，目前已分布于全世界71个国家和地区。苹果蠹蛾寄主众多，每年给世界水果种植业造成严重危害。我国于1957年首次在新疆报道了苹果蠹蛾，该虫目前已扩散至新疆全境、甘肃河西走廊地区、宁夏中卫、内蒙古阿拉善盟及黑龙江东南部地区。
据报道，苹果蠹蛾对不同生境和气候条件具有较强的适应性，当其成功入侵到一新的地区后，往往随着时间的推移而发生遗传分化和演变，从而形成了具有不同生理特性及生物学特性的种群，增加了害虫防治的难度。所以，了解苹果蠹蛾入侵到中国之后的微进化进程、种群的遗传多样性及遗传结构，探讨分化成因及追溯扩散历史，对于制定有效的苹果蠹蛾防治策略及拦截措施具有重要意义。另外，物种的分化源于种群的分化。对于古老种群而言，迁移和遗传漂变的平衡影响着种群的遗传结构及分化模式。对于新的入侵种群，诸多的进化事件如瓶颈效应（或奠基者效应）、地理隔离及入侵历史等影响着种群遗传多样性及遗传结构形成的模式。因而，研究苹果蠹蛾在中国这样一个新的入侵生态系统中的微进化模式，同时具有重要的分子进化学上的意义。
本研究利用8个微卫星位点，从我国主要苹果蠹蛾疫区（新疆、甘肃、黑龙江）采集12个苹果蠹蛾地理种群，并利用德国、瑞士的2个苹果蠹蛾种群作为对照种群，首次对我国苹果蠹蛾的种群遗传学进行了微卫星分子标记研究。运用多种遗传多样性及遗传分化参数，结合分子方差分析、贝叶斯聚类分析及系统发育分析等研究方法，对全部14个苹果蠹蛾种群的遗传多样性及遗传结构进行了深入系统的分析。结果与结论如下：
1）扩增了中国苹果蠹蛾主要疫区的12个种群及德国、瑞士2个西欧种群共339头个体在8个微卫星位点上的等位基因片段。各种群的平均等位基因丰富度为4.17~12.23，观察杂合度为0.201~0.550。21.9%的成对位点显示出基因型连锁不平衡，但没有表现出在某一位点全部不平衡。无义等位基因频率在0.010~0.203，与多数鳞翅目昆虫的无义等位基因频率相当。14个种群中，4个种群显示出偏离哈迪-温伯格平衡，结合较高的近交系数0.097~0.486，说明中国疫区内苹果蠹蛾种群内部的杂合子较缺乏。
2）基于平均等位基因丰富度、杂合度水平等遗传多样性指标，发现本研究中所选取的西北地区的苹果蠹蛾种群的遗传多样性呈现出由西向东、由北向南逐渐降低的趋势。这一结果表明，苹果蠹蛾在入侵的过程中由于奠基者种群的不断拓展，新建立的种群较原有种群的遗传多样性显著降低。但是BOTTLENECK的分析表明，所有种群均没有经历瓶颈效应，可能是由于较短的入侵历史或者入侵过程中奠基者种群较大的个体数量。采自黑龙江的苹果蠹蛾种群具有比西北种群更高的遗传多样性。较短的入侵历史及较高的遗传多样性说明黑龙江种群经历了具有不同遗传起源的种群的多次入侵。同时，黑龙江苹果蠹蛾种群较高的遗传多样性也说明其不是西北种群扩散的结果，而是具有不同的入侵来源。另外，欧洲苹果蠹蛾种群较西北种群具有更高的遗传多样性，说明西北地区的苹果蠹蛾种群入侵历史相对较近。
3）基于分子方差分析、成对固定指数及贝叶斯聚类分析，发现中国疫区内的苹果蠹蛾种群具有明显的亚结构。其中，成对固定指数在多数种群中表现出了较高的分化程度（FST=0.040~0.337，P<0.05）；分子方差分析表明人为分组的新疆、甘肃、黑龙江及西欧苹果蠹蛾种群各组之间的遗传分化明显，占了全部遗传分化的9.64%；贝叶斯聚类分析表明，新疆北部的伊犁、精河、奎屯种群具有相似的遗传结构（平均从属系数，clusterred，Ili0.526，Jin0.896，Kuy0.577），结合较高的遗传多样性，说明3个种群可能具有相似的遗传起源且相对较长的入侵历史。尤其是伊犁种群，在西北苹果蠹蛾种群中具有最高的遗传多样性（R=9.16，Ho=0.356），由此推断伊犁种群可能最早入侵到西北地区。新疆南部的库尔勒种群具有与甘肃张掖种群相似的遗传结构（平均从属系数，clusteryellow，Kor0.760，Zha0.805），结合二者之间较低的固定指数、邻接系统树分析及苗木引种历史，可以推断张掖苹果蠹蛾是随着两地间苗木的调运而引入。黑龙江种群与西部种群具有不同的遗传结构，结合较高的固定指数（FST=0.157~0.324，P<0.05），进一步证明了黑龙江的苹果蠹蛾种群不是来自于西部苹果蠹蛾疫区。IBD分析（r=0.164，P=0.176）显示西北地区苹果蠹蛾种群间地理距离与遗传距离不存在明显的相关性，这表明人为协助的扩散在种群分化中起到了重要作用，而苹果蠹蛾本身较弱的飞行能力又限制了扩张种群与其他种群的基因交流，从而加速了遗传分化。
4）邻接系统树分析表明，新疆北部的精河、伊犁、奎屯种群具有较近的亲缘关系，这与贝叶斯聚类分析的结果一致。甘肃张掖种群与库尔勒种群聚为一个分支，进一步证明两地之间苹果蠹蛾种群通过人为因素进行长距离扩散的可能。黑龙江苹果蠹蛾种群与西欧种群具有较近的亲缘关系，这进一步证明了贝叶斯聚类分析的结果。要探明东北种群与西欧种群亲缘关系较近的原因，需要探明整个欧洲包括俄罗斯远东地区苹果蠹蛾种群的亲缘关系。系统发育关系并不能反映苹果蠹蛾在中国的传播路径，造成这一结果的原因是较短的入侵历史以及人为协助的被动扩散。
Cydia pomonella (L.)(Lepidoptera:Tortricidae), the codling moth, is the destructive fruit pest in fruit orchard and also the notorious invasive species, spreading to nearly all the apple growing areas over71countries or regions. Host plants for codling moth include many kinds of pome fruits. As a notoriously invasive pest, the codling moth has caused a great deal of damage to production of pomes. The first reported sightings of the Chinese codling moth were in1957in Xinjiang. It has now been observed throughout Xinjiang, Hexi Corridor in Gansu Zhongwei city of Ningxia, Alxa of Inner Mongolia and southeastern Heilongjiang.
The successful adaption of codling moth to different habitats and climates by forming various populations which may differ with physiological and biological traits enforces its local fitness and makes it more difficult to control. So, the understanding of the micro-evolutionary processes and the reasons caused population variation after successful invasion of codling moth in China, and also the investigation of invasive history are necessary in order to develop effective pest management and interception strategies. Furthermore, speciation primarily results from the population differentiation. For populations established over long period of time, the genetic equilibrium of drift and gene flow forms the population structuring and patterns of variation. In contrast, in newly established populations, the population genetic diversity and structure are often determined by the historical events, such as bottleneck effects (or founder effects), vicariance events and dispersal history. Studies of the micro-evolutionary of codling moth in such a newly invaded ecosystem in China has a significance for understanding the process of molecular evolution.
This dissertation deals with the genetic variations of12C. pomonella populations collected from the mainly distributed regions (Xinjiang, Gansu and Heilongjiang) in China and compared them with one German and one Swiss population using eight microsatellite loci. We deeply investigates the population genetic diversity and structure of14selected population based on many parameters of genetic variation, analysis of molecular variance, Bayesian clustering analysis and phylogenetic relationship. The results and conclusions of this dissertation are as follow:
1) We amplified the allelic sequences of eight microsatellite loci of339individuals from14populations, covering the potential distributions of codling moth in China. All of the eight selected loci were polymorphic and the number of alleles of each population per locus ranged from4.17to12.23, observed heterozygosity ranged from0.201to0.550.21.9%disequilibrium was found in392pairs of loci. The frequency of null alleles ranged from0.010 to0.203that is typical for lepidopteran. Four of the14populations revealed significant departures from HWE, together with high mean values of inbreeding index ranging from0.097to0.486, indicating the existence of heterozygote deficiencies.
2) A west-east and north-south gradient in genetic diversity was observed based on mean allele richness and level of heterozygosity. This result can be explained by the colonization of new areas via sequential founder populations or with bottleneck effects. However, the BOTTLENECK analysis revealed no clear genetic evidence for bottleneck effect in any of the studied populations. The lack of a bottleneck effect may be determined by the recent invasion history and successful colonisation by large numbers of migrants. Moreover, the two populations from Heilongjiang showed highest genetic diversities among the studied populations, which may result from the new invasion event from different genetic resources. Taking together the higher genetic diversity and distinct genetic structure revealing by cluster analysis, we can deduce that C. pomonella of Heilongjiang were not seeded by invasion populations from western China. Furthermore, the codling moth populations from Germany and Switzerland displayed a higher level of genetic diversity compared with that of populations from northwestern China. This result supports that the codling moth in China has relatively shorter history than that in southeastern Europe, the documented origin.
3) There was strong genetic structuring in14populations based on Bayesian clustering approach, AMOVA and pairwise FST. The values of pairwise FST ranged from0.040to0.337. Sixty-eight comparisons out of ninety-one showed high or very high genetic differentiations (P<0.05). AMOVA results indicated that9.64%of overall variation was explained by geographic locations which were arbitrarily grouped according to the collected regions including Xinjiang, Gansu, Heilongjiang and western Europe. Bayesian clustering analysis showed that Ili, Jinghe and Kuytun populations from northern Xinjiang had similar genetic structure (average membership coefficient, cluster red, Ili0.526, Jin0.896, Kuy0.577). The results linking to relatively higher genetic diversity estimates of the three populations suggests these three populations were established by individuals belonging to the same maternal lineage. Genetic diversity of C. pomonella population from Ili was highest among populations from northwestern China (a=9.16, Ho=0.356), suggests that Ili region is most likely to be the origin center of codling moth in northwestern China. Bayesian clustering analysis also indicated that the populations from Zhangye and Korla had similar genetic structures (average membership coefficient, cluster yellow, Kor0.760, Zha0.805), together with the results of low pairwise FST, the analysis of NJ phylogenetic tree and the records of seeding transport, suggesting that similarity of genetic structures is due to human activity associated with the movement of nursery material. The level of genetic differentiation between populations from northeastern and northwestern China was great (FST=0.157～0.324,P<0.05). The results further supports the hypothesis that the invasion of codling moth in China from at least two different path ways. In the present study, the result of Mantel test (r=0.164,P=0.176) indicated that the pattern of variation was weakly associated with geographic distance among populations from northwestern China. The weak flight capacity and the human-aided dispersal improve the differentiation of geographic populations.
4) Phylogenetic analysis based on NJ tree indicated that the Jinghe, Ili and Kuytun populations form northern Xinjiang had a close phylogenetic relationship. This result is consistent with the result of Bayesian clustering analysis. The close phylogenetic relationship between populations from Zhangye and Korla further confirms the probability of human-aided dispersal over large geographic distance. We also found the populations from Heilongjiang had similar genetic structure with those of western European populations. A phylogenetic study based on a greater number of collection sites is necessary to clarify the relationship between C. pomonella populations from Eropean countries before precise conclusions can be drawn, especially the phylogenetic relationship of populations from western Europe and far east region of Russia, the latter is close to Heilongjiang and was documented as distributed region of codling moth. The neighbor joining tree did not show distinct phylogenetic relationship associated with geographic distribution, which can be explained by relatively short history or passive dispersal by anthropic factors.
据报道，苹果蠹蛾对不同生境和气候条件具有较强的适应性，当其成功入侵到一新的地区后，往往随着时间的推移而发生遗传分化和演变，从而形成了具有不同生理特性及生物学特性的种群，增加了害虫防治的难度。所以，了解苹果蠹蛾入侵到中国之后的微进化进程、种群的遗传多样性及遗传结构，探讨分化成因及追溯扩散历史，对于制定有效的苹果蠹蛾防治策略及拦截措施具有重要意义。另外，物种的分化源于种群的分化。对于古老种群而言，迁移和遗传漂变的平衡影响着种群的遗传结构及分化模式。对于新的入侵种群，诸多的进化事件如瓶颈效应（或奠基者效应）、地理隔离及入侵历史等影响着种群遗传多样性及遗传结构形成的模式。因而，研究苹果蠹蛾在中国这样一个新的入侵生态系统中的微进化模式，同时具有重要的分子进化学上的意义。
本研究利用8个微卫星位点，从我国主要苹果蠹蛾疫区（新疆、甘肃、黑龙江）采集12个苹果蠹蛾地理种群，并利用德国、瑞士的2个苹果蠹蛾种群作为对照种群，首次对我国苹果蠹蛾的种群遗传学进行了微卫星分子标记研究。运用多种遗传多样性及遗传分化参数，结合分子方差分析、贝叶斯聚类分析及系统发育分析等研究方法，对全部14个苹果蠹蛾种群的遗传多样性及遗传结构进行了深入系统的分析。结果与结论如下：
1）扩增了中国苹果蠹蛾主要疫区的12个种群及德国、瑞士2个西欧种群共339头个体在8个微卫星位点上的等位基因片段。各种群的平均等位基因丰富度为4.17~12.23，观察杂合度为0.201~0.550。21.9%的成对位点显示出基因型连锁不平衡，但没有表现出在某一位点全部不平衡。无义等位基因频率在0.010~0.203，与多数鳞翅目昆虫的无义等位基因频率相当。14个种群中，4个种群显示出偏离哈迪-温伯格平衡，结合较高的近交系数0.097~0.486，说明中国疫区内苹果蠹蛾种群内部的杂合子较缺乏。
2）基于平均等位基因丰富度、杂合度水平等遗传多样性指标，发现本研究中所选取的西北地区的苹果蠹蛾种群的遗传多样性呈现出由西向东、由北向南逐渐降低的趋势。这一结果表明，苹果蠹蛾在入侵的过程中由于奠基者种群的不断拓展，新建立的种群较原有种群的遗传多样性显著降低。但是BOTTLENECK的分析表明，所有种群均没有经历瓶颈效应，可能是由于较短的入侵历史或者入侵过程中奠基者种群较大的个体数量。采自黑龙江的苹果蠹蛾种群具有比西北种群更高的遗传多样性。较短的入侵历史及较高的遗传多样性说明黑龙江种群经历了具有不同遗传起源的种群的多次入侵。同时，黑龙江苹果蠹蛾种群较高的遗传多样性也说明其不是西北种群扩散的结果，而是具有不同的入侵来源。另外，欧洲苹果蠹蛾种群较西北种群具有更高的遗传多样性，说明西北地区的苹果蠹蛾种群入侵历史相对较近。
3）基于分子方差分析、成对固定指数及贝叶斯聚类分析，发现中国疫区内的苹果蠹蛾种群具有明显的亚结构。其中，成对固定指数在多数种群中表现出了较高的分化程度（FST=0.040~0.337，P<0.05）；分子方差分析表明人为分组的新疆、甘肃、黑龙江及西欧苹果蠹蛾种群各组之间的遗传分化明显，占了全部遗传分化的9.64%；贝叶斯聚类分析表明，新疆北部的伊犁、精河、奎屯种群具有相似的遗传结构（平均从属系数，clusterred，Ili0.526，Jin0.896，Kuy0.577），结合较高的遗传多样性，说明3个种群可能具有相似的遗传起源且相对较长的入侵历史。尤其是伊犁种群，在西北苹果蠹蛾种群中具有最高的遗传多样性（R=9.16，Ho=0.356），由此推断伊犁种群可能最早入侵到西北地区。新疆南部的库尔勒种群具有与甘肃张掖种群相似的遗传结构（平均从属系数，clusteryellow，Kor0.760，Zha0.805），结合二者之间较低的固定指数、邻接系统树分析及苗木引种历史，可以推断张掖苹果蠹蛾是随着两地间苗木的调运而引入。黑龙江种群与西部种群具有不同的遗传结构，结合较高的固定指数（FST=0.157~0.324，P<0.05），进一步证明了黑龙江的苹果蠹蛾种群不是来自于西部苹果蠹蛾疫区。IBD分析（r=0.164，P=0.176）显示西北地区苹果蠹蛾种群间地理距离与遗传距离不存在明显的相关性，这表明人为协助的扩散在种群分化中起到了重要作用，而苹果蠹蛾本身较弱的飞行能力又限制了扩张种群与其他种群的基因交流，从而加速了遗传分化。
4）邻接系统树分析表明，新疆北部的精河、伊犁、奎屯种群具有较近的亲缘关系，这与贝叶斯聚类分析的结果一致。甘肃张掖种群与库尔勒种群聚为一个分支，进一步证明两地之间苹果蠹蛾种群通过人为因素进行长距离扩散的可能。黑龙江苹果蠹蛾种群与西欧种群具有较近的亲缘关系，这进一步证明了贝叶斯聚类分析的结果。要探明东北种群与西欧种群亲缘关系较近的原因，需要探明整个欧洲包括俄罗斯远东地区苹果蠹蛾种群的亲缘关系。系统发育关系并不能反映苹果蠹蛾在中国的传播路径，造成这一结果的原因是较短的入侵历史以及人为协助的被动扩散。
Cydia pomonella (L.)(Lepidoptera:Tortricidae), the codling moth, is the destructive fruit pest in fruit orchard and also the notorious invasive species, spreading to nearly all the apple growing areas over71countries or regions. Host plants for codling moth include many kinds of pome fruits. As a notoriously invasive pest, the codling moth has caused a great deal of damage to production of pomes. The first reported sightings of the Chinese codling moth were in1957in Xinjiang. It has now been observed throughout Xinjiang, Hexi Corridor in Gansu Zhongwei city of Ningxia, Alxa of Inner Mongolia and southeastern Heilongjiang.
The successful adaption of codling moth to different habitats and climates by forming various populations which may differ with physiological and biological traits enforces its local fitness and makes it more difficult to control. So, the understanding of the micro-evolutionary processes and the reasons caused population variation after successful invasion of codling moth in China, and also the investigation of invasive history are necessary in order to develop effective pest management and interception strategies. Furthermore, speciation primarily results from the population differentiation. For populations established over long period of time, the genetic equilibrium of drift and gene flow forms the population structuring and patterns of variation. In contrast, in newly established populations, the population genetic diversity and structure are often determined by the historical events, such as bottleneck effects (or founder effects), vicariance events and dispersal history. Studies of the micro-evolutionary of codling moth in such a newly invaded ecosystem in China has a significance for understanding the process of molecular evolution.
This dissertation deals with the genetic variations of12C. pomonella populations collected from the mainly distributed regions (Xinjiang, Gansu and Heilongjiang) in China and compared them with one German and one Swiss population using eight microsatellite loci. We deeply investigates the population genetic diversity and structure of14selected population based on many parameters of genetic variation, analysis of molecular variance, Bayesian clustering analysis and phylogenetic relationship. The results and conclusions of this dissertation are as follow:
1) We amplified the allelic sequences of eight microsatellite loci of339individuals from14populations, covering the potential distributions of codling moth in China. All of the eight selected loci were polymorphic and the number of alleles of each population per locus ranged from4.17to12.23, observed heterozygosity ranged from0.201to0.550.21.9%disequilibrium was found in392pairs of loci. The frequency of null alleles ranged from0.010 to0.203that is typical for lepidopteran. Four of the14populations revealed significant departures from HWE, together with high mean values of inbreeding index ranging from0.097to0.486, indicating the existence of heterozygote deficiencies.
2) A west-east and north-south gradient in genetic diversity was observed based on mean allele richness and level of heterozygosity. This result can be explained by the colonization of new areas via sequential founder populations or with bottleneck effects. However, the BOTTLENECK analysis revealed no clear genetic evidence for bottleneck effect in any of the studied populations. The lack of a bottleneck effect may be determined by the recent invasion history and successful colonisation by large numbers of migrants. Moreover, the two populations from Heilongjiang showed highest genetic diversities among the studied populations, which may result from the new invasion event from different genetic resources. Taking together the higher genetic diversity and distinct genetic structure revealing by cluster analysis, we can deduce that C. pomonella of Heilongjiang were not seeded by invasion populations from western China. Furthermore, the codling moth populations from Germany and Switzerland displayed a higher level of genetic diversity compared with that of populations from northwestern China. This result supports that the codling moth in China has relatively shorter history than that in southeastern Europe, the documented origin.
3) There was strong genetic structuring in14populations based on Bayesian clustering approach, AMOVA and pairwise FST. The values of pairwise FST ranged from0.040to0.337. Sixty-eight comparisons out of ninety-one showed high or very high genetic differentiations (P<0.05). AMOVA results indicated that9.64%of overall variation was explained by geographic locations which were arbitrarily grouped according to the collected regions including Xinjiang, Gansu, Heilongjiang and western Europe. Bayesian clustering analysis showed that Ili, Jinghe and Kuytun populations from northern Xinjiang had similar genetic structure (average membership coefficient, cluster red, Ili0.526, Jin0.896, Kuy0.577). The results linking to relatively higher genetic diversity estimates of the three populations suggests these three populations were established by individuals belonging to the same maternal lineage. Genetic diversity of C. pomonella population from Ili was highest among populations from northwestern China (a=9.16, Ho=0.356), suggests that Ili region is most likely to be the origin center of codling moth in northwestern China. Bayesian clustering analysis also indicated that the populations from Zhangye and Korla had similar genetic structures (average membership coefficient, cluster yellow, Kor0.760, Zha0.805), together with the results of low pairwise FST, the analysis of NJ phylogenetic tree and the records of seeding transport, suggesting that similarity of genetic structures is due to human activity associated with the movement of nursery material. The level of genetic differentiation between populations from northeastern and northwestern China was great (FST=0.157～0.324,P<0.05). The results further supports the hypothesis that the invasion of codling moth in China from at least two different path ways. In the present study, the result of Mantel test (r=0.164,P=0.176) indicated that the pattern of variation was weakly associated with geographic distance among populations from northwestern China. The weak flight capacity and the human-aided dispersal improve the differentiation of geographic populations.
4) Phylogenetic analysis based on NJ tree indicated that the Jinghe, Ili and Kuytun populations form northern Xinjiang had a close phylogenetic relationship. This result is consistent with the result of Bayesian clustering analysis. The close phylogenetic relationship between populations from Zhangye and Korla further confirms the probability of human-aided dispersal over large geographic distance. We also found the populations from Heilongjiang had similar genetic structure with those of western European populations. A phylogenetic study based on a greater number of collection sites is necessary to clarify the relationship between C. pomonella populations from Eropean countries before precise conclusions can be drawn, especially the phylogenetic relationship of populations from western Europe and far east region of Russia, the latter is close to Heilongjiang and was documented as distributed region of codling moth. The neighbor joining tree did not show distinct phylogenetic relationship associated with geographic distribution, which can be explained by relatively short history or passive dispersal by anthropic factors.
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