濒危植物长叶榧不同尺度遗传结构及种群历史动态
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摘要
物种遗传结构对其生存和发展起着重要作用,探讨濒危物种的遗传多样性水平及其分布可以为制定合理有效的保护策略提供依据。浙闽山地是我国陆地生物多样性关键地区,对该地区特有物种遗传结构及其种群历史的研究能够增进我们对生物多样性形成和维持机制的理解,同时对于生物多样性保护也具有重要的理论和实践意义。本研究选取浙闽山地的特有濒危树种,隶属于红豆杉科(Taxaceae)榧树属(Torreya Arn.)的长叶榧(Torreya jackii Chun)为对象,开发并筛选出富含多态性的微卫星标记并应用于不同种群、亚种群的遗传结构以及小尺度空间遗传格局分析,同时结合叶绿体DNA和线粒体DNA序列变异分析其种群历史动态,为长叶榧以及类似濒危物种采取有针对性的挽救和保护措施提供科学依据,也为研究浙闽山地特有种的进化历史提供参考。主要结果如下：
1.采用改进的生物素链霉亲和素捕获法从长叶榧基因组中分离和筛选得到8对多态性微卫星引物,为研究长叶榧的种群遗传结构提供了有效的工具。
2.采用微卫星标记对整个分布区范围的长叶榧种群进行遗传结构分析。8对微卫星引物共检测到42个等位基因,种群观察杂合度的范围介于0.3641-0.6336,平均为0.5012；期望杂合度在0.3657～0.6047之间,平均为0.4830。AMOVA分析表明长叶榧遗传变异主要分布于种群内。长叶榧种群间遗传分化程度较低(FST=0.155,RsT=0.195),STRUCTURE聚类分析和主坐标分析都表明各种群间具有较高的混合比(?)。Mantel检验显示长叶榧种群间的遗传距离与地理距离无显著相关性。长叶榧各个种群的有效种群大小介于15.12～185.48,平均为44.08。BOTTLENECK分析显示,缙云、邵武、永嘉、仙居、松阳种群在近期经历了瓶颈。从种群遗传贡献来看,缙云、松阳、桐庐、仙居种群总体遗传贡献率较大,这4个种群应当作为优先保护对象。
3.采用微卫星标记分析长叶榧亚种群的空间遗传格局。8对微卫星引物在7个长叶榧亚种群中共检测到41个等位基因,观察杂合度的范围为0.4688～0.6027,平均为0.5427；期望杂合度介于0.4453～0.5471,平均为0.5060。AMOVA分析显示长叶榧的遗传变异主要分布在亚种群内,亚种群间遗传分化较低(FST=0.064,RST=0.089)。长叶榧小尺度范围内全部植株以及各年龄级植株均存在显著的空间遗传结构,其中幼苗和幼树的空间遗传结构强度大于成年植株。长叶榧的基因有效扩散距离为23.79m。从7个亚种群分布区域来看,长叶榧在0-0.4km地域范围存在显著的空间遗传结构。
4.从39对叶绿体引物中筛选得到存在变异位点的trnD-trnT、atpH-atpI、 rpoB-trnC、rps16-trnQ片段,对这4个序列进行联合分析后得到6种叶绿体单倍型,其中有1种为所有种群共享单倍型,其它均为特有单倍型,仅存在于松阳、仙居、资溪和浦城种群。叶绿体单倍型多样性为0.168,种群间的遗传分化系数FST为0.188,GST为0.221。分子方差分析表明遗传变异主要来自于种群内。采用Tajima's D和Fu's Fs进行中性检验,各个种群均没有达到显著水平,但整个物种水平显示经历了扩张。采用失配分布分析也进一步支持这一结果。长叶榧cpDNA的单倍型网络图呈现出以共享单倍型H1为中心的星状结构。MP树与Bayesian树得到相同的拓扑结构,均表明6个单倍型之间不存在明显的分枝。采用红豆杉科植物化石进行校准,通过分子钟模型计算得到长叶榧6个单倍型的分化时间大约开始于14.37百万年前。
5.筛选18对线粒体引物仅得到1个具有变异位点的coxⅠ片段,共2种单倍型,特有单倍型仅存在于浦城种群,另一单倍型为所有种群所共享。线粒体单倍型多样性为0.022,种群间的遗传分化系数FST为0.333,GST为0.316。分子方差分析表明遗传变异主要来自于种群内。
6.采用msvar基于贝叶斯方法推算长叶榧的种群动态,结果显示长叶榧当前种群大小平均值为4417.74,祖先种群大小平均值为1945.36,当前种群大小为祖先种群大小的2.27倍,表明长叶榧种群在历史上曾经历扩张,种群开始扩张的时间大约为距今2351.26～12909.22年前。
The genetic structure of a species plays a crucial role in its survival and development. Exploring genetic diversity and their distribution of endangered species can lay the basis for reasonable and effective protection strategy. Zhejiang-Fujian Mountains is one of the key terrestrial biodiversity hotspots in China. Genetic structure and population history can indicate the evolution and ecological processes of the plant and the biodiversiy maintaining mechanisms in this area. At the same time, it is important for the theoretical and practical biodiversity consevation. Torreya jackii Chun (Taxaceae) is an endangered species endemic to this area. Multi-scale spatial genetic structure of T. jackii were studied using SSR molecular marker. In addition, we combined the variation information of the chloroplast DNA and mitochondria DNA to infer the population demographic history which can provide scientific basis for the further protection. It can also provide a reference for the study of the evolutionary history of the endemic species in the Zhejiang-Fujian Mountains. The main results were as following.
1. Eight polymorphic microsatellite primers were developed for T. jackii to investigate the genetic structure using the improved biotin-streptavidin capture method.
2. We analyzed the genetic structure of all populations collected in the whole distritution areas using8pairs of SSR markers. Fourty-two alleles were found. The observed heterozygosity were0.3641～0.6336with an average of0.5012. The expected heterozygosity ranged from0.3657to0.6047with an average of0.4830. AMOVA analysis showed that the genetic variation was mainly found within population, the genetic differentiation among populations was low (FST=0.155, RST=0.195). STRUCTURE cluster analysis and PCoA analysis showed that there have a higher mixing ratio among populations. Mantel test showed that there was no significant relationship between genetic distance and geographic distance. The effective population size ranged from15.12to185.48with an average of44.08. BOTTLENECK analysis showed that recent bottleneck effects were found in population of Jinyun, Shaowu, Yonjia, Xianju and Songyang. In terms of the population genetic contribution, population Jinyun, Songyang, Tonglu, Xianju was comparatively large. So, we suggested that those four populations should be the priority to be protected.
3. The spatial genetic structure (SGS) of the subpopulations were studied using SSR markers. Fourty-one alleles were found in the7subpopulations using8pairs of SSR primers. The observed heterozygosity were0.4688～0.6027with the average of0.5427. The expected heterozygosity ranged from0.4453to0.5471with the average of0.5060. AMOVA analysis showed that the genetic variation was mainly found within subpopulation, the genetic differentiation among subpopulations was low (FST=0.064, RST=0.089). Significant SGS occurred in all individuals and each age level of the T.jackii in fine-scale, and the SGS intensity of the seedlings and juveniles were greater than the adult trees. The effective gene dispersal distance of T. jackii was23.79m. Judging from the distribution area of the7subpopulations, significant SGS was found in the0～0.4km regional scale.
4. Among39cpDNA fragments screened, four, i.e., trnD-trnT, atpH-atpI, rpoB-trnC and rps16-trnQ, were polymorphic. Joint analysis of these four fragments, We found6haplotypes. One common haplotype was found in all populations, and the other five were unique haplotype, existing in population Songyang, Xianju, Zixi and Pucheng, respectively. The haplotype diversity was0.168. The genetic differentiation value (FST) was0.188, GST was0.221. AMOVA analysis showed that the genetic variation was mainly found within population. Neutrality test (including Tajima's and Fu's Fs) and mismatch analysis indicated that each population of T. jackii had not undergone recent population expansion, but in its whole species level had undergone recent expansion. H1was the center of the TCS network. cpDNA haplotypes relationship was "star-like", with five rare haplotypes linked to the ancestral interior haplotype H1. Both MP and Bayesian tree showed that the six haplotypes did not form distinct separated clades. Using a fossil come from Taxaceae for calibration, we obtained the divergence time of these6haplotypes began about14.37million years ago by calculating with molecular clock model.
5. Only mitochondria fragment coxI was variable among the18pairs of primers, and two haplotypes were found. Unique haplotype was found in population Pucheng, another one was shared in all populations. The haplotype diversity of mitochondria fragments was0.022. The genetic differentiation value (FST) was0.333, GST was0.316. AMOVA analysis showed that the genetic variation was mainly found within population.
6. Population dynamics analysis by msvar based on Bayesian method showed that the current population size of T. jackii was4417.74, which was2.27times larger than the ancestral populations (1945.36), which indicated that the population of T. jackii had undergone expansion. Further analysis showed that the expantion time was about2351.26～12909.22years ago.
1.采用改进的生物素链霉亲和素捕获法从长叶榧基因组中分离和筛选得到8对多态性微卫星引物,为研究长叶榧的种群遗传结构提供了有效的工具。
2.采用微卫星标记对整个分布区范围的长叶榧种群进行遗传结构分析。8对微卫星引物共检测到42个等位基因,种群观察杂合度的范围介于0.3641-0.6336,平均为0.5012；期望杂合度在0.3657～0.6047之间,平均为0.4830。AMOVA分析表明长叶榧遗传变异主要分布于种群内。长叶榧种群间遗传分化程度较低(FST=0.155,RsT=0.195),STRUCTURE聚类分析和主坐标分析都表明各种群间具有较高的混合比(?)。Mantel检验显示长叶榧种群间的遗传距离与地理距离无显著相关性。长叶榧各个种群的有效种群大小介于15.12～185.48,平均为44.08。BOTTLENECK分析显示,缙云、邵武、永嘉、仙居、松阳种群在近期经历了瓶颈。从种群遗传贡献来看,缙云、松阳、桐庐、仙居种群总体遗传贡献率较大,这4个种群应当作为优先保护对象。
3.采用微卫星标记分析长叶榧亚种群的空间遗传格局。8对微卫星引物在7个长叶榧亚种群中共检测到41个等位基因,观察杂合度的范围为0.4688～0.6027,平均为0.5427；期望杂合度介于0.4453～0.5471,平均为0.5060。AMOVA分析显示长叶榧的遗传变异主要分布在亚种群内,亚种群间遗传分化较低(FST=0.064,RST=0.089)。长叶榧小尺度范围内全部植株以及各年龄级植株均存在显著的空间遗传结构,其中幼苗和幼树的空间遗传结构强度大于成年植株。长叶榧的基因有效扩散距离为23.79m。从7个亚种群分布区域来看,长叶榧在0-0.4km地域范围存在显著的空间遗传结构。
4.从39对叶绿体引物中筛选得到存在变异位点的trnD-trnT、atpH-atpI、 rpoB-trnC、rps16-trnQ片段,对这4个序列进行联合分析后得到6种叶绿体单倍型,其中有1种为所有种群共享单倍型,其它均为特有单倍型,仅存在于松阳、仙居、资溪和浦城种群。叶绿体单倍型多样性为0.168,种群间的遗传分化系数FST为0.188,GST为0.221。分子方差分析表明遗传变异主要来自于种群内。采用Tajima's D和Fu's Fs进行中性检验,各个种群均没有达到显著水平,但整个物种水平显示经历了扩张。采用失配分布分析也进一步支持这一结果。长叶榧cpDNA的单倍型网络图呈现出以共享单倍型H1为中心的星状结构。MP树与Bayesian树得到相同的拓扑结构,均表明6个单倍型之间不存在明显的分枝。采用红豆杉科植物化石进行校准,通过分子钟模型计算得到长叶榧6个单倍型的分化时间大约开始于14.37百万年前。
5.筛选18对线粒体引物仅得到1个具有变异位点的coxⅠ片段,共2种单倍型,特有单倍型仅存在于浦城种群,另一单倍型为所有种群所共享。线粒体单倍型多样性为0.022,种群间的遗传分化系数FST为0.333,GST为0.316。分子方差分析表明遗传变异主要来自于种群内。
6.采用msvar基于贝叶斯方法推算长叶榧的种群动态,结果显示长叶榧当前种群大小平均值为4417.74,祖先种群大小平均值为1945.36,当前种群大小为祖先种群大小的2.27倍,表明长叶榧种群在历史上曾经历扩张,种群开始扩张的时间大约为距今2351.26～12909.22年前。
The genetic structure of a species plays a crucial role in its survival and development. Exploring genetic diversity and their distribution of endangered species can lay the basis for reasonable and effective protection strategy. Zhejiang-Fujian Mountains is one of the key terrestrial biodiversity hotspots in China. Genetic structure and population history can indicate the evolution and ecological processes of the plant and the biodiversiy maintaining mechanisms in this area. At the same time, it is important for the theoretical and practical biodiversity consevation. Torreya jackii Chun (Taxaceae) is an endangered species endemic to this area. Multi-scale spatial genetic structure of T. jackii were studied using SSR molecular marker. In addition, we combined the variation information of the chloroplast DNA and mitochondria DNA to infer the population demographic history which can provide scientific basis for the further protection. It can also provide a reference for the study of the evolutionary history of the endemic species in the Zhejiang-Fujian Mountains. The main results were as following.
1. Eight polymorphic microsatellite primers were developed for T. jackii to investigate the genetic structure using the improved biotin-streptavidin capture method.
2. We analyzed the genetic structure of all populations collected in the whole distritution areas using8pairs of SSR markers. Fourty-two alleles were found. The observed heterozygosity were0.3641～0.6336with an average of0.5012. The expected heterozygosity ranged from0.3657to0.6047with an average of0.4830. AMOVA analysis showed that the genetic variation was mainly found within population, the genetic differentiation among populations was low (FST=0.155, RST=0.195). STRUCTURE cluster analysis and PCoA analysis showed that there have a higher mixing ratio among populations. Mantel test showed that there was no significant relationship between genetic distance and geographic distance. The effective population size ranged from15.12to185.48with an average of44.08. BOTTLENECK analysis showed that recent bottleneck effects were found in population of Jinyun, Shaowu, Yonjia, Xianju and Songyang. In terms of the population genetic contribution, population Jinyun, Songyang, Tonglu, Xianju was comparatively large. So, we suggested that those four populations should be the priority to be protected.
3. The spatial genetic structure (SGS) of the subpopulations were studied using SSR markers. Fourty-one alleles were found in the7subpopulations using8pairs of SSR primers. The observed heterozygosity were0.4688～0.6027with the average of0.5427. The expected heterozygosity ranged from0.4453to0.5471with the average of0.5060. AMOVA analysis showed that the genetic variation was mainly found within subpopulation, the genetic differentiation among subpopulations was low (FST=0.064, RST=0.089). Significant SGS occurred in all individuals and each age level of the T.jackii in fine-scale, and the SGS intensity of the seedlings and juveniles were greater than the adult trees. The effective gene dispersal distance of T. jackii was23.79m. Judging from the distribution area of the7subpopulations, significant SGS was found in the0～0.4km regional scale.
4. Among39cpDNA fragments screened, four, i.e., trnD-trnT, atpH-atpI, rpoB-trnC and rps16-trnQ, were polymorphic. Joint analysis of these four fragments, We found6haplotypes. One common haplotype was found in all populations, and the other five were unique haplotype, existing in population Songyang, Xianju, Zixi and Pucheng, respectively. The haplotype diversity was0.168. The genetic differentiation value (FST) was0.188, GST was0.221. AMOVA analysis showed that the genetic variation was mainly found within population. Neutrality test (including Tajima's and Fu's Fs) and mismatch analysis indicated that each population of T. jackii had not undergone recent population expansion, but in its whole species level had undergone recent expansion. H1was the center of the TCS network. cpDNA haplotypes relationship was "star-like", with five rare haplotypes linked to the ancestral interior haplotype H1. Both MP and Bayesian tree showed that the six haplotypes did not form distinct separated clades. Using a fossil come from Taxaceae for calibration, we obtained the divergence time of these6haplotypes began about14.37million years ago by calculating with molecular clock model.
5. Only mitochondria fragment coxI was variable among the18pairs of primers, and two haplotypes were found. Unique haplotype was found in population Pucheng, another one was shared in all populations. The haplotype diversity of mitochondria fragments was0.022. The genetic differentiation value (FST) was0.333, GST was0.316. AMOVA analysis showed that the genetic variation was mainly found within population.
6. Population dynamics analysis by msvar based on Bayesian method showed that the current population size of T. jackii was4417.74, which was2.27times larger than the ancestral populations (1945.36), which indicated that the population of T. jackii had undergone expansion. Further analysis showed that the expantion time was about2351.26～12909.22years ago.
引文
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