青藏高原特有植物垫状点地梅的种群遗传结构
摘要
青藏高原独特的地理特征和气候变化与该地区植物物种遗传多样性的空间分布格局的形成过程具有不可分割的联系。对该地区植物物种的遗传结构、空间分布格局及其成因的研究能够增进我们对植物的进化和生态过程,以及该地区过去地质气候变化过程的理解。以垫状点地梅(Androsace tapete Maxim)为例,它是报春花科点地梅属的一种多年生草本植物,分布于高寒草原和高原草甸之上,是地球上海拔分布最高的被子植物之一,同是也是青藏高原上特有的分布最广,数量最大的一类垫状植物,是我们研究物种遗传多样性和青藏高原的高寒生态系统、地质和气候环境变化历史事件的理想材料。
本文利用微卫星分子标记和叶绿体非编码区基因序列来分析垫状点地梅的遗传结构和进化潜力,评估垫状点地梅对气候变暖的响应能力,探讨影响或造成垫状点地梅空间遗传结构的生物学、地质事件和气候环境变化历史过程。旨在通过对垫状点地梅的遗传多样性和空间遗传结构的基础研究,为更好的保护和修复青藏高原高寒的生态系统的结构和功能完整性提供有价值的基础数据；结合青藏高原第四纪气候变迁历史,推测垫状点地梅第四冰期的可能避难所以及种群的扩散路线,通过模拟数据和垫状点地梅数据分析不同抽样策略(抽样大小和抽样方法)对研究精细尺度的空间遗传结构的影响,为研究垫状点地梅的繁殖和扩散行为提供可靠的方法。主要结果如下：
(1)通过磁珠富集法筛选垫状点地梅的微卫星分子标记基因组DNA后,用Rsal限制性内切酶酶切并连接接头,再用接头引物进行PCR扩增,得到的扩增产物与生物素标记的(AC)15,(AT)1 5,(CT)12,(ATC)10和(CCA)10探针杂交,杂交复合物用链亲和素包裹磁珠进行吸附,得到微卫星单链目标DNA片段,经PCR扩增,连接PMD19-T载体,转化到感受态大肠杆菌,得到微卫星富集小插入片段DNA文库。经阳性克隆和测序分析得到16个有效的微卫星序列,重复碱基数以双核苷重复最为常见,其中又以(GA) n/(CT)n重复最多,还观察到ATG、TCT重复单位。完美型(重复次数8-17次)的微卫星有9个,占56.25%；非完美型的微卫星有5个,占31.25%；混合型的微卫星有2个,占12.5%。这些序列在GenBank上的登录号分别是：FJ824648-FJ824656、GQ121408-GQ121415。16个有效的微卫星位点成功设计了16对引物,经用48个受试样本进行初步筛选,16对均表现出多态性,其中8个微卫星位点符合Hardy-Weinberg平衡。
(2)应用6对微卫星引物研究了唐古拉山两侧的垫状点地梅种群的遗传多样性、遗传结构和有效种群历史动态过程。在8个采样种群中,共检测到31.8个等位基因,观察等位基因数为3-9.87个,等位基因丰富度为4.484-5.577,平均期望杂合度(HE)为0.579-0.659,平均观察杂合度(Ho)为0.335-0.547,垫状点地梅总体表现为显著的杂合子缺失,近交系数为0.313；在4个种群中检测到连锁不平衡现象；垫状点地梅种群间的遗传分化程度很低,遗传分化系数Fst=0.028和Rst=0.026,而且AMOVA结果表明超过95%以上遗传变异发生在种群内；虽然8个种群内都发生了近交繁殖(Fis为0.233-0.430),但垫状点地梅种群间的基因交流仍很频繁(Nm>1),主坐标分析、距离法(NJ)和贝斯法(MCMC)的聚类分析结果显示垫状点地梅个体间混合程度较高,唐古拉山两侧的垫状点地梅种群间的基因交流并没有受到地理阻碍；用Mantel检验表明随着地理距离与遗传距离之间是显著相关的,即能表现出一定的地理隔离(isolation by distance)特征,但用地理距离来预测遗传距离会产生很大的误差。8个种群中有5个显著偏离期望漂移-突变平衡,可能近期经历了瓶颈效应,位点显著偏离Hardy-Weinberg平衡,杂合度不足(P<0.05)以及连锁不平衡的存在也间接支持这一结论。但瓶颈效应并没有显著影响垫状点地梅的遗传多样性。垫状点地梅种群内较高的遗传多样性表明这些瓶颈事件发生的时间不是很长,短期瓶颈对遗传多样性影响不大。
(3)对垫状点地梅的52个种群414个体的叶绿体trnL-trnF和rps16基因区间进行了PCR扩增片段的全序列测定,叶绿体trnL-trnF和rps16分别得到12和21个单倍型,经分区同质性检验后将两基因合并分析,得到34种单倍型,特有的单倍型占总的单倍型的比例都很高,都达到58%以上。其单倍型系统发育树和Network图表明52个种群分为主要分为两大分支和一小分支,其中一大分支的单倍型主要分布那曲地区南部与山南地区北部之间和日喀则地区的吉隆附近,另一大分支单倍型分布除山南地区外的所有采样区域,而一小分支的单倍型分布在青海的称多种群、西藏的那曲地区南部和山南地区北部之间的高原台面。无论是单个叶绿体单倍型分析还是两叶绿体联合的AMOVA分析结果都一致支持垫状点地梅的遗传变异主要存在种群间,占总遗传变异64%以上,叶绿体rps16片段和两基因联合得到的NsT显著大于GsT(P<0.05),显示垫状点地梅存在显著的谱系地理结构,但SAMOVA对所有的种群进行分组,无论是单个叶绿体基因片段还是两个叶绿体基因片段联合三个结果都检测不到有意义的K值,推测因两两种群间的分化很大,大部分种群在拥有广布的单倍型的同时也拥有一个或两个以上独特的单倍型,这样独特的谱系地理结构导致不能有效根据地理距离分组。我们在研究中推测垫状点地梅可能有多个避难所,位于藏南谷地特别是山南地区和位于青海地区称多地区；种群历史动态分析表明垫状点地梅在末次冰期的间冰期或间冰段可能有过一次种群扩张,并产生和留下了丰富的遗传多样性较高的单倍型,在随后的冰期对垫状点地梅在高原面上的种群可能没有影响,形成了在青藏高原地区现存的特有的分布格局。
(4)目前高山植物精细尺度的空间遗传结构(SGS)的研究越来越得到重视,这种空间遗传结构可以通过种子和花粉的分散推断出。然而,对SGS的估计更多的取决于抽样策略,包括抽样的大小和空间抽样方法。在本研究中,我们研究了抽样大小和三种空间抽样策略(随机抽样策略,样线抽样策略和随机聚簇抽样策略)对点地梅SGS估计的影响,点地梅是青藏高原特有的高山垫状植物。使用了真实和模拟的显性分子标记,我们得出以下结果：1)SGS的估计对抽样策略敏感,尤其是在样本量相对较小的情况下(如,<100)；2)相比Sp统计量,常用的SGS参数估计(自相关的截距)更容易受到抽样策略影响；3)随机聚簇抽样法会导致参数估计的显著偏差,即使样本量相对大的情况下(如,>200),而样线抽样法在参数估计上优于简单随机抽样,并在覆盖抽样空间范围方面比简单随机抽样法更有效。模拟数据和真实数据之间的一致性,意味着这些研究结果也可能适用于其他高山植物。
本文利用微卫星分子标记和叶绿体非编码区基因序列来分析垫状点地梅的遗传结构和进化潜力,评估垫状点地梅对气候变暖的响应能力,探讨影响或造成垫状点地梅空间遗传结构的生物学、地质事件和气候环境变化历史过程。旨在通过对垫状点地梅的遗传多样性和空间遗传结构的基础研究,为更好的保护和修复青藏高原高寒的生态系统的结构和功能完整性提供有价值的基础数据；结合青藏高原第四纪气候变迁历史,推测垫状点地梅第四冰期的可能避难所以及种群的扩散路线,通过模拟数据和垫状点地梅数据分析不同抽样策略(抽样大小和抽样方法)对研究精细尺度的空间遗传结构的影响,为研究垫状点地梅的繁殖和扩散行为提供可靠的方法。主要结果如下：
(1)通过磁珠富集法筛选垫状点地梅的微卫星分子标记基因组DNA后,用Rsal限制性内切酶酶切并连接接头,再用接头引物进行PCR扩增,得到的扩增产物与生物素标记的(AC)15,(AT)1 5,(CT)12,(ATC)10和(CCA)10探针杂交,杂交复合物用链亲和素包裹磁珠进行吸附,得到微卫星单链目标DNA片段,经PCR扩增,连接PMD19-T载体,转化到感受态大肠杆菌,得到微卫星富集小插入片段DNA文库。经阳性克隆和测序分析得到16个有效的微卫星序列,重复碱基数以双核苷重复最为常见,其中又以(GA) n/(CT)n重复最多,还观察到ATG、TCT重复单位。完美型(重复次数8-17次)的微卫星有9个,占56.25%；非完美型的微卫星有5个,占31.25%；混合型的微卫星有2个,占12.5%。这些序列在GenBank上的登录号分别是：FJ824648-FJ824656、GQ121408-GQ121415。16个有效的微卫星位点成功设计了16对引物,经用48个受试样本进行初步筛选,16对均表现出多态性,其中8个微卫星位点符合Hardy-Weinberg平衡。
(2)应用6对微卫星引物研究了唐古拉山两侧的垫状点地梅种群的遗传多样性、遗传结构和有效种群历史动态过程。在8个采样种群中,共检测到31.8个等位基因,观察等位基因数为3-9.87个,等位基因丰富度为4.484-5.577,平均期望杂合度(HE)为0.579-0.659,平均观察杂合度(Ho)为0.335-0.547,垫状点地梅总体表现为显著的杂合子缺失,近交系数为0.313；在4个种群中检测到连锁不平衡现象；垫状点地梅种群间的遗传分化程度很低,遗传分化系数Fst=0.028和Rst=0.026,而且AMOVA结果表明超过95%以上遗传变异发生在种群内；虽然8个种群内都发生了近交繁殖(Fis为0.233-0.430),但垫状点地梅种群间的基因交流仍很频繁(Nm>1),主坐标分析、距离法(NJ)和贝斯法(MCMC)的聚类分析结果显示垫状点地梅个体间混合程度较高,唐古拉山两侧的垫状点地梅种群间的基因交流并没有受到地理阻碍；用Mantel检验表明随着地理距离与遗传距离之间是显著相关的,即能表现出一定的地理隔离(isolation by distance)特征,但用地理距离来预测遗传距离会产生很大的误差。8个种群中有5个显著偏离期望漂移-突变平衡,可能近期经历了瓶颈效应,位点显著偏离Hardy-Weinberg平衡,杂合度不足(P<0.05)以及连锁不平衡的存在也间接支持这一结论。但瓶颈效应并没有显著影响垫状点地梅的遗传多样性。垫状点地梅种群内较高的遗传多样性表明这些瓶颈事件发生的时间不是很长,短期瓶颈对遗传多样性影响不大。
(3)对垫状点地梅的52个种群414个体的叶绿体trnL-trnF和rps16基因区间进行了PCR扩增片段的全序列测定,叶绿体trnL-trnF和rps16分别得到12和21个单倍型,经分区同质性检验后将两基因合并分析,得到34种单倍型,特有的单倍型占总的单倍型的比例都很高,都达到58%以上。其单倍型系统发育树和Network图表明52个种群分为主要分为两大分支和一小分支,其中一大分支的单倍型主要分布那曲地区南部与山南地区北部之间和日喀则地区的吉隆附近,另一大分支单倍型分布除山南地区外的所有采样区域,而一小分支的单倍型分布在青海的称多种群、西藏的那曲地区南部和山南地区北部之间的高原台面。无论是单个叶绿体单倍型分析还是两叶绿体联合的AMOVA分析结果都一致支持垫状点地梅的遗传变异主要存在种群间,占总遗传变异64%以上,叶绿体rps16片段和两基因联合得到的NsT显著大于GsT(P<0.05),显示垫状点地梅存在显著的谱系地理结构,但SAMOVA对所有的种群进行分组,无论是单个叶绿体基因片段还是两个叶绿体基因片段联合三个结果都检测不到有意义的K值,推测因两两种群间的分化很大,大部分种群在拥有广布的单倍型的同时也拥有一个或两个以上独特的单倍型,这样独特的谱系地理结构导致不能有效根据地理距离分组。我们在研究中推测垫状点地梅可能有多个避难所,位于藏南谷地特别是山南地区和位于青海地区称多地区；种群历史动态分析表明垫状点地梅在末次冰期的间冰期或间冰段可能有过一次种群扩张,并产生和留下了丰富的遗传多样性较高的单倍型,在随后的冰期对垫状点地梅在高原面上的种群可能没有影响,形成了在青藏高原地区现存的特有的分布格局。
(4)目前高山植物精细尺度的空间遗传结构(SGS)的研究越来越得到重视,这种空间遗传结构可以通过种子和花粉的分散推断出。然而,对SGS的估计更多的取决于抽样策略,包括抽样的大小和空间抽样方法。在本研究中,我们研究了抽样大小和三种空间抽样策略(随机抽样策略,样线抽样策略和随机聚簇抽样策略)对点地梅SGS估计的影响,点地梅是青藏高原特有的高山垫状植物。使用了真实和模拟的显性分子标记,我们得出以下结果：1)SGS的估计对抽样策略敏感,尤其是在样本量相对较小的情况下(如,<100)；2)相比Sp统计量,常用的SGS参数估计(自相关的截距)更容易受到抽样策略影响；3)随机聚簇抽样法会导致参数估计的显著偏差,即使样本量相对大的情况下(如,>200),而样线抽样法在参数估计上优于简单随机抽样,并在覆盖抽样空间范围方面比简单随机抽样法更有效。模拟数据和真实数据之间的一致性,意味着这些研究结果也可能适用于其他高山植物。
引文
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