中国近海重要生态建群红藻真江蓠的群体遗传多样性
刘若愚, 孙忠民, 姚建亭, 胡自民, 段德麟. 2016,中国近海重要生态建群红藻真江蓠的群体遗传多样性[J]. 生物多样性, 24(7): 781-790
Ruoyu Liu, Zhongmin Sun, Jianting Yao, Zimin Hu, Delin Duan.
2016,Genetic diversity of the habitat-forming red alga
Gracilaria vermiculophylla along Chinese coasts [J]. Biodiversity Science, 24(7): 781-79010.17520/biods.2016038&&
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中国近海重要生态建群红藻真江蓠的群体遗传多样性
刘若愚1,2,
孙忠民1,3,
姚建亭1,4,
胡自民1,4*,*,
段德麟1,4*,*
1 .中国科学院海洋研究所实验海洋生物学重点实验室, 山东青岛 266071
2 .中国科学院大学, 北京 100049
3 .中国科学院海洋研究所海洋生物分类与系统演化实验室, 山东青岛 266071
4 .青岛海洋科学与技术国家重点实验室, 山东青岛 266237
* 共同通讯作者 Co-authors for correspondence. E-mail:;
基金: 国家自然科学基金()
真江蓠( Gracilaria vermiculophylla)是中国近海潮间带生态系统结构组成和功能维持的重要支撑物种, 但有关其群体遗传结构和多样性分布模式的研究目前仍较缺乏。本研究利用线粒体 cox1序列对我国近海19个真江蓠地理群体进行了系统发育和群体遗传分析。461个长度为641 bp的 cox1序列片段共含有21个多态位点, 产生15个单倍型。基于 cox1序列的系统进化分析、单倍型分析和主成分分析显示, 19个真江蓠群体分化为南北两个类群, 其中浙江嵊泗以北的13个群体形成北方类群, 福建厦门以南的6个群体形成南方类群。遗传距离和分子方差分析显示真江蓠南北各类群内的遗传分化较小, 南北类群间的遗传分化达到亚种水平。南北类群间的差异是我国近海真江蓠群体遗传变异的主要来源。
Gracilaria vermiculophylla;
线粒体 cox1;
遗传多样性;
群体遗传分化
Genetic diversity of the habitat-forming red alga
Gracilaria vermiculophylla along Chinese coasts
Ruoyu Liu1,2,
Zhongmin Sun1,3,
Jianting Yao1,4,
Zimin Hu1,4,*,
Delin Duan1,4,*
1 Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071
2 University of Chinese Academy of Sciences, Beijing 100049
3 Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071
4 Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237
As a habitat-forming species, the red alga Gracilaria vermiculophylla has been noted to play an essential role in shaping coastal marine communities and maintaining intertidal ecosystems along Chinese coasts. However, few studies have been conducted that analyze the genetic structure of the population and the distribution patterns of genetic variation. In this study, we compiled partial mitochondrial DNA cytochrome c oxidase subunit I gene ( cox1) of 19 G. vermiculophylla populations (461 individuals) and performed phylogenetic analysis and population genetic surveys. A total of 461 mt-DNA cox1 sequences were obtained and edited into 641 bp, which contained 21 polymorphic sites and yielded 15 haplotypes. Phylogenetic inferences, haplotype networking, and principal coordinate analysis consistently indicated that G. vermiculophylla populations diverged into two groups: the northern group is comprised of specimens from the Yellow-Bohai Sea and the Shengsi Islands, while the southern group is comprised of specimens from six locations south to Xiamen, Fujian Province. Analysis of the molecular variance and Nei’s genetic distances indicated low genetic differentiation between populations in each group while group-level genetic divergence is comparable to the degree of subspecies differentiation.
Gracilaria vermiculophylla;
mitochondrial cox1;
phylogenetics;
genetic diversity;
population genetic differentiation
真江蓠(Gracilaria vermiculophylla)隶属于红藻门真红藻纲江蓠目江蓠科, 是一种可食用的大型经济海藻()。真江蓠藻体直立, 线形圆柱状, 常为紫褐色, 亚软骨质, 向上分枝, 分枝基部不缢缩或略缢缩, 半圆形的囊果、紫红色十字形分裂的四分孢子囊和V型的精子囊结构是其形态分类鉴定的重要依据()。真江蓠是潮间带生态群落的初级生产者和重要建群物种。最新研究表明, 在贫瘠海岸引入真江蓠可为小型底栖生物提供避难所和栖息地, 无脊椎动物的丰度和生物量会随着真江蓠海藻床的扩展而增加, 进而逐步形成复杂的生态群落()。此外, 真江蓠还是一种良好的重金属吸附藻类, 能明显改善水质环境()。真江蓠是太平洋西岸的地方种()。自Bellorin等(2004)首次在墨西哥的下加利福尼亚地区(Baja California)发现真江蓠后, 在太平洋东岸()、大西洋两岸(; ; )陆续报道了真江蓠的大范围入侵。近10年来, 真江蓠在太平洋东岸和大西洋两岸的入侵范围呈现出快速扩大的趋势, 改变了当地的生物多样性组成、潮间带群落结构和生态系统功能(; ), 引起学者们的广泛关注。在西北太平洋地区, 现有的研究主要集中在真江蓠的分类鉴定、个体遗传多态性检测以及入侵起源地的探索等方面(; ; ), 有关真江蓠群体遗传结构和多态性地理分布的研究则鲜有报道。真江蓠在中国近海分布广泛, 早期的文献记录显示其最北端分布位于辽宁省的大连市, 最南端分布位于广西省的防城港市()。目前, 国内只有少量关于真江蓠分子标记研究的报道(; ), 且主要集中于DNA条形码开发和系统进化分析, 所用材料仅限于少量采样地点的个别样品。Gulbransen等(2012)通过扩大样本(包括采样范围和每个地点的样品数量)发现美国弗吉尼亚湾的真江蓠群体具有较高的遗传多样性特征和单倍型丰度, 表明样品采集数量对研究真江蓠群体遗传结构的分布模式可能会产生重要的影响。本研究共收集19个地理群体的461株真江蓠样品的线粒体cox1序列, 在分子水平进行物种鉴定的基础上对不同群体的遗传多样性组成、分布特征和群体遗传分化模式进行了深入分析, 探讨形成这种遗传结构和地理分布格局的可能因子, 以期为真江蓠野生资源的保护监管和开发利用提供科学依据。1 材料和方法1.1 样品采集和地理分布在年间, 研究团队沿中国近海由北向南在18个地点采集到456株真江蓠样品, 每株个体用硅胶干燥保存。为扩大样本的覆盖区域, 采自厦门杏林湾的5株野生真江蓠个体的线粒体cox1序列(KF789526- KF789530)。扩大后的样本地点达19个, 共计461株个体。采样详细信息见。表1Table 1表1(Table 1)
表1 真江蓠19个群体的代号、地理位置、样本量(N)、多态位点数(Np)、单倍型数(Nh)、单倍型类型(数量)(Hn(n))、单倍型多态性(Hd)、核苷酸多态性(π )、采集时间和采样人
Table 1 Sampling information of 19 Gracilaria vermiculophylla populations, including abbreviation codes, geographic location, sample size (N), number of polymorphic sites (Np), number of haplotypes (Nh), types of haplotype (H(n)), haplotype diversity (Hd), nucleotide diversity (π ), collecting date and collectors代号Code地理位置Location经纬度Longitude/ LatitudeNNpNhHn(n)Hdπ (× 10-2)采样人Collectors南方群体 Region SouthYT北海银滩 Yingtang beach, Beihai109.34 � E, 21.45 � N2474H0(21), H2, H3, H40.2390.143刘若愚, 胡自民 Ruoyu Liu, Zimin HuJH北海金海岸 Jinhaian, Beihai109.11 � E, 21.49 � N3312H0(32), H20.0610.009刘若愚, 胡自民 Ruoyu Liu, Zimin HuTC湛江特呈岛 Techeng island, Zhanshan, 110.44 � E, 21.15 � N3001H0(30)0.0000.000孙忠民, 姚建亭 Zhongmin Sun, Jianting YaoNA汕头南澳岛 Nanao island, Shantou117.04 � E, 23.45 � N2312H0(19), H1(4)0.3000.047孙忠民, 姚建亭 Zhongmin Sun, Jianting YaoZP漳州漳浦六鳌 Zhangpu liuao, Zhanzhou, 117.77 � E, 23.92 � N3501H0(35)0.0000.000孙忠民, 黄超华 Zhongmin Sun, Chaohua HuangXL厦门杏林湾 Xingling bay, Xiamen118.08 � E, 24.60 � N512H0(4), H1(1)0.4000.062钟晨辉等 Chenhui Zhong et al小计 Subtotal15085H0(141), H1(5), H2(2), H3, H40.1160.027北方群体 Region NorthSS舟山嵊泗岛 Shengsi island, Zhoushan122.44 � E, 30.68 � N1901H6(19)0.0000.000胡自民 Zimin HuYY青岛一浴 No. 1 beach, Qingdao120.34 � E, 36.05 � N2123H5(19), H7, H100.1860.030刘若愚 Ruoyu LiuEY青岛二浴 No. 2 beach, Qingdao120.34 � E, 36.05 � N2101H5(21)0.0000.000刘若愚 Ruoyu LiuSY青岛三浴 No. 3 beach120.36 � E, 36.05 � N3901H5(39)0.0000.000刘若愚 Ruoyu LiuYH青岛银海国际 Yinhai, Qingdao120.42 � E, 36.06 � N3623H5(26), H8(9), H130.4270.069刘若愚 Ruoyu LiuLR青岛石老人 Shilaoren sea, Qingdao120.49 � E, 36.09 � N3623H5(32), H9(3), H120.2080.033刘若愚 Ruoyu LiuSD威海石岛 Stone island, Weihai122.41 � E, 36.91 � N1301H5(13)0.0000.000李晶晶, 张杰 Jingjing Li, Jie ZhangDC威海东楮岛 Dongchu island, Weihai122.56 � E, 37.04 � N3212H5(16), H14(16)0.5160.081刘若愚, 胡自民Ruoyu Liu, Zimin HuJM威海鸡鸣岛 Jiming island, Weihai122.48 � E, 37.45 � N701H5(7)0.0000.000李晶晶, 张杰 Jingjing Li, Jie ZhangCD烟台长岛 Long island, Yantai120.72 � E, 37.94 � N1601H5(16)0.0000.000胡自民 Zimin HuHN大连黄泥川 Huangninchuan, Dalian121.56 � E, 38.82 � N3512H5(34), H110.0570.009刘若愚, 胡自民 Ruoyu Liu, Zimin HuHS大连黑石礁 Heshijiao, Dalian121.56 � E, 38.87 � N801H5(8)0.0000.000刘若愚, 胡自民 Ruoyu Liu, Zimin HuZZ大连獐子岛 Zhangzi island, Dalian122.74 � E, 39.04 � N2801H5(28)0.0000.000姚建亭, 孙忠民 Ruoyu Liu, Zimin Hu小计 Subtotal311910H5(259), H6(19), H7, H8(9), H9(3) H10, H11, H12, H13, H14(16)0.3000.050
表1 真江蓠19个群体的代号、地理位置、样本量(N)、多态位点数(Np)、单倍型数(Nh)、单倍型类型(数量)(Hn(n))、单倍型多态性(Hd)、核苷酸多态性(π )、采集时间和采样人
Table 1 Sampling information of 19 Gracilaria vermiculophylla populations, including abbreviation codes, geographic location, sample size (N), number of polymorphic sites (Np), number of haplotypes (Nh), types of haplotype (H(n)), haplotype diversity (Hd), nucleotide diversity (π ), collecting date and collectors1.2 DNA提取、PCR扩增和测序取30 mg干燥样品在双蒸水中浸泡, 用毛刷洗净藻体表面的附着物。样品晾干后加入液氮碾磨成藻粉, 利用植物基因组提取试剂盒DP305 (Tiangen, Beijing)提取真江蓠的基因组DNA, -20℃保存备用()。采用Saunders (2005)设计的红藻通用引物对GazF1: TCAACAAATCATAAAGATATTGG和GazR1: ACTTCTGGATGTCCAAAAA AYCA扩增真江蓠的线粒体cox1序列。扩增反应在TakaRa TP600型PCR仪上进行。采用50 µ L反应体系: 模板DNA 0.5 µ L, 10× Taq Buffer 5 µ L, dNTPs 4 µ L, 5 U/µ L的Taq DNA聚合酶(TransGen) 0.5 µ L, 引物2 µ L和超纯水38 µ L。PCR反应程序为: 94℃预变性2 min, 94℃变性30 s, 50℃退火30 s, 72℃延伸1 min, 30个循环; 72℃延伸8 min。扩增产物经1%的琼脂糖凝胶电泳检测后进行纯化, 在ABI 3730XL测序平台上进行正向测序。1.3 数据处理和系统发育树构建用BioEdit 5.0.6软件()对测序获得的线粒体cox1序列进行比对和手工校正。将编辑好的序列导入NCBI进行BLASTn搜索, 寻找相似度最高的已知序列。从GenBank中下载在藻类学专业期刊上公开发表的真江蓠和江蓠属其他物种及龙须菜(Gracilariopsis lemaneiformis)的cox1序列用作参考。这些序列包括: 真江蓠(EF434927、EF434936、EF434937、EF434938、EF434939、FJ499550、FJ499581、GU907103、GU907104、GU907105、GU907106、GU907108、GU907110、GU907111、GQ292864、GQ292865、GQ292866、GQ292867、GQ292868、KF789526、KF789527、KF789528、KF789529、KF789530), 缢江蓠(G. salicornia) (FJ499537), 壶果江蓠(G. tikvahiae) (FJ499538、FJ499539、FJ499548、FJ499549、FJ499542), G. parvispora (EF434921、EF434922、KC113593、 KC113594), 太平洋江蓠(G. pacifica) (FJ499517、FJ499531、FJ499533、FJ499534、FJ499536)和龙须菜(KF789531)。采用邻接法(neighbor-joining, NJ) 和最大似然法(maximum likelihood, ML)构建系统发育树。首先采用Model-test 3.7 ()的AIC标准(Akaike information criterion)确定最佳的核苷酸替代模型(HKY+I+G, I = 0.6193, G = 1.5714)。然后使用MEGA 6.0.6 ()的Kimura 2-parameter遗传距离模型构建NJ树, 在Hasegawa-Kishino-Yano模型下构建ML树。为方便ML树与NJ树的比较, ML Heuristic Method选择Nearest-Neighbor-Interchange。系统发育树分支节点的置信度均采用自展检验方法(bootstrap method)进行估算, 自展检验重复1, 000次。1.4 群体遗传学分析采用DnaSP 5.1 ()计算各群体的多态位点数(Np)、单倍型数(Nh)、单倍型多态性(Hd)和核苷酸多样性(π )。使用GenAlEx 6.5 ()计算群体间的Nei’ s遗传距离、基因流(Nm), 进行单倍型分析、主成分分析(principal component analysis, PCA)和分子方差分析(analysis of molecular variance, AMOVA)。利用Network 4.6.1.3 ()的Median-joining算法构建真江蓠线粒体cox1序列的单倍型网状图。2 结果2.1 线粒体cox1鉴定和系统进化分析 扩增获得的461个线粒体cox1序列长度为641 bp, 序列中无碱基缺失和插入。BLASTn搜索显示每条cox1序列与GenBank中公开发表的真江蓠序列的相似度在99-100%之间。NJ和ML系统树显示, 本研究新获得的cox1序列与从GenBank下载的全部真江蓠序列聚集为一个大分支, 自展支持率为100%, 同时该分支同江蓠属其他种类和龙须菜明显分开()。NJ和ML系统树同时还显示浙江嵊泗(SS)以北的13个群体的真江蓠cox1序列同采自朝鲜半岛西海岸及中国威海和青岛的真江蓠样品(GU907106、GU907108、GU907110、EF434936、GU907103)聚为一个北部分支, 而中国厦门以南6个群体的150个真江蓠cox1序列(YT、JH、TC、NA、ZP和XL)聚为一个南部分支()。这一结果表明中国近海的真江蓠群体存在南北地理分化。图1Fig. 1 图1 基于真江蓠线粒体cox1序列构建的NJ和ML树。数字表示各节点的自展支持率数值(> 50%, 斜线左为NJ树, 右为ML树)。群体代号同。Fig. 1 Neighbor-joining (NJ) and maximum-likelihood (ML) phylogenetic trees based upon mt-DNA cox1 sequences of Gracilaria vermiculophylla and some congeneric species. Numbers indicate bootstrap values (> 50%) of NJ (left) and ML (right) inferences. Population codes are the same as in .2.2 遗传多态性和单倍型分布461个线粒体cox1序列含有21个多态位点(核苷酸变异率3.27%), 共产生15个单倍型(, ), GenBank注册号为KU136374-KU136387和KF789527 ()。其中北方群体共计9个多态位点(占1.40%), 南方群体8个多态位点(占1.25%)。北方群体的核苷酸和单倍型多态性分别在0.081和0.000-0.516之间; 南方群体的核苷酸和单倍型多态性分别在0.43和0.000- 0.400之间。真江蓠北方类群的核苷酸和单倍型多态性(0.0)要高于南方类群(0.0) ()。中国近海19个真江蓠群体的核苷酸和单倍型多态性分别为0.0, 其中南方群体的TC、ZP和北方群体SS、EY、SY、SD、JM、CD、HS、ZZ均只检测到1个单倍型。线粒体cox1单倍型中介网状图()显示, 单倍型H5-H14以H5为中心呈星状散射, 各单倍型之间仅有1个碱基差异()。单倍型H0-H4以H0为中心呈星状散射, 各单倍型之间存在1-4个碱基差异。H0-H4和H5-H14的cox1序列在位点346、517、562和604处存在明显的特征变异()。另外, 单倍型H5-H14仅分布在浙江嵊泗(SS)以北的13个群体里, 其中H5是北方群体的主要共享单倍型(占比83.28%)。H0-H4仅分布在福建厦门杏林湾(XL)以南的6个群体里, 其中H0是南方群体的主要共享单倍型(占比94.00%) (, )。图2Fig. 2 图2 真江蓠的线粒体cox1单倍型中介网状图, 单倍型H0-H4仅在厦门杏林湾以南的南方群体中检测到, 单倍型H5-H14仅分布在浙江嵊泗到以北的北方群体中(群体代号同)。Fig. 2 Median-joining network of mitochondrialcox1 haplotypes in Gracilaria vermiculophylla populations. We only detected haplotype H0-H4 in the populations south to Xiamen, while H5-H14 only in the populations north to Shengsi Island. Population codes are the same as in .表2Table 2表2(Table 2)
表2 真江蓠15个线粒体cox1单倍型的核苷酸多态位点分布特征, 表中不同字体的字母表示各单倍型的多态位点。
Table 2 Polymorphic sites of 15 cox1 haplotypes in Gracilaria vermiculophylla. The letters with different font denote polymorphic sites.单倍型Haplotype单倍型数量Number核苷酸多态位点 Polymorphic sitesGenBank accession number425526465112151250346352370406433460517558562593604605634H0141TGAACGAAGTTTAGGCTGGGAKU136384H15TAAACGAAGTTTAGGCTGGGAKF789527H22TGAACGAAGTTTAGGCTGGGGKU136385H31TGTACTTAGTTTAGGCTTGAAKU136387H41AGAACGAAGTTTAGGCTGGGAKU136386H5259TGAACGAACTTTAGACCGTGAKU136374H619TGAACGAACGTTAGACCGTGAKU136375H716TGAGCGAACTTTAGACCGTGAKU136383H89TGAATGAACTTTAGACCGTGAKU136377H93TGAACGAACTATAGACCGTGAKU136378H101TGAACGAACTTCAGACCGTGAKU136379H111TGAACGAACTTTAGAACGTGAKU136380H121TGAACGAACTTTAAACCGTGAKU136381H131TGAACGATCTTTAGACCGTGAKU136382H141TGAACGAACTTTTGACCGTGAKU136376
表2 真江蓠15个线粒体cox1单倍型的核苷酸多态位点分布特征, 表中不同字体的字母表示各单倍型的多态位点。
Table 2 Polymorphic sites of 15 cox1 haplotypes in Gracilaria vermiculophylla. The letters with different font denote polymorphic sites.2.3 遗传距离和PCA分析Nei’ s遗传距离()显示, 厦门以南的6个真江蓠群体间遗传距离均较小, 最大值0.003出现在YT与XL群体之间。北方13个真江蓠群体间遗传距离也很小, 最大值为0.062。南方群体与北方群体间的遗传距离相对较大, 最小为0.211, 最大为0.277。南北两个地理类群之间的Nei’ s遗传距离为0.215。PCA分析结果显示中国南方的150株真江蓠个体聚集为一个南方类群, 嵊泗以北的311株真江蓠个体聚集为一个北方类群()。其中轴1 (Coord. 1)和轴2 (Coord. 2)解释了90.54%的变异来源。北方类群的真江蓠个体主要沿轴2方向分布, 仅占总遗传变异量的3.88%, 而南北类群之间的遗传变异则占总量的80.66% ()。图3Fig. 3 图3 基于线粒体cox1序列遗传距离的主成分分析(群体代号同)Fig. 3 Principal coordinate analysis of 461 mt-DNA cox1 sequences based on Nei’ s genetic distance. The amount of variation is explained by Coord. 1 and Coord. 2, respectively. Population codes are the same as in .表3Table 3表3(Table 3)
表3 真江蓠群体间的Nei’ s遗传距离(群体代号同)
Table 3 Pairwise Nei’ s genetic distances among Gracilaria vermiculophylla populations. Population codes see .YTJHTCNAZPXLSSYYEYSYYHLRSDDCJMCDHNHSZZYT0.000JH0.0000.000TC0.0000.0000.000NA0.0020.0010.0010.000ZP0.0000.0000.0000.0010.000XL0.0030.0020.0020.0000.0020.000SS0.2770.2720.2720.2760.2720.2770.000YY0.2170.2130.2130.2160.2130.2170.0490.000EY0.2150.2120.2110.2150.2110.2150.0490.0000.000SY0.2150.2120.2110.2150.2110.2150.0490.0000.0000.000YH0.2220.2180.2170.2210.2170.2220.0520.0030.0030.0030.000LR0.2170.2130.2130.2160.2130.2170.0490.0010.0000.0000.0030.000SD0.2150.2120.2110.2150.2110.2150.0490.0000.0000.0000.0030.0000.000DC0.2330.2300.2290.2330.2290.2340.0620.0120.0120.0120.0150.0130.0120.000JM0.2150.2120.2110.2150.2110.2150.0490.0000.0000.0000.0030.0000.0000.0120.000CD0.2150.2120.2110.2150.2110.2150.0490.0000.0000.0000.0030.0000.0000.0120.0000.000HN0.2160.2120.2120.2150.2120.2160.0490.0000.0000.0000.0030.0000.0000.0120.0000.0000.000HS0.2150.2120.2110.2150.2110.2150.0490.0000.0000.0000.0030.0000.0000.0120.0000.0000.0000.000ZZ0.2150.2120.2110.2150.2110.2150.0490.0000.0000.0000.0030.0000.0000.0120.0000.0000.0000.0000.000
表3 真江蓠群体间的Nei’ s遗传距离(群体代号同)
Table 3 Pairwise Nei’ s genetic distances among Gracilaria vermiculophylla populations. Population codes see .2.4 AMOVA分析将中国近海19个真江蓠群体视为1个类群进行AMOVA分析, 结果表明真江蓠的遗传变异主要来自于群体间(93%), 群体内仅为7%。同时, 真江蓠群体间存在显著的遗传分化(FST = 0.928, P< 0.001), 群体间的Nm值仅为0.039 ()。将真江蓠群体划分为南北两个地理类群, AMOVA分析表明93%的遗传变异来自南北类群间, 且两大类群间的遗传分化非常显著(FCT= 0.933, P< 0.001); 只有3%的变异来自群体间(FSC = 0.465, P< 0.001), 而群体内的遗传变异不到4% (FST = 0.964, P< 0.001)。真江蓠南北类群间Nm值为0.019 (), 显示南北类群间的基因交流非常有限。表4Table 4表4(Table 4)
表4 真江蓠群体的分子变异分析(AMOVA)
Table 4 Analysis of molecular variance (AMOVA) of Gracilaria vermiculopylla populations变异来源Source of variation自由度 df平方和Sums of squares变异组分Estimated variance变异百分比% of variation分化系数F-statistics基因流Nm一个类群 One group群体间 Among populations18434.04924.11493群体内 Within populations44234.1030.0777FST= 0.928* 0.039两个类群(南方群体, 北方群体) Two groups (Regions: South, North)类群间Among regions1405.675405.67593FCT= 0.933* 0.019类群内群体间Among populations1728.3741.6693FSC= 0.465* 群体内 Within populations44234.1030.0774FST= 0.964* FCT was calculated as the proportion of va FSC was calculated as the proportion of variance among popula FST was calculated as the proportion of variance within populations. * P �.FCT为类群间遗传分化系数, FSC为类群内群体间遗传分化系数, FST为群体间遗传分化系数。* P �。
表4 真江蓠群体的分子变异分析(AMOVA)
Table 4 Analysis of molecular variance (AMOVA) of Gracilaria vermiculopylla populations3 讨论在开发红藻条形码进行物种鉴定时发现, 红藻种内cox1序列核苷酸变异率在0-0.3%左右, 属内种间核苷酸变异率在4.5-13.6%左右。Yang等(2008)比较了韩国和日本部分地区的14个真江蓠线粒体cox1序列, 检测到的变异率为1.2%。Kim等(2010)比较了全球312株真江蓠的线粒体cox1序列, 检测到的变异率为1.98%。本研究中, 中国近海461株野生真江蓠的线粒体cox1序列核苷酸变异率为3.27%, 其中南方类群的变异率为1.25%、北方类群的变异率为1.40%, 南、北类群的cox1序列在346、517、562和604 bp碱基位点上存在明显的特征变异()。以上研究中真江蓠线粒体cox1序列的核苷酸变异率都介于Saunders (2005)界定的红藻种内到种间变异率的区间内。类似的结果也出现在对细江蓠(Gracilaria gracilis) (2.04%)、沙菜(Hypnea asiatica) (2.06%)和Mastcarpus stellatus (2.60%)等红藻的研究中(; )。Robbat等(2006)采纳Saunders (2005)界定的属种变异率标准对G. gracilis和M. stellatus进行研究和讨论, 认为较高的核苷酸变异率是雏形种形成(incipient speciation)的例证。Hebert等(2003)在分析线粒体cox1序列的遗传距离时发现种内遗传距离往往小于0.200, 同属种间的遗传距离一般为该属种内遗传距离的10倍左右。Chu等(2009)认为当种内遗传距离大于0.200时可能存在亚种或隐存种()。本研究南北类群内各群体间的遗传距离最大为0.062, 远低于0.200, 而南北类群间的遗传距离为0.215。借鉴郑文娟等(2009)、Cheang等(2010)和Boo等(2014)对泥蚶(Tegillarca granosa)、半叶马尾藻(Sargassum hemiphyllum)和石花菜(Gelidium crinale)地理亚种的研究, 结合本文的PCA分析、AMOVA结果和基因流数值可知, 中国近海红藻真江蓠南北类群间的分化已达种内亚种水平。这种分化随着人类影响的加剧(如人为引种和养殖)和近岸环境的变化(如黑潮驱动的由南向北的遗传交流)可能会逐渐变得细微。因此, 现有真江蓠南北类群野生资源的收集和保存对于真江蓠物种的可持续保护和利用具有重要实践意义。Kim等(2010)在美国弗吉尼亚湾仅检测到1种cox1单倍型。Gulbransen等(2012)增加了采样点和采样密度, 在同一地区检测到7种单倍型, 揭示了采样密度和样本量对真江蓠群体遗传结构分析的重要影响。本研究在中国沿海检测到15个真江蓠cox1单倍型, 高于之前的研究报道(), 这进一步凸显样本采集策略对红藻群体遗传结构和多样性分析的重要性。另外, 本文的结果并没有揭示出真江蓠南北类群分化的确切地理界限, 进而未能深入揭示真江蓠南北分化的潜在环境因素, 这有待于以后的持续采样加以探讨。虽然中国近海真江蓠的整体核苷酸变异率和单倍型多态性较高, 但在很多地理群体(如TC、ZP、SS、EY、SY、SD、JM、CD、HS和ZZ)中只检测到1个单倍型, 显示出高度的遗传均质性。对于藻类而言, 无性繁殖会促使群体内个体的基因型趋于纯合, 进而降低藻类群体遗传多样性。Peason和Murray (1997)发现红藻Lithothrix aspergillum在加利福利亚南部地区行有性繁殖的群体具有较高的遗传多样性, 而在北部行无性繁殖的群体其遗传多样性较低。这种现象在江蓠属海藻中亦有报道。例如, Guillemin等(2008)使用SSR标记研究智利江蓠(Gracilaria. chilensis)发现, 主要依靠断枝增殖的人工养殖群体的遗传多样性水平明显低于野外行有性生殖的自然群体。真江蓠为多年生海藻, 有性世代和无性世代可以在同一时期存在, 四分孢子体和雌、雄配子体可在同一时期分别长成植株体。除行有性繁殖外, 在自然界中具有顶端细胞的真江蓠断枝能够不断分裂生长, 萌发出新枝长成新的藻体(曾呈奎和陈淑芬, 1959; )。真江蓠一般生长在生态因子变化幅度相对较小、环境基质相对稳定、异质性较小的平静内湾(), 这种稳定的环境条件使得真江蓠面临的自然选择压力偏小, 群体变异水平趋低。无性繁殖和环境选择可能是中国近海某些真江蓠地理群体展现出高度遗传均质性的重要原因。气候变化和近岸海洋环境变迁是影响近海生物群体遗传分化的关键因素, 中国近海真江蓠群体的南北分化可能与北半球古气候变动引起的近海环境剧烈波动有关。中国海是太平洋西部的边缘海, 在新生代晚期形成后经历了剧烈的气候和环境变迁。在更新世冰期, 东中国海和中国南海海平面比现在低约100-150 m, 黄东海和南海分别为两个独立的分隔着的边缘海()。这些边缘海的低洼处在冰期充当封闭的避难所, 保存残留的海洋生物类群, 促进种内遗传谱系的分化(; )。中国近海真江蓠北方类群由单倍型H5-H14组成, 分布在黄东海; 南方类群由单倍型H0-H4组成, 分布在南海; 真江蓠南、北类群遗传分化显著, 基因交流有限(, )。这种遗传分布模式在西北太平洋营底栖生活的潮间带海藻中亦有类似报道。例如, 沙菜日韩群体的单倍型为C1-C9, 中国台湾群体的单倍型为C10-C15 ()。羊栖菜的南海群体、东海群体和黄海群体表现出截然不同的线粒体cox1单倍型分布()。Cheang等(2010)的研究表明西北太平洋边缘海的隔离导致了半叶马尾藻福建以南群体与长江以北的日韩群体之间的遗传谱系分化。我们据此推测历史气候变化造成的黄东海和南海两大边缘海的分隔可能是导致真江蓠形成目前地理分布格局的重要原因。真江蓠南北两个类群可能来自不同的冰期避难所, 它们具有共同的祖先, 在冰期退却后沿不同的线路扩散到现在的黄渤海、东海和南海沿岸。这一假设希望能在后续的研究中得到进一步验证。
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Genetic differentiation of Tegillarca granosa based on mitochondrial COI gene sequences.
, 30, 17-23. (in Chinese with English abstract)[郑文娟, 朱世华, 沈锡权, 刘必谦, 潘志崇, 叶央芳 (2009)
基于线粒体COI基因序列探讨泥蚶的遗传分化. , 30, 17-23. ]
[本文引用:1]
Zhong CH, Huang RF, Lin Q, Zheng YY, Li LB, Liu B (2014)
Molecular identification of a green type of Gracilaria vermiculophylla.
, 33, 183-189. (in Chinese with English abstract)[钟晨辉, 黄瑞芳, 林琪, 郑雅友, 李雷斌, 刘波 (2014)
一种绿色真江蓠的分子鉴定. , 33, 183-189. ]
[本文引用:1]
... 3 (Bandelt et al, 1999)的Median-joining算法构建真江蓠线粒体cox1序列的单倍型网状图 ...
... 这些边缘海的低洼处在冰期充当封闭的避难所, 保存残留的海洋生物类群, 促进种内遗传谱系的分化(Cheang et al, 2010 ...
Chen Z, Zhang J, Fu HF, Xu ZZ, Deng KZ, Zhang JY (2012)
On the validity of the species Phenacoccus solenopsis based on morphological and
mitochondrial COI data, with the description of a new body color variety.
, 20, 443-450. (in Chinese with English abstract)[陈哲, 张姜, 傅杭飞, 许争争, 邓坤正, 张加勇 (2012)
基于形态特征和线粒体COI基因探讨扶桑绵粉蚧物种的有效性并记述一体色变异型扶桑绵粉蚧. , 20, 443-450. ]
Phenacoccus solenopsis , an exotic invasive species, was firstly reported in 2008 in Guangdong, China. Since it&s discovery, P. solenopsis has been observed in Zhejiang, Guangxi and Yunnan provinces. To discuss whether two cryptic evolutionary lineages or the P. solenopsis complex species existed, we surveyed and sequenced P. solenopsis in Zhejiang Province. During surveys for P. solenopsis in Zhejiang Province, we found P. solenopsis individuals with yellowish color on the body and three pairs of yellow spots on the back. To evaluate potential genetic divergence among these phenotypes, we sequenced mtDNA COI gene sequences (694 bp) of 25 individuals from seven host plants in six locations. We analyzed these sequences and the known sequences of P. solenopsis from GenBank and discovered three haplotypes. Additionally, we calculated intra-species genetic distance of P. solenopsis and inter-species genetic distance of the genus Phenacoccus and constructed phylogenetic trees of P. solenopsis . We found that genetic divergence of P. solenopsis was 0&1.0% compared to samples from Chinese provinces (i.e., Zhejiang, Hainan, Guangdong), the United States (i.e., California), and Pakistan, and varied from 3&3.6% to samples collected from other areas of the United States (i.e., Florida). Further, intra-species genetic distance was obviously smaller than inter-species genetic distance in Phenacoccus(13.0&17.2%). Based on the morphological characters and mt COI gene sequence analysis, these individuals with phenotypic differences are likely true P. solenopsis . However, two distinct evolutionary lineages appear to exist in P. solenopsis, and further evidence is necessary to draw reliable conclusions on the existence of a P. solenopsis complex species.
扶桑绵粉蚧( Phenacoccus solenopsis )于2008年首次在广东发现, 到目前为止, 浙江、广西、云南等10多个省市均有其入侵的报道。为探讨入侵中国的扶桑绵粉蚧是否存在两大隐存谱系或姊妹种的复合种, 作者对浙江的该物种进行了调查。在调查过程中, 发现体色浅橘黄色、背部具三对黄色斑点的体色变异型个体, 通过形态特征比较和线粒体COI基因部分序列的分析, 证实该体色变异型粉蚧为扶桑绵粉蚧。同时对中国、巴基斯坦、美国的扶桑绵粉蚧COI基因序列进行碱基差异比较、遗传距离(genetic distance)分析, 发现所扩增的浙江省内6个地点7种不同寄主植物上的25条扶桑绵粉蚧COI基因(694 bp)可以分成3种单倍型, 这3种单倍型与中国海南、中国广州、巴基斯坦和美国加州的扶桑绵粉蚧遗传分歧较小(0&1.0%), 而与美国佛罗里达州的遗传分歧较大(3&3.6%); 但两者遗传距离小于绵粉蚧属内物种之间的遗传距离(13.0&17.2%)。综合形态特征和COI基因数据的分析结果显示, 扶桑绵粉蚧可能没有达到种间分化。基于碱基差异所构建的网络关系图、遗传分歧差异和系统发生关系分析, 扶桑绵粉蚧存在两个进化支系, 至于是否是复合种, 目前尚难作结论, 还有待更多证据。
... 200时可能存在亚种或隐存种(陈哲等, 2012) ...
... Geraldino et al, 2009) ...
... 例如, 沙菜日韩群体的单倍型为C1-C9, 中国台湾群体的单倍型为C10-C15 (Geraldino et al, 2009) ...
... 真江蓠(Gracilaria vermiculophylla)隶属于红藻门真红藻纲江蓠目江蓠科, 是一种可食用的大型经济海藻(Guiry #cod#x00026 ...
... Gulbransen et al, 2012)陆续报道了真江蓠的大范围入侵 ...
... 6软件(Hall, 1999)对测序获得的线粒体cox1序列进行比对和手工校正 ...
... Hu et al, 2013) ...
... 羊栖菜的南海群体、东海群体和黄海群体表现出截然不同的线粒体cox1单倍型分布(Hu et al, 2013) ...
... Hu #cod#x00026 ...
... Kim et al, 2010 ...
... Kim et al, 2010), 有关真江蓠群体遗传结构和多态性地理分布的研究则鲜有报道 ...
... 1 (Librado #cod#x00026 ...
... 本研究在中国沿海检测到15个真江蓠cox1单倍型, 高于之前的研究报道(Kim et al, 2010), 这进一步凸显样本采集策略对红藻群体遗传结构和多样性分析的重要性 ...
Li JJ, Zhang J, Hu ZM, Duan DL (2013)
Population genetics and
demographic history of red seaweed, Palmaria palmata, from the Canada-northwest Atlantic.
, 21, 306-314. (in Chinese with English abstract)[李晶晶, 张杰, 胡自民, 段德麟 (2013)
加拿大西北大西洋地区掌形藻的种群遗传结构与动态变化. , 21, 306-314. ]
摘 要： 探讨古气候波动（如更新世末期冰期）对典型生物的时空分布和有效种群大小变动的影响是生物地理学和进化遗传学的重要研究课题。本文利用线粒体cox2–3序列和RAPD两种分子标记,对分布于加拿大–西北大西洋地区8个地点（共138个个体）的掌形藻（Palmaria palmata）进行谱系地理学研究,试图阐明当更新世冰期来临时掌形藻如何衍生出适应性的进化机制,并形成当前的地理分布格局。结果表明,线粒体cox2–3间区序列共检测出11个单倍型,其中1个单倍型（C3）在所有种群中都有分布,并位于星状基因谱系的中心位置,可认为是祖先单倍型。St.Lawrence湾内北部的两个种群多样性最高,与其他地理种群分化最明显,这与基于RAPD数据的STRUCTURE聚类分析结果相一致。根据掌形藻遗传多样性及其单倍型谱系结构特征,推测掌形藻在加拿大–西北大西洋沿岸存在多个冰期避难所。分子多态性分析（AMOVA）显示掌形藻的遗传变异主要来自种群内,而St.Lawrence湾和Fundy湾群组间的遗传变异较小。cox2–3序列的Bayesianskylineplots分析结果反映出掌形藻种群在加拿大–西北大西洋沿岸经历了轻微的种群扩张,时间大概在0.18–0.13百万年前。St.Lawrence湾和Fundy湾群组间的K2P遗传距离为0.2%,相应的分化时间大约在0.36百万年前。由此推测,更新世末期的冰期及间冰期是影响掌形藻种群结构及变动的重要古气候环境因子。
... 样品晾干后加入液氮碾磨成藻粉, 利用植物基因组提取试剂盒DP305 (Tiangen, Beijing)提取真江蓠的基因组DNA, -20℃保存备用(李晶晶等, 2013) ...
... 5 (Peakall #cod#x00026 ...
... 7 (Posada #cod#x00026 ...
... 此外, 真江蓠还是一种良好的重金属吸附藻类, 能明显改善水质环境(Riosmena et al, 2009) ...
... 60%)等红藻的研究中(Robba et al, 2006 ...
... 自Bellorin等(2004)首次在墨西哥的下加利福尼亚地区(Baja California)发现真江蓠后, 在太平洋东岸(Saunders, 2009)、大西洋两岸(Rueness, 2005 ...
... Rueness, 2005) ...
... 真江蓠一般生长在生态因子变化幅度相对较小、环境基质相对稳定、异质性较小的平静内湾(Rueness, 2005), 这种稳定的环境条件使得真江蓠面临的自然选择压力偏小, 群体变异水平趋低 ...
... 3 讨论Saunders (2005)在开发红藻条形码进行物种鉴定时发现, 红藻种内cox1序列核苷酸变异率在0-0 ...
... 自Bellorin等(2004)首次在墨西哥的下加利福尼亚地区(Baja California)发现真江蓠后, 在太平洋东岸(Saunders, 2009)、大西洋两岸(Rueness, 2005 ...
... Saunders, 2009 ...
... 6 (Tamura et al, 2013)的Kimura 2-parameter遗传距离模型构建NJ树, 在Hasegawa-Kishino-Yano模型下构建ML树 ...
... 真江蓠是太平洋西岸的地方种(Terada #cod#x00026 ...
... 最新研究表明, 在贫瘠海岸引入真江蓠可为小型底栖生物提供避难所和栖息地, 无脊椎动物的丰度和生物量会随着真江蓠海藻床的扩展而增加, 进而逐步形成复杂的生态群落(Thomsen et al, 2013) ...
... 近10年来, 真江蓠在太平洋东岸和大西洋两岸的入侵范围呈现出快速扩大的趋势, 改变了当地的生物多样性组成、潮间带群落结构和生态系统功能(Thomsen et al, 2013 ...
... 真江蓠藻体直立, 线形圆柱状, 常为紫褐色, 亚软骨质, 向上分枝, 分枝基部不缢缩或略缢缩, 半圆形的囊果、紫红色十字形分裂的四分孢子囊和V型的精子囊结构是其形态分类鉴定的重要依据(曾呈奎, 2008) ...
Zheng WJ, Zhu SH, Shen XQ, Liu BQ, Pan ZC, Ye YF (2009)
Genetic differentiation of Tegillarca granosa based on mitochondrial COI gene sequences.
, 30, 17-23. (in Chinese with English abstract)[郑文娟, 朱世华, 沈锡权, 刘必谦, 潘志崇, 叶央芳 (2009)
基于线粒体COI基因序列探讨泥蚶的遗传分化. , 30, 17-23. ]
Partial sequences of the mitochondrial DNA cytochrome c oxidase subunit I gene ( COI ) of seven Tegillarca granosa populations, which were collected from China's coastal areas, were amplified by polymerase chain reaction (PCR). The length of COI gene of 38 Tegillarca granosa individuals from seven populations was all 660bp. One hundred and three variable sites were detected in the nucleotide sequences of 660 bp, and 17 different haplotypes were identified. The result showed that the seven populations could be divided into two groups based on the the genetic distance and phylogenetic analysis of their COI gene sequences. The two groups were classified as Group in the Northern Fujian (including Fujian) and Group in the Southern Fujian. Group in the Northern Fujian was composed of five populations and the genetic distance was 0.0016. Group in the Southern Fujian was composed of two populations and the genetic distance was 0.0006. However, the genetic distance between the two groups was significantly high (0.1529), which suggested significant genetic differentiation between the two groups. It suggested that Group in the North of Fujian (including Fujian) and Group in the South of Fujian should be the same species, but they were different subspecies.
采用PCR技术对我国沿海地区7个泥蚶群体的线粒体 COI 基因部分序列进行了测定和遗传分析。在来自7个群体的38个泥蚶样本均得到660 bp的 COI 基因片段序列，共103个多态位点，组成17种单倍型；数据分析表明：7个群体形成了二大类群：福建以北(包括福建)的5个群体（江苏盐城、浙江奉化、浙江乐清养殖和自然群体、福建福鼎）形成一个类群，类群内的遗传距离为0.0016；福建以南的类群（广东湛江、海南海口）形成一个类群，遗传距离为0.0006；二个类群之间的遗传距离为0.1529，表现为高度的分化。因此我国沿海泥蚶已分化形成福建以南和以北二大类群，二大类群之间的遗传分化已达到亚种水平。
... 在更新世冰期, 东中国海和中国南海海平面比现在低约100-150 m, 黄东海和南海分别为两个独立的分隔着的边缘海(Wang, 1999) ...
Zhong CH, Huang RF, Lin Q, Zheng YY, Li LB, Liu B (2014)
Molecular identification of a green type of Gracilaria vermiculophylla.
, 33, 183-189. (in Chinese with English abstract)[钟晨辉, 黄瑞芳, 林琪, 郑雅友, 李雷斌, 刘波 (2014)
一种绿色真江蓠的分子鉴定. , 33, 183-189. ]
应用rDNA-ITS和线粒体 cox1片段扩增序列,分析了厦门杏林湾的2株绿色未知江蓠(Gracilaria sp.;四分孢子体GR-1和雌配子体GR-2)及2株紫褐色真江蓠(G.四分孢子体PU-1和雌配子体PU-2).运 用MEGA5.0估算了4个供试样本与GenBank中相似度最高序列的遗传距离并构建了系统发育树.ITS序列分析显示绿色未知江蓠GR-1、GR-2 都与真江蓠聚集在一起,推断两者与真江蓠的亲缘关系非常近.cox1片段序列分析表明,绿色未知江蓠GR-1、GR-2和紫褐色真江蓠PU-1、PU-2 都与索引的真江蓠聚集在相同类群.其中GR-1、GR-2与真江蓠JQ619142、JQ619143的相似度都为100%,它们之间的遗传距离范围在 0.000~0.002,低于种群内部的遗传距离范围0.000~0.015,从分子水平上确定了绿色未知江蓠是真江蓠.联合ITS和cox1片段序列的 分子标记适用于真江蓠的种质鉴定.
... 为扩大样本的覆盖区域, 后续分析中整合了钟晨辉等(2014)采自厦门杏林湾的5株野生真江蓠个体的线粒体cox1序列(KF789526- KF789530) ...
中国近海重要生态建群红藻真江蓠的群体遗传多样性
[刘若愚1,2, 孙忠民1,3, 姚建亭1,4, 胡自民1,4*,*, 段德麟1,4*,*]
