中国明对虾和日本囊对虾遗传多样性及对虾科系统学初步研究
|
摘要
本文以中国沿海两种对虾类中国明对虾和日本囊对虾为研究对象，采用线粒体COI基因片段和控制区序列等标记技术开展了这两种虾类的群体遗传多样性研究，系统研究了这两种虾类的遗传多样性和群体遗传结构并探讨了其群体历史动态。另外，利用核基因ITS1序列和线粒体全长以及nd5假基因对对虾科虾类进行了系统分析，主要研究结果如下：
1、为了检测中国明对虾的群体遗传结构合群体历史动态，我们对中国明对虾分布区内5个群体共93个个体的线粒体细胞色素氧化酶I亚基基因(COI)序列和控制区序列(CR)进行了测定和分析。在COI序列中，共检测到20个多态性核苷酸位点，定义了20种单倍型，其核苷酸多态度和单倍型多态度都很低(H=0．4816±0．0639，π=0．0846±0．0711％)。长993bp的CR序列中，共检测到84个多态性核苷酸位点，定义了68种单倍型，其单倍型多态度较高(0．95±0．03-0．99±0．02)，而核苷酸多态度中等或较低(0．66±0．36％-0．84±0．46％)。群体分化指数FST值(FST=-0．02343-0．02112)和分子变异分析(AMOVA)都表明不同群体间的中国明对虾还没有出现明显的遗传分化。IM的结果显示中国明对虾朝鲜半岛西海岸群和黄渤海沿岸群出现分化，用IM所估算的分化时间约为12，800(7，400-18，600)前。因此，中国明对虾不同地理群体间分化很小或不存在遗传分化的原因是由于分化的时间尚短，不足以在不同群体间形成明显的遗传结构。中性检验和核苷酸不配对分布都表明中国明对虾经历了群体扩张事件。中国明对虾较低的遗传多样性水平、简单的基因谱系结构、星状结构的单倍型网络关系图和检验显著的负的Tajima’D值都提示分布于黄渤海的中国明对虾群体可能经历过近期的瓶颈效应或奠基者效应。
2、采用PCR技术扩增了日本囊对虾(Marsupenaeus japonicus)线粒体细胞色素氧化酶I亚基基因(COI)片段，PCR产物经测序得到858bp的核苷酸序列；分析了该片段的日本、浙江、福建、广东、广西5个自然群体85个个体的核苷酸序列多态性，共检测到106个多态性核苷酸位点、58种单倍型。结果表明，五个群体中以广西群体遗传多样性最高，日本群体最低；在日本囊对虾群体内存在两个明显的单倍型类群，这两个单倍型类群间的平均遗传距离为5．6％；分子变异分析(AMOVA)和群体间分化指数FST值均显示，不同自然分布区的日本囊对虾出现明显的遗传分化。中性检验和核苷酸不配对分布表明日本囊对虾两个单倍型类群都经历了更新世的群体扩张。
3、对采自不同群体的5个中国明对虾个体的核糖体第一内转录间隔区(ITS1)序列特点进行分析，并利用GeneBank数据库中已有的对虾科(Penaeidae)ITS1同源序列对对虾科虾类进行系统分析，探讨ITS1序列在对虾科系统及演化中的应用。结果表明，中国明对虾ITS1序列在个体间和个体内都表现出长度多态性，序列长度范围为637-652bp，这种长度多态性主要是由于微卫星DNA简单重复序列的重复次数不同所造成。在中国明对虾ITS1序列中发现8个微卫星位点，根据目前已知的12种对虾的ITS1序列，发现某些微卫星位点只存于一种对虾中，如(CAGC)2-4只存在于中国明对虾中，(CGGA)4-9只存在于斑节对虾中，(GCGA)4只存在于短沟对虾中。利用ITS1序列对12种对虾进行的系统分析表明，12种对虾分为四个类群，同种的不同个体，同属的不同种各自聚支，与形态分类比较吻合。对虾科属间遗传距离范围为0．313-0．977，平均值为0．633，远高于用线粒体基因片段得出的属间的遗传距离，支持将原对虾属的6个亚属提升为属的观点。
4、在扩增中国明对虾线粒体基因组全序列的过程中，我们发现疑似nd5基因片段的假基因，对该片段的特点和类型进行了分析，并以该片段为外群探讨了对虾科的系统关系。同时采用线粒体DNA全序列对十足目和对虾科的系统关系进行了研究。结果表明，用假基因为外群构建的对虾科的系统树与用线粒体蛋白编码基因核苷酸序列得出的系统树的拓扑结构一致，但不同于蛋白编码基因氨基酸序列得出的系统树的拓扑结构。要更多的了解对虾科的系统关系还需要更多的资料加以证实。
In this study,the genetic diversity and evolutionary demography ofFeneropenaeus chinensis and Marsupenaeus japonicus were studied by mtDNAmarkers.We discussed the role of Pleistocene ice ages and present environmentalfactors in shaping the phylogeographic pattern and genetic structures of the twospecies.In addition,ITS1,mt genome sequences and Numts were used as molecularmarkers for studying the phylogenetic relationships among species of penaeid shrimps.
1、Genetic structure and demographic history ofFeneropenaeus chinensis wasexamined using sequence data of partial mitochondrial cytochrome oxidase I (COI)gene and the complete mitochondrial control region (CR).Samples of 93 individualswere collected from 5 localities over most of the species' range in the Yellow Sea andthe Bohai Sea.For COI data,atotal of 20 nucleotide sites were detected variable,defining 20 haplotypes.The variation level was low,with H=0.4816±0.0639 and=0.0846±0.0711 (%),respectively.For CR data,there are 84 variable sites defining68 haplotypes.Haplotype diversity levels were very high (0.95±0.03-0.99±0.02),while that ofnucleotide diversitywere at moderate to low level (0.66±0.36%-0.84±0.46%).Analysis of molecular variance and the conventional population statisticFST revealed no significant genetic structure throughout the range of F.chinensis.However,Isolation with Migration (IM) coalescence results based on CR data suggestF.chinensis distributed along the coasts of northern China and Korean Peninsula(about 1000 km apart) diverged recently,and the estimated split time was 12,800 (7,400-18,600) years ago.Both mismatch distribution analyses and neutrality testsbased on COI data and CR data suggested a late Pleistocene or Holocene populationexpansion (12,100-28,500 years ago) for F.chinensis,which was consistent withthe geological period of formation of the Bohai Sea and the Yellow Sea.These results indicated that F.chinensis in the Bohai Sea and the Yellow Sea might have undergonea genetic bottleneck or founder event during the late Pleistocene globle glacial period.
2、DNA sequencing is very useful for the genetic diversity analysis at molycular level.Mitochondrial COI gene fragments of kuruma shrimp Marsupenaeus japonicus wereamplified via polymerase chain reaction (PCR),the PCR products were sequenced for85 individuals,5 population of China.858 base-pair nucleotide sequences wereexamined and analyzed for genetic polymorphism.Resultant sequences data analysisshowed that all 85 sequences were grouped into 58 haplotypes and there were 106variable nucleotide positions in this gene fragment.The genetic diversity indexesincluding S (polymorphic sites),π(nucleotide diversity) and H (haplotype diversity)were calculated and the results indicated that Guangxi population showed morevariation than others and more differences to others.Based on the mitochondrial DNAsequence data,the shrimps were separated into two distinct clades.Analyses ofmolecular variance and the population statistic FST revealed significant geneticstructure.Both mismatch distribution analyses and neutrality tests based suggested aPleistocene population expansion for Marsupenaeus japonicus.
3、The ribosomal DNA internal transcribed spacer 1 (ITS1) of Fenneropenaeuschinensis was cloned and sequenced.The objective of the present study is to estimatephylogenies and explore the feasibility of using ITS1 as a molecular marker forstudying the interspecific and intraspecific genetic variations among penaeid shrimps.Inter-and intraindividual polymorphisms of ITS 1 were clearly observed in F.chinensis.The length of the ITS1 ranged from 637 to 652bp,with a GC content of 66.9%.Repeats of microsatellite loci of ITS 1 plays an important role in length heteroplasmyat both between-and within-individual levels in this species.Eight microsatellite lociwere found in the ITS1 sequence of F.chinensis.According to existing data,somemicrosatellites were found in only one specie,(CAGC) 2-4 in F.chinensis,(GCGA)4in P.semisalcatus and (CGGA)4-9 in P.monodon.The DNA data of the penaeidshrimps were processed in neighbor-joining (NJ) methods to build phylogeneticrelationships within the family of Penaeidae.According to the NJ tree,differentindividuals of the same species,different species of the same genus were grouped together,in consistence with the morphological taxonomy.The genetic distancesamong different genus ranged from 0.313 to 0.977 and the average was 0.633,exceeding those estimated with COI and partial 16S rRNAgene sequences,and beingtherefore larger than the value among subgenera.The results of the present studyindicated that Fenneropenaeus,Litopenaeus,Farfanatepenaeus,Marsupenaeus andPenaeus are at a higher phylogenetic level than subgenus,which supports the opinionof the elevation of phylogenetic status of the four subgenera to genus level.Theseresults show that ITS 1 is highly divergent among different penaeid shrimps and couldbe an appropriate marker for molecular systematic studies at the species levels,although the presence of intragenomic variation needs to be taken into consideration.
4、Mt genome sequences have provided useful markers for investigating populationgenetic structures,systematics and phylogenetics of organisms.In this study,mtgenome sequences and Numts were used as molecular markers for studying the phylogeneticrelationships among species of penaeid shrimps.Phylogenetic analyses based onconcatenated amino acid and nucleic acid sequences of the 13 mt protein-codinggenes strongly support the monophyly of the Decapoda and Penaeidae.However,relationships among species within the Penaeidae based on the 13 mt protein-codinggenes and Numts could not be resolved,and further studies were necessary to becarried out based.on the increasing number of mitochondrial genome sequences,inorder to better understand the relationships among species of Penaeidae.
1、为了检测中国明对虾的群体遗传结构合群体历史动态，我们对中国明对虾分布区内5个群体共93个个体的线粒体细胞色素氧化酶I亚基基因(COI)序列和控制区序列(CR)进行了测定和分析。在COI序列中，共检测到20个多态性核苷酸位点，定义了20种单倍型，其核苷酸多态度和单倍型多态度都很低(H=0．4816±0．0639，π=0．0846±0．0711％)。长993bp的CR序列中，共检测到84个多态性核苷酸位点，定义了68种单倍型，其单倍型多态度较高(0．95±0．03-0．99±0．02)，而核苷酸多态度中等或较低(0．66±0．36％-0．84±0．46％)。群体分化指数FST值(FST=-0．02343-0．02112)和分子变异分析(AMOVA)都表明不同群体间的中国明对虾还没有出现明显的遗传分化。IM的结果显示中国明对虾朝鲜半岛西海岸群和黄渤海沿岸群出现分化，用IM所估算的分化时间约为12，800(7，400-18，600)前。因此，中国明对虾不同地理群体间分化很小或不存在遗传分化的原因是由于分化的时间尚短，不足以在不同群体间形成明显的遗传结构。中性检验和核苷酸不配对分布都表明中国明对虾经历了群体扩张事件。中国明对虾较低的遗传多样性水平、简单的基因谱系结构、星状结构的单倍型网络关系图和检验显著的负的Tajima’D值都提示分布于黄渤海的中国明对虾群体可能经历过近期的瓶颈效应或奠基者效应。
2、采用PCR技术扩增了日本囊对虾(Marsupenaeus japonicus)线粒体细胞色素氧化酶I亚基基因(COI)片段，PCR产物经测序得到858bp的核苷酸序列；分析了该片段的日本、浙江、福建、广东、广西5个自然群体85个个体的核苷酸序列多态性，共检测到106个多态性核苷酸位点、58种单倍型。结果表明，五个群体中以广西群体遗传多样性最高，日本群体最低；在日本囊对虾群体内存在两个明显的单倍型类群，这两个单倍型类群间的平均遗传距离为5．6％；分子变异分析(AMOVA)和群体间分化指数FST值均显示，不同自然分布区的日本囊对虾出现明显的遗传分化。中性检验和核苷酸不配对分布表明日本囊对虾两个单倍型类群都经历了更新世的群体扩张。
3、对采自不同群体的5个中国明对虾个体的核糖体第一内转录间隔区(ITS1)序列特点进行分析，并利用GeneBank数据库中已有的对虾科(Penaeidae)ITS1同源序列对对虾科虾类进行系统分析，探讨ITS1序列在对虾科系统及演化中的应用。结果表明，中国明对虾ITS1序列在个体间和个体内都表现出长度多态性，序列长度范围为637-652bp，这种长度多态性主要是由于微卫星DNA简单重复序列的重复次数不同所造成。在中国明对虾ITS1序列中发现8个微卫星位点，根据目前已知的12种对虾的ITS1序列，发现某些微卫星位点只存于一种对虾中，如(CAGC)2-4只存在于中国明对虾中，(CGGA)4-9只存在于斑节对虾中，(GCGA)4只存在于短沟对虾中。利用ITS1序列对12种对虾进行的系统分析表明，12种对虾分为四个类群，同种的不同个体，同属的不同种各自聚支，与形态分类比较吻合。对虾科属间遗传距离范围为0．313-0．977，平均值为0．633，远高于用线粒体基因片段得出的属间的遗传距离，支持将原对虾属的6个亚属提升为属的观点。
4、在扩增中国明对虾线粒体基因组全序列的过程中，我们发现疑似nd5基因片段的假基因，对该片段的特点和类型进行了分析，并以该片段为外群探讨了对虾科的系统关系。同时采用线粒体DNA全序列对十足目和对虾科的系统关系进行了研究。结果表明，用假基因为外群构建的对虾科的系统树与用线粒体蛋白编码基因核苷酸序列得出的系统树的拓扑结构一致，但不同于蛋白编码基因氨基酸序列得出的系统树的拓扑结构。要更多的了解对虾科的系统关系还需要更多的资料加以证实。
In this study,the genetic diversity and evolutionary demography ofFeneropenaeus chinensis and Marsupenaeus japonicus were studied by mtDNAmarkers.We discussed the role of Pleistocene ice ages and present environmentalfactors in shaping the phylogeographic pattern and genetic structures of the twospecies.In addition,ITS1,mt genome sequences and Numts were used as molecularmarkers for studying the phylogenetic relationships among species of penaeid shrimps.
1、Genetic structure and demographic history ofFeneropenaeus chinensis wasexamined using sequence data of partial mitochondrial cytochrome oxidase I (COI)gene and the complete mitochondrial control region (CR).Samples of 93 individualswere collected from 5 localities over most of the species' range in the Yellow Sea andthe Bohai Sea.For COI data,atotal of 20 nucleotide sites were detected variable,defining 20 haplotypes.The variation level was low,with H=0.4816±0.0639 and=0.0846±0.0711 (%),respectively.For CR data,there are 84 variable sites defining68 haplotypes.Haplotype diversity levels were very high (0.95±0.03-0.99±0.02),while that ofnucleotide diversitywere at moderate to low level (0.66±0.36%-0.84±0.46%).Analysis of molecular variance and the conventional population statisticFST revealed no significant genetic structure throughout the range of F.chinensis.However,Isolation with Migration (IM) coalescence results based on CR data suggestF.chinensis distributed along the coasts of northern China and Korean Peninsula(about 1000 km apart) diverged recently,and the estimated split time was 12,800 (7,400-18,600) years ago.Both mismatch distribution analyses and neutrality testsbased on COI data and CR data suggested a late Pleistocene or Holocene populationexpansion (12,100-28,500 years ago) for F.chinensis,which was consistent withthe geological period of formation of the Bohai Sea and the Yellow Sea.These results indicated that F.chinensis in the Bohai Sea and the Yellow Sea might have undergonea genetic bottleneck or founder event during the late Pleistocene globle glacial period.
2、DNA sequencing is very useful for the genetic diversity analysis at molycular level.Mitochondrial COI gene fragments of kuruma shrimp Marsupenaeus japonicus wereamplified via polymerase chain reaction (PCR),the PCR products were sequenced for85 individuals,5 population of China.858 base-pair nucleotide sequences wereexamined and analyzed for genetic polymorphism.Resultant sequences data analysisshowed that all 85 sequences were grouped into 58 haplotypes and there were 106variable nucleotide positions in this gene fragment.The genetic diversity indexesincluding S (polymorphic sites),π(nucleotide diversity) and H (haplotype diversity)were calculated and the results indicated that Guangxi population showed morevariation than others and more differences to others.Based on the mitochondrial DNAsequence data,the shrimps were separated into two distinct clades.Analyses ofmolecular variance and the population statistic FST revealed significant geneticstructure.Both mismatch distribution analyses and neutrality tests based suggested aPleistocene population expansion for Marsupenaeus japonicus.
3、The ribosomal DNA internal transcribed spacer 1 (ITS1) of Fenneropenaeuschinensis was cloned and sequenced.The objective of the present study is to estimatephylogenies and explore the feasibility of using ITS1 as a molecular marker forstudying the interspecific and intraspecific genetic variations among penaeid shrimps.Inter-and intraindividual polymorphisms of ITS 1 were clearly observed in F.chinensis.The length of the ITS1 ranged from 637 to 652bp,with a GC content of 66.9%.Repeats of microsatellite loci of ITS 1 plays an important role in length heteroplasmyat both between-and within-individual levels in this species.Eight microsatellite lociwere found in the ITS1 sequence of F.chinensis.According to existing data,somemicrosatellites were found in only one specie,(CAGC) 2-4 in F.chinensis,(GCGA)4in P.semisalcatus and (CGGA)4-9 in P.monodon.The DNA data of the penaeidshrimps were processed in neighbor-joining (NJ) methods to build phylogeneticrelationships within the family of Penaeidae.According to the NJ tree,differentindividuals of the same species,different species of the same genus were grouped together,in consistence with the morphological taxonomy.The genetic distancesamong different genus ranged from 0.313 to 0.977 and the average was 0.633,exceeding those estimated with COI and partial 16S rRNAgene sequences,and beingtherefore larger than the value among subgenera.The results of the present studyindicated that Fenneropenaeus,Litopenaeus,Farfanatepenaeus,Marsupenaeus andPenaeus are at a higher phylogenetic level than subgenus,which supports the opinionof the elevation of phylogenetic status of the four subgenera to genus level.Theseresults show that ITS 1 is highly divergent among different penaeid shrimps and couldbe an appropriate marker for molecular systematic studies at the species levels,although the presence of intragenomic variation needs to be taken into consideration.
4、Mt genome sequences have provided useful markers for investigating populationgenetic structures,systematics and phylogenetics of organisms.In this study,mtgenome sequences and Numts were used as molecular markers for studying the phylogeneticrelationships among species of penaeid shrimps.Phylogenetic analyses based onconcatenated amino acid and nucleic acid sequences of the 13 mt protein-codinggenes strongly support the monophyly of the Decapoda and Penaeidae.However,relationships among species within the Penaeidae based on the 13 mt protein-codinggenes and Numts could not be resolved,and further studies were necessary to becarried out based.on the increasing number of mitochondrial genome sequences,inorder to better understand the relationships among species of Penaeidae.
引文
陈大刚。黄渤海渔业生态学。北京：海洋出版社，1991。
刘瑞玉，钟振如等。南海对虾类。北京：[M]农业出版社．1987，p114-120。
刘旭东，黄渤海中国对虾种群生化遗传学和七种虾类同工酶遗传标记的研究，[博士学位论文]。青岛：中科院海洋研究所，1995
刘萍，孟宪红，庄志猛，孔杰等．3种对虾种间RAPD遗传标记．海洋水产研究，2002，23(2)：1-6
孟宪红、马春艳等， 黄渤海中国对虾6个地理群的遗传结构及其遗传分化，高科技通报，2004，4：96—102
邱高峰，常林瑞等，中国对虾16SrRNA基因序列多态性的研究．动物学研究，2000，21(1)：35-40
邱芳、伏建民等，遗传多样性的分子检测．生物多样性，1998，6：143-150
庆宁。墨吉对虾Penaeusmerguiensis线粒体16SrRNA基因序列分析，华南师范大学学报(自然科学版)，2002，3：63～67．
石拓，孔杰，刘萍等，用随机引物扩增多态DNA技术对中国对虾遗传多样性的分析一朝鲜半岛西海岸群体的DNA多态性．海洋与湖沼，1999，30(6)：509-515
宋林生，相建海，李晨曦等．日本对虾野生种群和养殖种群遗传结构的RAPD标记研究。海洋与湖沼，1999，30(3)：261-265．
唐伯平，周开亚，宋大祥．核rDNA ITS区序列在无脊椎动物分子系统学中的应用。动物学杂志，2002，37(4)：67—73．
王献溥，生物多样性保护与利用的主要研究方向。 自然资源，1994(4)：1-6
许常德等，6个虾种基因组DNA多态性分析。 海洋科学，2001，25(1)：10-12
叶昌臣，刘传桢，李培军。对虾亲体数量和补充量之间的关系。水产学报，1980，4(1)：1-8
张煜，邓景耀．渤黄海对虾标志放流实验．海洋水产研究丛刊．1965，20：78～85
(?)lvarez I,Wendel JF(2003).Ribosomal ITS sequence and plant phylogenetic inference.Mol Phylogenet Evol,29:417—434
Anderson S,Bankier AT,Barrell BG.de Bruijn MHL,Coulson AR,Drouin J,Eperon IC,Nierlich DP,Roe BA,Sanger F,Schreier PH,Smith AJH,Staden R,Young IG.(1981) Sequence and organization of the human mitochondrial genome.Nature 290:457-465
A vise JC (1994) Molecular markers, Natural History and Evolution. Chamman & Hall, New York
Avise JC, Neigel JE, Arnold J (1984) Demographic influences on mitochondrial DNA lineage survivorship in animal populations. J Mol Evol 20:99-105
Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders N. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu. Rev. Ecol. Syst. 1987; 18: 489-522.
Avise JC. (2000) Phylogeography. Harvard Univ. Press, London, 447p
Baldwin JD, Bass AL, Bowen BW, Clark WC. Molecular phytogeny and biogeography of the marine shrimp Penaeus. Mol. Phylogenet. Evol. 1998; 10: 399-407
Bandelt HJ, Forster P, Sykes BC, Richards MB (1995) Mitochondrial portraits of human populations using median networks. Genetics 141:743-753
Bandelt HJ, Macaulay V, Richards M (2000) Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. Mol Phylogenet Evol 16:8-28 .
Baxevanis AD, Kappas I, Abatzopoulos TJ(2006). Molecular phylogenetics and asexuality in the brine shrimp Artemia. Mol Phylogenet Evol, 40(3): 724-738
Bensasson D, Zhang DX(2001). Mitochondrial pseudogenes; evolution's misplaced witnesses. Trends in Ecology and Evolution,16(6):314-322
Benzie AH, Bailment E, Frusher S(1993). Genetic structure of in Australia: concordant results from mtDNA and allozymes. Aquaculture, 111: 89-93
Brown DD, Wensink PC, Jordan EA(1972). comparison of the ribosomal DNA's of Xenopus laevis and Xenopus mulleri: the evolution of tandem gene. J Mol Biol, 63: 57-73
Burkenroad MD(1934). The Penaeidae of Louisiana, with a discussion of their world relationships. Bull Amer Mus Nat Hist, 68: 61-143.
Cha HK, Oh CW, Hong SY, Park KY (2002) Reproduction and population dynamics of Penaeus chinensis (Decapoda: Penaeidae) on the western coast of Korea, Yellow Sea. Fish Res 56:25-36
Chappell J. Sea level changes forced ice breakouts in the last Glacial cycle: new results from coal terraces. Quat. Sci. Rev. 2002; 21: 1229-1240
Chen CA. Chen CP, Fan TY, Yu JK, Hsieh HL(2002). Nucleotide sequences of ribosomal internal transcribed spacers and their utility in distinguishing closely related Perinereis polychaetes(Annelida; Polychaeta; Nereididae). Mar Btotech, 4:17-29
Chu KH, Li PC, Ho YH(2001). The first internal transcribed spacer (ITS-1) of ribosomal DNA as a molecular marker for phylogenetic and population analyses in Crustacea. Mar Biotechnol, 3: 355-361
Chu KH, Li CP, Tam YK, Lavery S (2003) Application of mitochondrial control region in population genetic studies of the shrimp Penaeus. Mol Ecol Notes 3:120-122
Crespi BJ, Fulton MJ(2004). Molecular systematics of Salmonidae: combined nuclear data yields a robust phylogeny. Mol Phylogenet Evol, 31: 658-679
Cui ZX, Li CP, Jang IK, Chu KH (2007) Lack of Genetic Differentiation in the Shrimp Penaeus chinensis in the Northwestern Pacific. Biochem Genet 45:579-588
Deng JY, Zhu JS, Jiang YW (1983) A summary of surveys of the penaeid shrimp spawning ground in the Bohai Bay. Mar Fish Res (in Chinese) 5:17-32
Deng JY, Ye C, Liu Y (1990) Penaeus chinensis in the Bohai Sea and the Yellow Sea and its Management. In: (ed. By Deng JY), pp. 48-91. Ocean press, Beijing, China
Deng JY, Zhao CY (1991) Marine Fishery Biology. Agriculture Press, Beijing, China
Dover GA(1986). Molecular drive in multigene families, how biological novelties arise, spread and assimilated. Trends in Genetics, 2: 159-165
Dubuyhg, Riley L (1967). Hybridization between the nuclear and kinetoplast DNA S of Leishmania enriettii and between nuclear and mitochondrial DNA'S of mouse liver. Proe Natl Acad Sci USA, 57:790-797
Durent L, Mouchiroud D. (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila and Arabidopsis. Proc Natl Acad Sci USA 96: 4482-4487
Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131:479-491
Excoffier L (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Eco 13:853-864
Farfame PI(1969). Western Atlantic shrimps of the genus Penaeus. Fish Bull US Fish and Wildlife Service, 67:461-591
Fauvelot C, Bernardi G, Planes S. Reductions in the mitochondrial DNA diversity of coral reef fish provide evidence of population bottlenecks resulting from Holocene sea-level change. Evolution 2003; 57 (7): 1571-1583
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
Freeland JR. Molecular Ecology. Wiley & Sons, Chichester. 2005
Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915-925
Funk DJ. Molecular systematics of cytochrome oxidase I and 16S from Neochlamisus leaf beetles and the importance of sampling. Mol. Biol Evol. 1999; 16: 67-82
Garcia-Machado E, Dennebouy N, Suarez MO. Partial sequence of the shrimp Penaeus notialis mitochondrial genome. C. R. Acad. Sci. Paris, Sci. Vie. 1996; 319, 473-486
Garcia-Machado E., Pempera M., Dennebouy N., Oliva-Suarez M., Mounolou J.C., Monnerot M. (1999) Mitochondrial genes collectively suggest the paraphyly of Crustacea with respect to Insecta. J Mol Evol 49: 142-149
Grant WS, Bowen BW (1998) Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered 89:415-426
Hall TA. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98
Harpending HC (1994) Signature of ancient population growth in a low resolution mitochondrial DNA mismatch distribution. Hum Biol 66:591-600
Harpending H, Rogers A. Genetic perspectives on human origins and differentiation. Annu. Rev. Genomics. Hum. Genet. 2000; 1: 361-385
Hartl DL, Clark AG (1989) Principles of Population Genetics, 3rd edn. Sinauer, Sunderland, MA
Hasegawa M, Kishino H, Yano K. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174
He M, Huang L, Shi J, Jiang Y(2005). Variability of ribosomal DNA ITS-2 and its utility in detecting genetic relatedness of pearl oyster. Mar Btotech, 7: 40-45
Hedrick PW, Miller PS (1992) Conservation genetics: techniques and fundamentals. Ecol Appl 2:30-46
Hewitt GM. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 1996; 58: 247-276
Hewitt GM. The genetic legacy of the Quaternary ice ages. Nature 2000; 405: 907-913
Hey J, Nielsen (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760
Hey J (2005) On the number of new world founders: a population genetic portrait of the peopling of the Americas. PLoS Biol 3:el93
Hillis DM, Dixon MT(1991). Ribosomal DNA: molecular evolution and phylogenetic inference. Quarterly Review of Biology, 66: 411-453
Hualkasin W, Sirimontaporn P, Chotigeat W, Querci J, Phongdara A (2003) Molecular phylogenetic analysis of white prawns species and the existence of two clades in Penaeus merguiensis. J Exp Mar Biol Ecol 296:1-11
Hudson RR. Gene genealogies and the coalescent process. In: Futuyma D, Antonovies J (Eds). Oxford Surveys in Evolutionary biology. Oxford University Press, New York. 1990; 7:1-44
Huelsenbeck JP, Rannala B (1997) Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227-232
Huyse T, Houdt JV, Volckaert AM(2004). Paleoclimatic history and vicariant speciation in the "sand goby" group (Gobiidae, Teleostei). Mol Phylogenet Evol, 32: 324-336
Hwang GL (1996) Stock characterization of the fleshy prawn (Penaeus chinensis) in the Yellow Sea by intraspecific sequence variation of the cytochrome c oxidase subunit I gene. J Korean Fish Soc 29:876-881
Hwang GL, Lee YC, Chang CS (1997) Mitochondrial DNA analysis of the fleshy prawn (Penaeus chinensis) for stock discrimination in the Yellow Sea. J Korean Fish Soc 30:88-94
Jansen G, Devaere S, Weekers PHH(2006). Phylogenetic relationships and divergence time estimate of African anguilliform catfish (Silurformes: Clariidae) inferred from ribosomal gene and spacer sequences. Mol Phylogenet Evol, 38: 65-78
Jerry DR, Preston N, Crocos PJ(2004). Parentage determination of Kuruma prawn shrimp Penaeus {Marsupenaeus) japonicus using microsatellite markers. Aquaculture, 235: 237 - 247
Kim B. Studies on the distribution and migration of Korean shrimp, Penaeus orientalis Kishinouye, in Yellow Sea. Bull Fish Dev Agency, Busan 1973; 11: 7-23.
Klinbunga S, Siludjai D, Wudthijinda W, Tassanakajon A, Jarayabhand P, Menasveta P (2001) Genetic heterogeneity of the giant tiger shrimp (Penaeus monodon) in Thailand revealed by RAPD and mitochondrial DNA RFLP analyses. Mar Biotechnol 3:428-438
Kubo I(1949). Studies of the penaeids of Japanese and its adjacent waters. J Tokyo Coll Fish, 36: 1-467
Kumar S, Tamura K, Nei M (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. http://www.megasoftware.net/
Lee WJ, Conroy J, Howell WH, Kocher TD (1995) Structure and evolution of teleost mitochondrial control regions. J Mol Evol 41:58-66
Li WH. Molecular Evolution. Sinauer Associates, Inc., Publishers, Sunderland, Massachusetts. 1997
Liu P, Kong J, Shi T, Zhuang ZM, Deng JY, Xu HS, Han LL (2000a) RAPD analysis of wild stock of penaeid shrimp (Penaeus chinensis) in the China's coastal waters of Huanghai and Bohai Seas. Acta Ocean Sinica (in Chinese) 5:88-94
Liu P, Kong J, Shi T, Liu ZH, Zhuang ZM, Deng JY, Xu HS, Han LL (2000b) RAPD analysis of genetic diversity in two HUANG BO SEA stock families of Penaeus chinensis. Acta Ocean Sinica (in Chinese) 1:13-21
Liu P, Meng XH, Kong J, Zhuang ZM, HE YY, Wang QY (2006) Polymorphic analysis of microsatellite DNA in wild populations of Chinese shrimp (Fenneropenaeus chinensis). Aquac Res 37:556-562
Liu RY. Present status and future prospects for shrimp mariculture in China. In: Main KL and Fulks W (eds). The Culture of Cold-Tolerant Shrimp. Proc. Asian-US. Workshop on Shrimp Culture2-4 October 1989, Honolulu, HI, The Oceanic Institute, Honolulu, HI. 1990; 10-28.
Liu RY (2003) On the unification of the scientific name of penaeid shrimp (Crustacea: Decapoda). Trans Chinese Crust Soc (in Chinese) 4:106-124
Lopez JV(1994). Numt, a recent transfer and tandem amplification of mitoehondrial DNA to the nuclear genome of the domestic eat. J Mol Evol, 39:174-190
McMillan-Jackson AL, Bert TM (2003) Disparate patterns of population genetic structure and population history in two sympatric penaeid shrimp species {Farfantepenaeus aztecus and Litopenaeus setiferus) in the eastern United States. Mol Eco 12:275-288
McMillan-Jackson AL, Bert TM (2004) Genetic diversity in the mtDNA control region and population structure in the pink shrimp Farfantepenaeus duorarum. J Crustac Biol 24:101-109
Miller AD, Austin CM. (2006) The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences. Mol Phylogenet Evol 38: 565-574
Mukha D, Wiegmann BM, Schal C(2002). Evolution and phylogenetic information content of the ribosomal DNA repeat unit in the Blattodea (Insecta). Insect Biochem Mol Biol, 32: 951-960
Munro JL, Bell JD (1997) Enhancement of marine fisheries resources. Rev Fish Sci 5: 185-222
Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
Palumbi SR, Benzie J. Large mitochondrial DNA differences between morphologically similar Penaeus shrimp. Mol. Mar. Biol. Biotechnol. 1991; 1: 27-34.
Palumbi SR. Population genetics, demographic connectivity, and the design of marine reserves. Ecol. Appl. 2003; 13 (1):S146-S158.Supplement.
Perez-Farfante I and Kensley B(1997). Penaeoid and Sergestoid Shrimps and Prawns of the World. Editions du Museum National d'Histoire Naturelle, Paris
Pfeiler E, Hurtado LA, Knowles LL, Torre-Cosio, Bourillon-Moreno L,Marquez-Farias JF, Montemayor-Lopez G Population genetics of the swimming crab Callinectes bellicosus (Brachyura: Portunidae) from the eastern Pacific Ocean. Mar. Biol. 2005; 146: 559-569
Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818
Presa P, Pardo BG, Martinez P(2002). Phylogeographic Congruence Between mtDNA and rDNA ITS Markers in Brown Trout. Mol Biol Evo, 19(12): 2161-2175
Quan JX, Lu X.M, Zhuang ZM, Dai JX, Deng JY, Zhang YP (2001) Low Genetic Variation of Penaeus chinensis as Revealed by Mitochondrial COI and 16S rRNA Gene Sequences. Biochem Genet 39:279-284
Ray N, Currat M, Excoffier L (2003) Intra-deme molecular diversity in spatially expanding populations. Mol Biol Evol 20:76-86
Raymond M, Rousset F(1995). An exact text for population differentiation. Evolution, 49: 1280-1283
Remigio EA, Blair D(1997). Relationships among problematic North American stagnicoline snails(Pulmonata: Lymnaeidae)reinvestigated using nuclear ribosomal DNA internal transcribed spacer sequences. Can. J. Zool, 75: 1540-1545
Rodrigo Maggioni, Alex D Rogers, Norman Maclean(2001). Molecular Phylogeny of Western Atlantic Farfantepenaeus and Litopenaeus Shrimp Based on Mitochondrial 16S Partial Sequences. Mol Phylogenet Evol, 18: 66-73
Rodriguez-Trelles F, Tarrio R, Ayala FJ(2000). Evidence for a high ancestral GC content in Drosophila. Mol Biol Evol, 17: 1710-1717
Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552-569
Rogers AR. (1995) Genetic evidence for a Pleistocene population expansion. Evolution 49:608-615
Roman J, Palumbi SR. A global invader at home: population structure of the green crab, Carcinus maenas, in Europe. Mol. Ecol. 2004; 13 (10): 2891-2898
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574
Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
Salgueiro P, Carvalho G, Collares-Pereira MJ, Coelho MM (2003) Microsatellite analysis of genetic population structure of the endangered cyprinid Anaecypris hispanica in Portugal: implications for conservation. Biological conservation 109: 47-56
Schneider S, Excoffier L (1999) Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152:1079-1089
Schneider S, Roessli D, Excoffier L (2000) ARLEQUIN, version 2.0: a software for population genetic data analysis. Geneva: University of Geneva
Schlotterer C, Tautz D(1992). Slippage synthesis of simple sequence DNA [J]. Nucleic Acids Res, 20:211-215
Schulenburg JHG, Hancock JM, Pagnamenta A(2001). Extreme length and length variation in the first ribosomal internal transcribed spacer of ladybird beetles (Coleoptera: Coccinellidae). Mol Biol Evol, 18(4): 648-660
Shane Lavery, Chan TY, Tam YK, Chu K H(2004). Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus s.l. derived from mitochondrial DNA. Mol Phylogenet Evol, 31: 39-49
Shen X, Ren JF, Cui ZX, Sha Zhongli, Wang B, Xiang JH, Liu B(2007). The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations. Gene, 403: 98-109
Shi T, Zhuang ZM, Kong J, Liu P, Liu Z, Meng XH, Deng JY (2001) Genetic diversity analysis of Penaeus chinensis by RAPD. Pro Nat Sci (in Chinese) 4:360-364
Sirawut Klinbunga, David J. Penman, Brendan J. McAndrew(1998). A preliminary study of ribosomal DNA polymorphism in the tiger shrimp, Penaeus monodon. J Mar Biotechnol, 6:186-188
Slatkin M, Hudson RH (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555-562
Slatkin M. Isolation by distance in equilibrium and non-equilibrium populations. Evolution 1993; 47:264-279
Spicer GS. Phylogenetic utility of the mitochondrial cytochrome oxidase gene: molecular evolution of the Drosophila buzzatii species complex. J. Mol. Evol. 1995; 41: 749-759.
Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods), version 4. Sinauer Associates, Sunderland, Massachusetts.
Tajima F (1989) The effect of change in population size on population DNA polymorphism. Genetics 123:597-601
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526
Tamura K, Dudley J, Nei M, Kumar S. MEGA 4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007; 24 (8): 1596-1599.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DJ (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 24:4876-4882
Tsoi KH, Wang ZY, Chu KH(2005). Genetic divergence between two morphologically similar varieties of the kururaa shrimp Penaeus japonicus. Marine Biology, 147: 367-379
Tsoi KH, Chan TY, Chu KH (2007) Molecular population structure of the kuruma shrimp Penaeus japonicus species complex in western Pacific. Mar Biol 150:1345-1364
Tzeng TD, Yeh SY, Hui CF (2004) Population genetic structure of the kuruma prawn (Penaeus japonicus) in East Asia inferred from mitochondrial DNA sequences. J Mar Sci 61:913-920
Valles-Jimenez R, Gaffhey PM, Perez-Enriquez R (2006) RFLP analysis of the mtDNA control region in white shrimp (Litopenaeus vannamei) populations from the eastern pacific. Mar Biol 148:867-873
Walton C, Handley JM, Tun-Lin W, Collins FH, Harbach RE, Baimai V, Butlin RK. Population structure and population history of Anopheles dims mosquitoes in Southeast Asia. Mol. Biol. Evol. 2000; 17: 962-974
Wang P. Paleontological evidence for the formation of the seas neighbouring China. In: Wang P (eds). Proceeding of Paleontology on Marine Corpuscle. Ocean Press, Beijing. 1980
Wang P. Response of Western Pacific marginal seas to glacial cycles: paleoceanographic and sedimentological features. Mar. Geol. 1999,156: 5-39
Wang P, Sun X. Last glacial maximum in China: comparison of land and sea. Catena. 1994; 23: 341-353
Wanna W, Chotigeat W, Phongdara A(1972). Sequence variations of the first ribosomal internal transcribed spacer of Penaeus species in Thailand. Journal of Experimental Marine Biology and Ecology, 2006, 331: 64-73.
Watterson GA (1984) Allele frequencies after a bottleneck. Theor Popul Biol 26:387-407
Xu X, Oda M. Surface-water evolution of the eastern East China Sea during the last 36,000 years. Mar. Geol. 1999; 156: 285-304
Yamauchi MM, Miya MU, Nishida M. (2002) Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda). Gene 295: 89-96
Yu SS, Kong XY, Li YL, Xu H(2007). The complete sequence of mitochondrial COII gene of Fenneropenaeus chinensis and its applicability as a marker for phylogenetic analysis. Journal of Ocean University of China, 6: 187-192
Zhu S, Wang W, Hu L (1998) Study on climate variations in the region of Guanzhong in the historical period. Quaternary Sci (in Chinese)1:l-11
Zhuang ZM, Meng XH, Quan JX (2000). Genetic diversity in the wild population and hatchery stock of Penaeus japonicus shrimp by isoenzyme analysis. Zoological Research,21(4): 323 - 326
Zhuang ZM, Shi T, Kong J, Liu P, Liu ZH, Meng XH, Deng JY (2001) Genetic diversity in Penaeus chinensis shrimp as revealed by RAPD technique. Prog Nat Sci (in Chinese) 11:432-438
刘瑞玉，钟振如等。南海对虾类。北京：[M]农业出版社．1987，p114-120。
刘旭东，黄渤海中国对虾种群生化遗传学和七种虾类同工酶遗传标记的研究，[博士学位论文]。青岛：中科院海洋研究所，1995
刘萍，孟宪红，庄志猛，孔杰等．3种对虾种间RAPD遗传标记．海洋水产研究，2002，23(2)：1-6
孟宪红、马春艳等， 黄渤海中国对虾6个地理群的遗传结构及其遗传分化，高科技通报，2004，4：96—102
邱高峰，常林瑞等，中国对虾16SrRNA基因序列多态性的研究．动物学研究，2000，21(1)：35-40
邱芳、伏建民等，遗传多样性的分子检测．生物多样性，1998，6：143-150
庆宁。墨吉对虾Penaeusmerguiensis线粒体16SrRNA基因序列分析，华南师范大学学报(自然科学版)，2002，3：63～67．
石拓，孔杰，刘萍等，用随机引物扩增多态DNA技术对中国对虾遗传多样性的分析一朝鲜半岛西海岸群体的DNA多态性．海洋与湖沼，1999，30(6)：509-515
宋林生，相建海，李晨曦等．日本对虾野生种群和养殖种群遗传结构的RAPD标记研究。海洋与湖沼，1999，30(3)：261-265．
唐伯平，周开亚，宋大祥．核rDNA ITS区序列在无脊椎动物分子系统学中的应用。动物学杂志，2002，37(4)：67—73．
王献溥，生物多样性保护与利用的主要研究方向。 自然资源，1994(4)：1-6
许常德等，6个虾种基因组DNA多态性分析。 海洋科学，2001，25(1)：10-12
叶昌臣，刘传桢，李培军。对虾亲体数量和补充量之间的关系。水产学报，1980，4(1)：1-8
张煜，邓景耀．渤黄海对虾标志放流实验．海洋水产研究丛刊．1965，20：78～85
(?)lvarez I,Wendel JF(2003).Ribosomal ITS sequence and plant phylogenetic inference.Mol Phylogenet Evol,29:417—434
Anderson S,Bankier AT,Barrell BG.de Bruijn MHL,Coulson AR,Drouin J,Eperon IC,Nierlich DP,Roe BA,Sanger F,Schreier PH,Smith AJH,Staden R,Young IG.(1981) Sequence and organization of the human mitochondrial genome.Nature 290:457-465
A vise JC (1994) Molecular markers, Natural History and Evolution. Chamman & Hall, New York
Avise JC, Neigel JE, Arnold J (1984) Demographic influences on mitochondrial DNA lineage survivorship in animal populations. J Mol Evol 20:99-105
Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders N. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu. Rev. Ecol. Syst. 1987; 18: 489-522.
Avise JC. (2000) Phylogeography. Harvard Univ. Press, London, 447p
Baldwin JD, Bass AL, Bowen BW, Clark WC. Molecular phytogeny and biogeography of the marine shrimp Penaeus. Mol. Phylogenet. Evol. 1998; 10: 399-407
Bandelt HJ, Forster P, Sykes BC, Richards MB (1995) Mitochondrial portraits of human populations using median networks. Genetics 141:743-753
Bandelt HJ, Macaulay V, Richards M (2000) Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. Mol Phylogenet Evol 16:8-28 .
Baxevanis AD, Kappas I, Abatzopoulos TJ(2006). Molecular phylogenetics and asexuality in the brine shrimp Artemia. Mol Phylogenet Evol, 40(3): 724-738
Bensasson D, Zhang DX(2001). Mitochondrial pseudogenes; evolution's misplaced witnesses. Trends in Ecology and Evolution,16(6):314-322
Benzie AH, Bailment E, Frusher S(1993). Genetic structure of in Australia: concordant results from mtDNA and allozymes. Aquaculture, 111: 89-93
Brown DD, Wensink PC, Jordan EA(1972). comparison of the ribosomal DNA's of Xenopus laevis and Xenopus mulleri: the evolution of tandem gene. J Mol Biol, 63: 57-73
Burkenroad MD(1934). The Penaeidae of Louisiana, with a discussion of their world relationships. Bull Amer Mus Nat Hist, 68: 61-143.
Cha HK, Oh CW, Hong SY, Park KY (2002) Reproduction and population dynamics of Penaeus chinensis (Decapoda: Penaeidae) on the western coast of Korea, Yellow Sea. Fish Res 56:25-36
Chappell J. Sea level changes forced ice breakouts in the last Glacial cycle: new results from coal terraces. Quat. Sci. Rev. 2002; 21: 1229-1240
Chen CA. Chen CP, Fan TY, Yu JK, Hsieh HL(2002). Nucleotide sequences of ribosomal internal transcribed spacers and their utility in distinguishing closely related Perinereis polychaetes(Annelida; Polychaeta; Nereididae). Mar Btotech, 4:17-29
Chu KH, Li PC, Ho YH(2001). The first internal transcribed spacer (ITS-1) of ribosomal DNA as a molecular marker for phylogenetic and population analyses in Crustacea. Mar Biotechnol, 3: 355-361
Chu KH, Li CP, Tam YK, Lavery S (2003) Application of mitochondrial control region in population genetic studies of the shrimp Penaeus. Mol Ecol Notes 3:120-122
Crespi BJ, Fulton MJ(2004). Molecular systematics of Salmonidae: combined nuclear data yields a robust phylogeny. Mol Phylogenet Evol, 31: 658-679
Cui ZX, Li CP, Jang IK, Chu KH (2007) Lack of Genetic Differentiation in the Shrimp Penaeus chinensis in the Northwestern Pacific. Biochem Genet 45:579-588
Deng JY, Zhu JS, Jiang YW (1983) A summary of surveys of the penaeid shrimp spawning ground in the Bohai Bay. Mar Fish Res (in Chinese) 5:17-32
Deng JY, Ye C, Liu Y (1990) Penaeus chinensis in the Bohai Sea and the Yellow Sea and its Management. In: (ed. By Deng JY), pp. 48-91. Ocean press, Beijing, China
Deng JY, Zhao CY (1991) Marine Fishery Biology. Agriculture Press, Beijing, China
Dover GA(1986). Molecular drive in multigene families, how biological novelties arise, spread and assimilated. Trends in Genetics, 2: 159-165
Dubuyhg, Riley L (1967). Hybridization between the nuclear and kinetoplast DNA S of Leishmania enriettii and between nuclear and mitochondrial DNA'S of mouse liver. Proe Natl Acad Sci USA, 57:790-797
Durent L, Mouchiroud D. (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila and Arabidopsis. Proc Natl Acad Sci USA 96: 4482-4487
Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131:479-491
Excoffier L (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Eco 13:853-864
Farfame PI(1969). Western Atlantic shrimps of the genus Penaeus. Fish Bull US Fish and Wildlife Service, 67:461-591
Fauvelot C, Bernardi G, Planes S. Reductions in the mitochondrial DNA diversity of coral reef fish provide evidence of population bottlenecks resulting from Holocene sea-level change. Evolution 2003; 57 (7): 1571-1583
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
Freeland JR. Molecular Ecology. Wiley & Sons, Chichester. 2005
Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915-925
Funk DJ. Molecular systematics of cytochrome oxidase I and 16S from Neochlamisus leaf beetles and the importance of sampling. Mol. Biol Evol. 1999; 16: 67-82
Garcia-Machado E, Dennebouy N, Suarez MO. Partial sequence of the shrimp Penaeus notialis mitochondrial genome. C. R. Acad. Sci. Paris, Sci. Vie. 1996; 319, 473-486
Garcia-Machado E., Pempera M., Dennebouy N., Oliva-Suarez M., Mounolou J.C., Monnerot M. (1999) Mitochondrial genes collectively suggest the paraphyly of Crustacea with respect to Insecta. J Mol Evol 49: 142-149
Grant WS, Bowen BW (1998) Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered 89:415-426
Hall TA. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98
Harpending HC (1994) Signature of ancient population growth in a low resolution mitochondrial DNA mismatch distribution. Hum Biol 66:591-600
Harpending H, Rogers A. Genetic perspectives on human origins and differentiation. Annu. Rev. Genomics. Hum. Genet. 2000; 1: 361-385
Hartl DL, Clark AG (1989) Principles of Population Genetics, 3rd edn. Sinauer, Sunderland, MA
Hasegawa M, Kishino H, Yano K. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174
He M, Huang L, Shi J, Jiang Y(2005). Variability of ribosomal DNA ITS-2 and its utility in detecting genetic relatedness of pearl oyster. Mar Btotech, 7: 40-45
Hedrick PW, Miller PS (1992) Conservation genetics: techniques and fundamentals. Ecol Appl 2:30-46
Hewitt GM. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 1996; 58: 247-276
Hewitt GM. The genetic legacy of the Quaternary ice ages. Nature 2000; 405: 907-913
Hey J, Nielsen (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760
Hey J (2005) On the number of new world founders: a population genetic portrait of the peopling of the Americas. PLoS Biol 3:el93
Hillis DM, Dixon MT(1991). Ribosomal DNA: molecular evolution and phylogenetic inference. Quarterly Review of Biology, 66: 411-453
Hualkasin W, Sirimontaporn P, Chotigeat W, Querci J, Phongdara A (2003) Molecular phylogenetic analysis of white prawns species and the existence of two clades in Penaeus merguiensis. J Exp Mar Biol Ecol 296:1-11
Hudson RR. Gene genealogies and the coalescent process. In: Futuyma D, Antonovies J (Eds). Oxford Surveys in Evolutionary biology. Oxford University Press, New York. 1990; 7:1-44
Huelsenbeck JP, Rannala B (1997) Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227-232
Huyse T, Houdt JV, Volckaert AM(2004). Paleoclimatic history and vicariant speciation in the "sand goby" group (Gobiidae, Teleostei). Mol Phylogenet Evol, 32: 324-336
Hwang GL (1996) Stock characterization of the fleshy prawn (Penaeus chinensis) in the Yellow Sea by intraspecific sequence variation of the cytochrome c oxidase subunit I gene. J Korean Fish Soc 29:876-881
Hwang GL, Lee YC, Chang CS (1997) Mitochondrial DNA analysis of the fleshy prawn (Penaeus chinensis) for stock discrimination in the Yellow Sea. J Korean Fish Soc 30:88-94
Jansen G, Devaere S, Weekers PHH(2006). Phylogenetic relationships and divergence time estimate of African anguilliform catfish (Silurformes: Clariidae) inferred from ribosomal gene and spacer sequences. Mol Phylogenet Evol, 38: 65-78
Jerry DR, Preston N, Crocos PJ(2004). Parentage determination of Kuruma prawn shrimp Penaeus {Marsupenaeus) japonicus using microsatellite markers. Aquaculture, 235: 237 - 247
Kim B. Studies on the distribution and migration of Korean shrimp, Penaeus orientalis Kishinouye, in Yellow Sea. Bull Fish Dev Agency, Busan 1973; 11: 7-23.
Klinbunga S, Siludjai D, Wudthijinda W, Tassanakajon A, Jarayabhand P, Menasveta P (2001) Genetic heterogeneity of the giant tiger shrimp (Penaeus monodon) in Thailand revealed by RAPD and mitochondrial DNA RFLP analyses. Mar Biotechnol 3:428-438
Kubo I(1949). Studies of the penaeids of Japanese and its adjacent waters. J Tokyo Coll Fish, 36: 1-467
Kumar S, Tamura K, Nei M (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. http://www.megasoftware.net/
Lee WJ, Conroy J, Howell WH, Kocher TD (1995) Structure and evolution of teleost mitochondrial control regions. J Mol Evol 41:58-66
Li WH. Molecular Evolution. Sinauer Associates, Inc., Publishers, Sunderland, Massachusetts. 1997
Liu P, Kong J, Shi T, Zhuang ZM, Deng JY, Xu HS, Han LL (2000a) RAPD analysis of wild stock of penaeid shrimp (Penaeus chinensis) in the China's coastal waters of Huanghai and Bohai Seas. Acta Ocean Sinica (in Chinese) 5:88-94
Liu P, Kong J, Shi T, Liu ZH, Zhuang ZM, Deng JY, Xu HS, Han LL (2000b) RAPD analysis of genetic diversity in two HUANG BO SEA stock families of Penaeus chinensis. Acta Ocean Sinica (in Chinese) 1:13-21
Liu P, Meng XH, Kong J, Zhuang ZM, HE YY, Wang QY (2006) Polymorphic analysis of microsatellite DNA in wild populations of Chinese shrimp (Fenneropenaeus chinensis). Aquac Res 37:556-562
Liu RY. Present status and future prospects for shrimp mariculture in China. In: Main KL and Fulks W (eds). The Culture of Cold-Tolerant Shrimp. Proc. Asian-US. Workshop on Shrimp Culture2-4 October 1989, Honolulu, HI, The Oceanic Institute, Honolulu, HI. 1990; 10-28.
Liu RY (2003) On the unification of the scientific name of penaeid shrimp (Crustacea: Decapoda). Trans Chinese Crust Soc (in Chinese) 4:106-124
Lopez JV(1994). Numt, a recent transfer and tandem amplification of mitoehondrial DNA to the nuclear genome of the domestic eat. J Mol Evol, 39:174-190
McMillan-Jackson AL, Bert TM (2003) Disparate patterns of population genetic structure and population history in two sympatric penaeid shrimp species {Farfantepenaeus aztecus and Litopenaeus setiferus) in the eastern United States. Mol Eco 12:275-288
McMillan-Jackson AL, Bert TM (2004) Genetic diversity in the mtDNA control region and population structure in the pink shrimp Farfantepenaeus duorarum. J Crustac Biol 24:101-109
Miller AD, Austin CM. (2006) The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences. Mol Phylogenet Evol 38: 565-574
Mukha D, Wiegmann BM, Schal C(2002). Evolution and phylogenetic information content of the ribosomal DNA repeat unit in the Blattodea (Insecta). Insect Biochem Mol Biol, 32: 951-960
Munro JL, Bell JD (1997) Enhancement of marine fisheries resources. Rev Fish Sci 5: 185-222
Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
Palumbi SR, Benzie J. Large mitochondrial DNA differences between morphologically similar Penaeus shrimp. Mol. Mar. Biol. Biotechnol. 1991; 1: 27-34.
Palumbi SR. Population genetics, demographic connectivity, and the design of marine reserves. Ecol. Appl. 2003; 13 (1):S146-S158.Supplement.
Perez-Farfante I and Kensley B(1997). Penaeoid and Sergestoid Shrimps and Prawns of the World. Editions du Museum National d'Histoire Naturelle, Paris
Pfeiler E, Hurtado LA, Knowles LL, Torre-Cosio, Bourillon-Moreno L,Marquez-Farias JF, Montemayor-Lopez G Population genetics of the swimming crab Callinectes bellicosus (Brachyura: Portunidae) from the eastern Pacific Ocean. Mar. Biol. 2005; 146: 559-569
Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818
Presa P, Pardo BG, Martinez P(2002). Phylogeographic Congruence Between mtDNA and rDNA ITS Markers in Brown Trout. Mol Biol Evo, 19(12): 2161-2175
Quan JX, Lu X.M, Zhuang ZM, Dai JX, Deng JY, Zhang YP (2001) Low Genetic Variation of Penaeus chinensis as Revealed by Mitochondrial COI and 16S rRNA Gene Sequences. Biochem Genet 39:279-284
Ray N, Currat M, Excoffier L (2003) Intra-deme molecular diversity in spatially expanding populations. Mol Biol Evol 20:76-86
Raymond M, Rousset F(1995). An exact text for population differentiation. Evolution, 49: 1280-1283
Remigio EA, Blair D(1997). Relationships among problematic North American stagnicoline snails(Pulmonata: Lymnaeidae)reinvestigated using nuclear ribosomal DNA internal transcribed spacer sequences. Can. J. Zool, 75: 1540-1545
Rodrigo Maggioni, Alex D Rogers, Norman Maclean(2001). Molecular Phylogeny of Western Atlantic Farfantepenaeus and Litopenaeus Shrimp Based on Mitochondrial 16S Partial Sequences. Mol Phylogenet Evol, 18: 66-73
Rodriguez-Trelles F, Tarrio R, Ayala FJ(2000). Evidence for a high ancestral GC content in Drosophila. Mol Biol Evol, 17: 1710-1717
Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552-569
Rogers AR. (1995) Genetic evidence for a Pleistocene population expansion. Evolution 49:608-615
Roman J, Palumbi SR. A global invader at home: population structure of the green crab, Carcinus maenas, in Europe. Mol. Ecol. 2004; 13 (10): 2891-2898
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574
Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
Salgueiro P, Carvalho G, Collares-Pereira MJ, Coelho MM (2003) Microsatellite analysis of genetic population structure of the endangered cyprinid Anaecypris hispanica in Portugal: implications for conservation. Biological conservation 109: 47-56
Schneider S, Excoffier L (1999) Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152:1079-1089
Schneider S, Roessli D, Excoffier L (2000) ARLEQUIN, version 2.0: a software for population genetic data analysis. Geneva: University of Geneva
Schlotterer C, Tautz D(1992). Slippage synthesis of simple sequence DNA [J]. Nucleic Acids Res, 20:211-215
Schulenburg JHG, Hancock JM, Pagnamenta A(2001). Extreme length and length variation in the first ribosomal internal transcribed spacer of ladybird beetles (Coleoptera: Coccinellidae). Mol Biol Evol, 18(4): 648-660
Shane Lavery, Chan TY, Tam YK, Chu K H(2004). Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus s.l. derived from mitochondrial DNA. Mol Phylogenet Evol, 31: 39-49
Shen X, Ren JF, Cui ZX, Sha Zhongli, Wang B, Xiang JH, Liu B(2007). The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations. Gene, 403: 98-109
Shi T, Zhuang ZM, Kong J, Liu P, Liu Z, Meng XH, Deng JY (2001) Genetic diversity analysis of Penaeus chinensis by RAPD. Pro Nat Sci (in Chinese) 4:360-364
Sirawut Klinbunga, David J. Penman, Brendan J. McAndrew(1998). A preliminary study of ribosomal DNA polymorphism in the tiger shrimp, Penaeus monodon. J Mar Biotechnol, 6:186-188
Slatkin M, Hudson RH (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555-562
Slatkin M. Isolation by distance in equilibrium and non-equilibrium populations. Evolution 1993; 47:264-279
Spicer GS. Phylogenetic utility of the mitochondrial cytochrome oxidase gene: molecular evolution of the Drosophila buzzatii species complex. J. Mol. Evol. 1995; 41: 749-759.
Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods), version 4. Sinauer Associates, Sunderland, Massachusetts.
Tajima F (1989) The effect of change in population size on population DNA polymorphism. Genetics 123:597-601
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526
Tamura K, Dudley J, Nei M, Kumar S. MEGA 4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007; 24 (8): 1596-1599.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DJ (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 24:4876-4882
Tsoi KH, Wang ZY, Chu KH(2005). Genetic divergence between two morphologically similar varieties of the kururaa shrimp Penaeus japonicus. Marine Biology, 147: 367-379
Tsoi KH, Chan TY, Chu KH (2007) Molecular population structure of the kuruma shrimp Penaeus japonicus species complex in western Pacific. Mar Biol 150:1345-1364
Tzeng TD, Yeh SY, Hui CF (2004) Population genetic structure of the kuruma prawn (Penaeus japonicus) in East Asia inferred from mitochondrial DNA sequences. J Mar Sci 61:913-920
Valles-Jimenez R, Gaffhey PM, Perez-Enriquez R (2006) RFLP analysis of the mtDNA control region in white shrimp (Litopenaeus vannamei) populations from the eastern pacific. Mar Biol 148:867-873
Walton C, Handley JM, Tun-Lin W, Collins FH, Harbach RE, Baimai V, Butlin RK. Population structure and population history of Anopheles dims mosquitoes in Southeast Asia. Mol. Biol. Evol. 2000; 17: 962-974
Wang P. Paleontological evidence for the formation of the seas neighbouring China. In: Wang P (eds). Proceeding of Paleontology on Marine Corpuscle. Ocean Press, Beijing. 1980
Wang P. Response of Western Pacific marginal seas to glacial cycles: paleoceanographic and sedimentological features. Mar. Geol. 1999,156: 5-39
Wang P, Sun X. Last glacial maximum in China: comparison of land and sea. Catena. 1994; 23: 341-353
Wanna W, Chotigeat W, Phongdara A(1972). Sequence variations of the first ribosomal internal transcribed spacer of Penaeus species in Thailand. Journal of Experimental Marine Biology and Ecology, 2006, 331: 64-73.
Watterson GA (1984) Allele frequencies after a bottleneck. Theor Popul Biol 26:387-407
Xu X, Oda M. Surface-water evolution of the eastern East China Sea during the last 36,000 years. Mar. Geol. 1999; 156: 285-304
Yamauchi MM, Miya MU, Nishida M. (2002) Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda). Gene 295: 89-96
Yu SS, Kong XY, Li YL, Xu H(2007). The complete sequence of mitochondrial COII gene of Fenneropenaeus chinensis and its applicability as a marker for phylogenetic analysis. Journal of Ocean University of China, 6: 187-192
Zhu S, Wang W, Hu L (1998) Study on climate variations in the region of Guanzhong in the historical period. Quaternary Sci (in Chinese)1:l-11
Zhuang ZM, Meng XH, Quan JX (2000). Genetic diversity in the wild population and hatchery stock of Penaeus japonicus shrimp by isoenzyme analysis. Zoological Research,21(4): 323 - 326
Zhuang ZM, Shi T, Kong J, Liu P, Liu ZH, Meng XH, Deng JY (2001) Genetic diversity in Penaeus chinensis shrimp as revealed by RAPD technique. Prog Nat Sci (in Chinese) 11:432-438