环渤海红条毛肤石鳖种群遗传多样性研究
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摘要
以线粒体细胞色素c氧化酶亚基Ⅰ(COⅠ)为遗传标记分析了环渤海红条毛肤石鳖Acanthochiton rubrolineatus 9个种群的遗传多样性及遗传结构。126只个体经PCR扩增测序获得654 bp的COⅠ基因序列,41个多态位点产生29种单倍型,单倍型多样性为0. 899±0. 013,核苷酸多样性为0. 013 3±0. 006 8。种群遗传多样性与纬度(r=-0. 808,P <0. 05)及年平均温度变异系数(r=-0. 795,P <0. 05)呈显著负相关,表明红条毛肤石鳖适应低纬度及温度稳定的海洋环境。分子方差分析表明,遗传变异主要发生在种群内(83. 26%,P <0. 001)。系统发生树与单倍型网络图没有呈现明显的谱系地理结构。种群历史动态结果显示,红条毛肤石鳖在早更新世晚期(第二温暖期)间冰期经历了种群扩张。
The genetic diversity and genetic structure of 9 populations of Acanthochiton rubrolineatus in the Bohai Rim were analyzed using mitochondrial cytochrome c oxidase subunit Ⅰ( CO Ⅰ). The COⅠ gene( 654 bp) of 126 A. rubrolineatus individuals were amplified and sequenced. Finally,a total of 29 haplotypes were detected by 41 polymorphic loci. The haplotype diversity of all samples was 0. 899 ± 0. 013,and the nucleotide diversity was 0. 013 3 ± 0. 006 8.There was a significant negative correlation between the population genetic diversity and latitude( r =-0. 808,P < 0. 05)and annual mean temperature variation coefficient( r =-0. 795,P < 0. 05),indicating that A. rubrolineatus was adaptive in the marine environment with low latitudes and stable temperature. The result of analysis of molecular variance showed that genetic variation occurred mainly within populations( 83. 26%,P < 0. 001). Phylogenetic tree and haplotype network did not show obvious phylogeographic structure. Demographic results showed that A. rubrolineatus had experienced population expansion during the late period of early Pleistocene( the second warm period) and interglacial period.
The genetic diversity and genetic structure of 9 populations of Acanthochiton rubrolineatus in the Bohai Rim were analyzed using mitochondrial cytochrome c oxidase subunit Ⅰ( CO Ⅰ). The COⅠ gene( 654 bp) of 126 A. rubrolineatus individuals were amplified and sequenced. Finally,a total of 29 haplotypes were detected by 41 polymorphic loci. The haplotype diversity of all samples was 0. 899 ± 0. 013,and the nucleotide diversity was 0. 013 3 ± 0. 006 8.There was a significant negative correlation between the population genetic diversity and latitude( r =-0. 808,P < 0. 05)and annual mean temperature variation coefficient( r =-0. 795,P < 0. 05),indicating that A. rubrolineatus was adaptive in the marine environment with low latitudes and stable temperature. The result of analysis of molecular variance showed that genetic variation occurred mainly within populations( 83. 26%,P < 0. 001). Phylogenetic tree and haplotype network did not show obvious phylogeographic structure. Demographic results showed that A. rubrolineatus had experienced population expansion during the late period of early Pleistocene( the second warm period) and interglacial period.
引文
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Shen KN,Jamandre BW,Hsu CC,et al.2011.Plio-Pleistocene sea level and temperature fluctuations in the northwestern Pacific promoted speciation in the globally-distributed flathead mullet Mugil cephalus[J].BMC Evolutionary Biology,11:83.
Surhone LM,Tennoe MT,Henssonow SF,et al.2010.Tree view[M].Hong Kong:Betascript Publishing:28-143.
Yu JH,Song JH,Minchul C,et al.2009.Effects of water temperature change on immune function in surf clams,Mactra veneriformis(Bivalvia:Mactridae)[J].Journal of Invertebrate Pathology,102(1):30-35.
Zhou N,Shen H,Cheng C,et al.2016.Genetic structure of Onchidium“struma”(Mollusca:Gastropoda:Eupulmonata)from the coastal area of China based on mt COⅠ[J].Mitochondrial DNA Part A:DNA Mapping Sequencing&Analysis,27(2):1319-1323.
王玲,李琪,孔令锋,等.2018.基于COⅠ基因的中国沿海青蚶野生种群遗传结构及种群动态研究[J].海洋与湖沼,49(1):87-95.
张均龙,史振平,王承,等.2015.基于壳板和齿舌形态对中国沿岸几种常见多板纲软体动物的分类研究[J].海洋科学,39(11):96-107.
赵青松,金珊,陈寅儿.2007.石鳖的结构与习性[J].水生态学杂志,27(3):46-47.
史博洋,李媛媛,王儒晓,等.2017.基于线粒体16S rR NA探讨渤海海区矮拟帽贝的种群生态遗传[J].四川动物,36(4):386-391.
Bandelt HJ,Forster P,R9hl A.1999.Median-joining networks for inferring intraspecific phylogenies[J].Molecular Biology and Evolution,16:37-48.
Coakes SJ.2013.SPSS version 20.0 for Windows[M].New York:John Wiley&Sons.
Cordero D,Delgado M,Liu B,et al.2017.Population genetics of the Manila clam(Ruditapes philippinarum)introduced in north America and Europe[J].Scientific Reports,7:39745.DOI:10.1038/srep39745.
Darriba D,Taboada GL,Doallo R,et al.2012.jM odelTest 2:more models,new heuristics and parallel computing[J].Nature Methods,9(8):772.DOI:10.1038/nmeth.2019.
Excoffier L,Lischer HEL.2010.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows[J].Molecular Ecology Resources,10(3):564-567.
Folmer O,Black M,Hoeh W,et al.1994.DNA primers for amplification of mitochondrial cytochrome c oxidase subunitⅠfrom diverse metazoan invertebrates[J].Molecular Marine Biology and Biotechnology,3(5):294-299.
Grant W,Bowen B.1998.Shallow population histories in deep evolutionary lineages of marine fishes:insights from sardines and anchovies and lessons for conservation[J].Journal of Heredity,89(5):415-426.
Guindon S,Delsuc F,Dufayard JF,et al.2010.Estimating maximum likelihood phylogenies with PhyM L[J].Methods in Molecular Biology,537:113-137.
Larkin MA,Blackshields G,Brown NP,et al.2007.Clustal Wand Clustal X version 2.0[J].Bioinformatics,23(21):2947-2948.
Lee HJ,Boulding EG.2010.Spatial and temporal population genetic structure of four northeastern Pacific littorinid gastropods:the effect of mode of larval development on variation at one mitochondrial and two nuclear DNA markers[J].Molecular Ecology,18(10):2165-2184.
Li S,Li Q,Yu H,et al.2015.Genetic variation and population structure of the Pacific oyster Crassostrea gigas,in the northwestern Pacific inferred from mitochondrial COⅠsequences[J].Fisheries Science,81(6):1071-1082.
Librado P,Rozas J.2009.DnaS P v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,25(11):1451-1452.
Monari M,Matozzo V,Foschi J,et al.2007.Effects of high temperatures on functional responses of haemocytes in the clam Chamelea gallina[J].Fish&Shellfish Immunology,22(1):98-114.
Ni G,Li Q,Kong L,et al.2012.Phylogeography of bivalve Cyclina sinensis:testing the historical glaciations and Changjiang River outflow hypotheses in northwestern Pacific[J].PLoS ONE,7(11):1-11.
Nylander JAA.2004.MRMODELTEST,version 2.0.Program distributed by the author[J].Evolutionary Biology Centre Uppsala University,2:1-2.
Palumbi SR.1994.Genetic divergence,reproductive isolation,and marine speciation[J].Annual Review of Ecology&Systematics,25(25):547-572.
Polzin T,Daneshmand SV.2003.On Steiner trees and minimum spanning trees in hypergraphs[J].Operations Research Letters,31(1):12-20.
Ronquist F,Teslenko M,Mark PVD,et al.2012.MrBayes3.2:efficient Bayesian phylogenetic inference and model choice across a large model space[J].Systematic Biology,61(3):539-542.
Shen KN,Jamandre BW,Hsu CC,et al.2011.Plio-Pleistocene sea level and temperature fluctuations in the northwestern Pacific promoted speciation in the globally-distributed flathead mullet Mugil cephalus[J].BMC Evolutionary Biology,11:83.
Surhone LM,Tennoe MT,Henssonow SF,et al.2010.Tree view[M].Hong Kong:Betascript Publishing:28-143.
Yu JH,Song JH,Minchul C,et al.2009.Effects of water temperature change on immune function in surf clams,Mactra veneriformis(Bivalvia:Mactridae)[J].Journal of Invertebrate Pathology,102(1):30-35.
Zhou N,Shen H,Cheng C,et al.2016.Genetic structure of Onchidium“struma”(Mollusca:Gastropoda:Eupulmonata)from the coastal area of China based on mt COⅠ[J].Mitochondrial DNA Part A:DNA Mapping Sequencing&Analysis,27(2):1319-1323.