环境因子对中国海矮拟帽贝种群遗传多样性的影响
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摘要
采用聚合酶链式反应和直接测序的方法研究了中国海矮拟帽贝(Patelloida pygmaea) 13个地理种群环境因子对其遗传多样性的影响。137个样本的COI部分序列(601 bp)中共发现217个多态位点,转换颠换比1. 25,界定30个单倍型。汕头种群呈现较高的遗传多样性,威海种群呈现较低的遗传多样性。与环境因子相关性分析发现,矮拟帽贝遗传多样性与年均温度、年均降水量、年均水汽压呈显著正相关(P <0. 05),与纬度、年均温度变异系数、日照百分率、日照时数呈显著负相关(P <0. 05)。形态主成分分析矮拟帽贝长重比(L/DW)、宽重比(W/DW)、高重比(H/DW)为形态变异主成分,且与年均降水量变异系数呈显著负相关(P <0. 05)。温度、降水、日照、水汽压是影响中国海矮拟帽贝遗传多样性的主导因子,南方种群比北方种群有更高的遗传多样性。
Patelloida pygmaea,widely distributed in the intertidal zone along the coast of China,can be used as a model organism for the study of ecological genetics,because it is suitable for a wide range of living environments and is significantly influenced by historical events,current environmental and climatic factors.In this study,the mitochondrion DNA cytochrome c oxidase subunit I( mt DNA COI) gene of P. pygmaea was selected as a molecular marker to study the effects of environmental factors on morphological variation and genetic diversity of P. pygmaea. We collected 137 samples from 13 populations along the coast of China. A total of 10 absolute morphology measurements were selected and converted into relative measurements. The partial sequence of mt DNA COI gene( 601 bp) was obtained by polymerase chain reaction( PCR) and DNA sequencing. The base content of mt DNA COI gene was A 24. 10%,T 37. 27%,C 16. 53%,G 22. 10%,and a total of 217 polymorphic loci were found,containing 139 transformations and 110 transversions( transformation/transversion = 1. 25),and 30 haplotypes were defined( 21. 89% of the total sample).Compared with 13 populations of P. pygmaea,the Shantou population showed higher genetic diversity and haplotype diversity was 0. 855 ± 0. 08 5,the nucleotide diversity was 0. 091 4 ± 0. 048 3,and the Weihai population showed the lowest genetic diversity( haplotype diversity 0. 200 ± 0. 154; nucleotide diversity0. 003 ± 0. 000 5). The results of AMOVA showed that the genetic variation of P. pygmaea was mainly derived from among populations( 89. 57%,P < 0. 001). The correlation analysis between environmental factors and genetic diversity showed that the genetic diversity of P. pygmaea was significantly positively correlated with annual average temperature,annual average precipitation and annual average vapor pressure( P < 0. 05),and was significantly negatively correlated with latitude,variation coefficient annual average temperature,sunshine duration and sunshine percentage( P < 0. 05). The results of correlation analysis between environmental factors and morphological factors showed that the principal components of morphological variation( length/dry weight,width/dry weight and height/dry weight) were significantly negatively correlated with the annual average precipitation( P < 0. 05). Temperature and precipitation were the dominant factors affecting the genetic diversity of P. pygmaea,and southern populations had higher genetic diversity than northern populations in China. The higher the annual mean temperature is,the higher the genetic diversity of the population is. It is speculated that environmental temperature is the direct factor affecting P. pygmaea metabolism and sexual maturity,and then affects population genetic diversity. The more stable the temperature is,the higher the genetic diversity is,which is basically consistent with other mollusc ecological research results. The effect of precipitation on water vapor content in the air is another major factor affecting genetic diversity of P. pygmaea. And rainfall shortens sunshine hours, ultimately leading to increased genetic diversity. The stable environment leads to higher population genetic diversity for P.pygmaea along the coast of China.
Patelloida pygmaea,widely distributed in the intertidal zone along the coast of China,can be used as a model organism for the study of ecological genetics,because it is suitable for a wide range of living environments and is significantly influenced by historical events,current environmental and climatic factors.In this study,the mitochondrion DNA cytochrome c oxidase subunit I( mt DNA COI) gene of P. pygmaea was selected as a molecular marker to study the effects of environmental factors on morphological variation and genetic diversity of P. pygmaea. We collected 137 samples from 13 populations along the coast of China. A total of 10 absolute morphology measurements were selected and converted into relative measurements. The partial sequence of mt DNA COI gene( 601 bp) was obtained by polymerase chain reaction( PCR) and DNA sequencing. The base content of mt DNA COI gene was A 24. 10%,T 37. 27%,C 16. 53%,G 22. 10%,and a total of 217 polymorphic loci were found,containing 139 transformations and 110 transversions( transformation/transversion = 1. 25),and 30 haplotypes were defined( 21. 89% of the total sample).Compared with 13 populations of P. pygmaea,the Shantou population showed higher genetic diversity and haplotype diversity was 0. 855 ± 0. 08 5,the nucleotide diversity was 0. 091 4 ± 0. 048 3,and the Weihai population showed the lowest genetic diversity( haplotype diversity 0. 200 ± 0. 154; nucleotide diversity0. 003 ± 0. 000 5). The results of AMOVA showed that the genetic variation of P. pygmaea was mainly derived from among populations( 89. 57%,P < 0. 001). The correlation analysis between environmental factors and genetic diversity showed that the genetic diversity of P. pygmaea was significantly positively correlated with annual average temperature,annual average precipitation and annual average vapor pressure( P < 0. 05),and was significantly negatively correlated with latitude,variation coefficient annual average temperature,sunshine duration and sunshine percentage( P < 0. 05). The results of correlation analysis between environmental factors and morphological factors showed that the principal components of morphological variation( length/dry weight,width/dry weight and height/dry weight) were significantly negatively correlated with the annual average precipitation( P < 0. 05). Temperature and precipitation were the dominant factors affecting the genetic diversity of P. pygmaea,and southern populations had higher genetic diversity than northern populations in China. The higher the annual mean temperature is,the higher the genetic diversity of the population is. It is speculated that environmental temperature is the direct factor affecting P. pygmaea metabolism and sexual maturity,and then affects population genetic diversity. The more stable the temperature is,the higher the genetic diversity is,which is basically consistent with other mollusc ecological research results. The effect of precipitation on water vapor content in the air is another major factor affecting genetic diversity of P. pygmaea. And rainfall shortens sunshine hours, ultimately leading to increased genetic diversity. The stable environment leads to higher population genetic diversity for P.pygmaea along the coast of China.
引文
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[8]JAFFE A L,CAMPBELL-STATON S C,LOSOS JB.Geographical variation in morphology and its environmental correlates in a widespread North American lizard,Anolis carolinensis(Squamata:Dactyloidae)[J].Biological Journal of the Linnean Society,2016,117(4):760-774.
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[10]TZENG T.Morphological variation between populations of spotted mackerel(Scomber australasicus)off Taiwan[J].Fisheries Research,2004,68(1):45-55.
[11]PEPIN P.Morphlogical,meristic,and genetic analysis of stock structure in juvenile Atlantic cod(Gadus morhua)from the Newfoundland shelf[J].Canadian Journal of Fisheries and Aquatic Sciences,1993,50(9):1924-1933.
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[13]WAYNE R K.Molecular markers,natural history and evolution[M].New York:Sinauer Associates,2004.
[14]HONDA M,YASUKAWA Y,REN H,et al.Phylogenetic relationships of the asian Box turtles of the genus Cuora sensu lato(Reptilia:Bataguridae)inferred from mitochondrial DNA sequences[J].Zoological Science,2002,19(11):1305-1312.
[15]SURHONE L M,TENNOE M T,HENSSONOW SF.Patelloida Pygmaea[M].Montana:Betascript Publishing,2010.
[16]LINDBERG D R.Systematics of Potamacmaea fluviatilis(Blanford):Abrackishwater Patellogastropod(Patelloidinae:Lottiidae)[J].Journal of Molluscan Studies,1990,56(2):309-316.
[17]NAKANO T,OZAWA T.Worldwide phylogeography of limpets of the order Patellogastropoda:Molecular,morphological and palaeontological evidence[J].Journal of Molluscan Studies,2007,73(1):79-99.
[18]KIRKENDALE L A,MEYER C P.Phylogeography of the Patelloida profunda group(Gastropoda:Lottidae):Diversification in a dispersal-driven marine system[J].Molecular Ecology,2010,13(9):2749-2762.
[19]TAKENORI S,TAKASHI O.Anatomy and systematic position of yayoiacmea,a new genus for Japanese tiny limpet“Collisella”oyamai Habe,1955(Gastropoda:Lottiidae)[J].The Japanese Journal of Malacology,1993,52(3):193-209.
[20]NI G,LI Q,KONG L,et al.Phylogeography of bivalve,Cyclina sinensis:Testing the historical glaciations and Changjiang River outflow hypotheses in Northwestern Pacific[J].Plos One,2012,7(11):e49487.
[21]史博洋,李媛媛,王儒晓,等.基于线粒体16SrRNA探讨渤海海区矮拟帽贝的种群生态遗传[J].四川动物,2017,36(4):386-391.SHI B Y,LI Y Y,WANG R X,et al.Population ecological genetics of Patelloida pygmaea based on mitochondrial 16S rRNA fragment sequences in the Bohai Sea[J].Sichuan Journal of Zoology,2017,36(4):386-391.
[22]FOLMER O,BLACK M,HOEH W,et al.DNAprimers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates[J].Molecular Marine Biology&Biotechnology,1994,3(5):294-299.
[23]KIRKPATRICK L A,FEENEY B C.A simple guide to IBM SPSS statistics for version 20.0[M].Cambridge:Wadsworth Publishing,2012.
[24]LIBRADO P,ROZAS J.Dna SP v5:A software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452.
[25]EXCOFFIER L,LISCHER H E L.Arlequin suite ver 3.5:A new series of programs to perform population genetics analyses under Linux and Windows[J].Molecular Ecology Resources,2010,10(3):564-567.
[26]KUMAR S,STECHER G,TAMURA K.MEGA7:Molecular evolutionary genetics analysis version 7.0for bigger datasets[J].Molecular Biology&Evolution,2016,33(7):1870.
[27]GRANT W S,BOWEN B W.Shallow population histories in deep evolutionary lineages of marine fishes:Insights from sardines and anchovies and lessons for conservation[J].Journal of Heredity,1998,89(5):415-426.
[28]MICHOD R E.Ecological genetics[J].Science,1981,212(4491):154-155.
[29]NEVO E.Genetic variation and climatic selection in the lizard Agama stellio in Israel and Sinai[J].Theoretical&Applied Genetics,1981,60(6):369-380.
[30]JIN Y T,LIU N F.Ecological genetics of Phrynocephalus vlangalii on the north Tibetan(Qinghai)Plateau:Correlation between environmental factors and population genetic variability[J].Biochemical Genetics,2008,46(9-10):598-604.
[31]KIM M,AHN I Y,CHEON J,et al.Molecular cloning and thermal stress-induced expression of a pi-class glutathione S-transferase(GST)in the Antarctic bivalve Laternula elliptica[J].Comparative Biochemistry&Physiology Part AMolecular&Integrative Physiology,2009,152(2):207-213.
[32]DGREMONT L,ERNANDE B,BéDIER E,et al.Summer mortality of hatchery-produced Pacific oyster spat(Crassostrea gigas).I.Estimation of genetic parameters for survival and growth[J].Aquaculture,2007,262(1):41-53.
[33]MALHAM S K,COTTER E,O’KEEFFE S,et al.Summer mortality of the Pacific oyster,Crassostrea gigas,in the Irish Sea:The influence of temperature and nutrients on health and survival[J].Aquaculture,2009,287(1):128-138.
[34]ELIZABETH C,SHELAGHK M,SELENA O K,et al.Summer mortality of the Pacific oyster,Crassostrea gigas,in the Irish Sea:The influence of growth,biochemistry and gametogenesis[J].Aquaculture,2010,303(1):8-21.
[35]JOHNSON Z I,ZINSER E R,COE A,et al.Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients[J].Science,2006,311(5768):1737-1740.
[36]MONARI M,MATOZZO V,FOSCHI J,et al.Effects of high temperatures on functional responses of haemocytes in the clam Chamelea gallina[J].Fish&Shellfish Immunology,2007,22(1):98-114.
[37]VANHALA T,RIJN C,BUNTJER J,et al.Environmental,phenotypic and genetic variation of wild barley(Hordeum spontaneum)from Israel[J].Euphytica,2004,137(3):297-309
[38]KOCHBA M,GAMBASH S,AVNIMELECH Y.Studies on slow release fertilizers:I.Effects of temperature,soil moisture,and water vapor pressure[J].Soil Science,1990,149(6):339.
[39]PORTER S C,AN Z.Correlation between climate events in the North Atlantic and China during the last glaciation[J].Nature,1995,375(6529):305-308.
[40]SORIA G,MERINO G,BRAND E V.Effect of increasing salinity on physiological response in juvenile scallops Argopecten purpuratus at two rearing temperatures[J].Aquaculture,2007,270(1):451-463.
[41]VERWEEN A,VINCX M,DEGRAER S.The effect of temperature and salinity on the survival of Mytilopsis leucophaeata larvae(Mollusca,Bivalvia):the search for environmental limits[J].Journal of Experimental Marine Biology&Ecology,2007,348(1-2):111-120.
[42]HA M,LI W H,CHEN Z J.External factors accelerate expression divergence between duplicate genes[J].Trends in Genetics,2007,23(4):162-166.
[43]KINSEY S T,ORSOY T,BERT T M,et al.Population structure ofthe Spanish sardine Sardinella aurita:natural morphological variation in a genetically homogeneous population[J].Marine Biology,1994,118(2):309-317.
[44]HUANG Z,LIU N,LUO S,et al.Ecological genetics of rusty-necklaced partridge(Alectoris magna):Evironmental factors and population genetic variability correlations[J].Korean Journal of Genetics,2007,29(2):115-120.
[45]CORRE V L,ROUX F,REBOUD X.DNApolymorphism at the FRIGIDA gene in Arabidopsis thaliana:Extensive nonsynonymous variation is consistent with local selection for flowering time[J].Molecular Biology&Evolution,2002,19(8):1261-1271.
[2]OSOVITZ C J,HOFMANN G E.Thermal historydependent expression of the hsp70 gene in purple sea urchins:Biogeographic patterns and the effect of temperature acclimation[J].Journal of Experimental Marine Biology&Ecology,2005,327(2):134-143.
[3]SCHNEIDER C J,CUNNINGHAM M,MORITZ C.Comparative phylogeography and the history of endemic vertebrates in the wet tropics rainforests of Australia[J].Molecular Ecology,2010,7(4):487-498.
[4]GEORGINA M.Scaling:Why is animal size so important?[J]Trends in Neurosciences,1985,8(61):548-549.
[5]YOMTOV Y,GEFFEN E.Recent spatial and temporal changes in body size of terrestrial vertebrates:probable causes and pitfalls[J].Biological Reviews,2011,86(2):531-541.
[6]MCNAB B K.On the ecological significance of Bergmann’s rule[J].Ecology,1971,52(5):845-854.
[7]MARTINEZ P A,MARTI D A,MOLINA W F,et al.Bergmann’s rule across the equator:a case study in Cerdocyon thous(Canidae)[J].Journal of Animal Ecology,2013,82(5):997-1008.
[8]JAFFE A L,CAMPBELL-STATON S C,LOSOS JB.Geographical variation in morphology and its environmental correlates in a widespread North American lizard,Anolis carolinensis(Squamata:Dactyloidae)[J].Biological Journal of the Linnean Society,2016,117(4):760-774.
[9]ROBY D,LAMBERT J D,SEVIGNY J.Morphometric and electrophoretic approaches to discrimination of capel[J].Journal Canadien Des Sciences Halieutiques,1991,48(11):2040-2050.
[10]TZENG T.Morphological variation between populations of spotted mackerel(Scomber australasicus)off Taiwan[J].Fisheries Research,2004,68(1):45-55.
[11]PEPIN P.Morphlogical,meristic,and genetic analysis of stock structure in juvenile Atlantic cod(Gadus morhua)from the Newfoundland shelf[J].Canadian Journal of Fisheries and Aquatic Sciences,1993,50(9):1924-1933.
[12]SCHEINER S M.Genetics and evolution of phenotypic plasticity[J].Annual Review of Ecology&Systematics,1993,24(1):35-68.
[13]WAYNE R K.Molecular markers,natural history and evolution[M].New York:Sinauer Associates,2004.
[14]HONDA M,YASUKAWA Y,REN H,et al.Phylogenetic relationships of the asian Box turtles of the genus Cuora sensu lato(Reptilia:Bataguridae)inferred from mitochondrial DNA sequences[J].Zoological Science,2002,19(11):1305-1312.
[15]SURHONE L M,TENNOE M T,HENSSONOW SF.Patelloida Pygmaea[M].Montana:Betascript Publishing,2010.
[16]LINDBERG D R.Systematics of Potamacmaea fluviatilis(Blanford):Abrackishwater Patellogastropod(Patelloidinae:Lottiidae)[J].Journal of Molluscan Studies,1990,56(2):309-316.
[17]NAKANO T,OZAWA T.Worldwide phylogeography of limpets of the order Patellogastropoda:Molecular,morphological and palaeontological evidence[J].Journal of Molluscan Studies,2007,73(1):79-99.
[18]KIRKENDALE L A,MEYER C P.Phylogeography of the Patelloida profunda group(Gastropoda:Lottidae):Diversification in a dispersal-driven marine system[J].Molecular Ecology,2010,13(9):2749-2762.
[19]TAKENORI S,TAKASHI O.Anatomy and systematic position of yayoiacmea,a new genus for Japanese tiny limpet“Collisella”oyamai Habe,1955(Gastropoda:Lottiidae)[J].The Japanese Journal of Malacology,1993,52(3):193-209.
[20]NI G,LI Q,KONG L,et al.Phylogeography of bivalve,Cyclina sinensis:Testing the historical glaciations and Changjiang River outflow hypotheses in Northwestern Pacific[J].Plos One,2012,7(11):e49487.
[21]史博洋,李媛媛,王儒晓,等.基于线粒体16SrRNA探讨渤海海区矮拟帽贝的种群生态遗传[J].四川动物,2017,36(4):386-391.SHI B Y,LI Y Y,WANG R X,et al.Population ecological genetics of Patelloida pygmaea based on mitochondrial 16S rRNA fragment sequences in the Bohai Sea[J].Sichuan Journal of Zoology,2017,36(4):386-391.
[22]FOLMER O,BLACK M,HOEH W,et al.DNAprimers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates[J].Molecular Marine Biology&Biotechnology,1994,3(5):294-299.
[23]KIRKPATRICK L A,FEENEY B C.A simple guide to IBM SPSS statistics for version 20.0[M].Cambridge:Wadsworth Publishing,2012.
[24]LIBRADO P,ROZAS J.Dna SP v5:A software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452.
[25]EXCOFFIER L,LISCHER H E L.Arlequin suite ver 3.5:A new series of programs to perform population genetics analyses under Linux and Windows[J].Molecular Ecology Resources,2010,10(3):564-567.
[26]KUMAR S,STECHER G,TAMURA K.MEGA7:Molecular evolutionary genetics analysis version 7.0for bigger datasets[J].Molecular Biology&Evolution,2016,33(7):1870.
[27]GRANT W S,BOWEN B W.Shallow population histories in deep evolutionary lineages of marine fishes:Insights from sardines and anchovies and lessons for conservation[J].Journal of Heredity,1998,89(5):415-426.
[28]MICHOD R E.Ecological genetics[J].Science,1981,212(4491):154-155.
[29]NEVO E.Genetic variation and climatic selection in the lizard Agama stellio in Israel and Sinai[J].Theoretical&Applied Genetics,1981,60(6):369-380.
[30]JIN Y T,LIU N F.Ecological genetics of Phrynocephalus vlangalii on the north Tibetan(Qinghai)Plateau:Correlation between environmental factors and population genetic variability[J].Biochemical Genetics,2008,46(9-10):598-604.
[31]KIM M,AHN I Y,CHEON J,et al.Molecular cloning and thermal stress-induced expression of a pi-class glutathione S-transferase(GST)in the Antarctic bivalve Laternula elliptica[J].Comparative Biochemistry&Physiology Part AMolecular&Integrative Physiology,2009,152(2):207-213.
[32]DGREMONT L,ERNANDE B,BéDIER E,et al.Summer mortality of hatchery-produced Pacific oyster spat(Crassostrea gigas).I.Estimation of genetic parameters for survival and growth[J].Aquaculture,2007,262(1):41-53.
[33]MALHAM S K,COTTER E,O’KEEFFE S,et al.Summer mortality of the Pacific oyster,Crassostrea gigas,in the Irish Sea:The influence of temperature and nutrients on health and survival[J].Aquaculture,2009,287(1):128-138.
[34]ELIZABETH C,SHELAGHK M,SELENA O K,et al.Summer mortality of the Pacific oyster,Crassostrea gigas,in the Irish Sea:The influence of growth,biochemistry and gametogenesis[J].Aquaculture,2010,303(1):8-21.
[35]JOHNSON Z I,ZINSER E R,COE A,et al.Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients[J].Science,2006,311(5768):1737-1740.
[36]MONARI M,MATOZZO V,FOSCHI J,et al.Effects of high temperatures on functional responses of haemocytes in the clam Chamelea gallina[J].Fish&Shellfish Immunology,2007,22(1):98-114.
[37]VANHALA T,RIJN C,BUNTJER J,et al.Environmental,phenotypic and genetic variation of wild barley(Hordeum spontaneum)from Israel[J].Euphytica,2004,137(3):297-309
[38]KOCHBA M,GAMBASH S,AVNIMELECH Y.Studies on slow release fertilizers:I.Effects of temperature,soil moisture,and water vapor pressure[J].Soil Science,1990,149(6):339.
[39]PORTER S C,AN Z.Correlation between climate events in the North Atlantic and China during the last glaciation[J].Nature,1995,375(6529):305-308.
[40]SORIA G,MERINO G,BRAND E V.Effect of increasing salinity on physiological response in juvenile scallops Argopecten purpuratus at two rearing temperatures[J].Aquaculture,2007,270(1):451-463.
[41]VERWEEN A,VINCX M,DEGRAER S.The effect of temperature and salinity on the survival of Mytilopsis leucophaeata larvae(Mollusca,Bivalvia):the search for environmental limits[J].Journal of Experimental Marine Biology&Ecology,2007,348(1-2):111-120.
[42]HA M,LI W H,CHEN Z J.External factors accelerate expression divergence between duplicate genes[J].Trends in Genetics,2007,23(4):162-166.
[43]KINSEY S T,ORSOY T,BERT T M,et al.Population structure ofthe Spanish sardine Sardinella aurita:natural morphological variation in a genetically homogeneous population[J].Marine Biology,1994,118(2):309-317.
[44]HUANG Z,LIU N,LUO S,et al.Ecological genetics of rusty-necklaced partridge(Alectoris magna):Evironmental factors and population genetic variability correlations[J].Korean Journal of Genetics,2007,29(2):115-120.
[45]CORRE V L,ROUX F,REBOUD X.DNApolymorphism at the FRIGIDA gene in Arabidopsis thaliana:Extensive nonsynonymous variation is consistent with local selection for flowering time[J].Molecular Biology&Evolution,2002,19(8):1261-1271.