基于DNA条形码的物种丰富度估计:以宿迁地区鳞翅目蛾类为例
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摘要
为了探究基于DNA条形码方法量化物种多样性指标的可行性,本研究以江苏省宿迁地区蛾类群落为例,基于DNA条形码方法估计群落物种丰富度并绘制等级多度分布曲线(rank-abundance curves),同时与基于传统形态学的对应指标进行比较。结果表明:(1)基于DNA条形码的物种丰富度估计与基于形态的物种丰富度估计之间没有显著差异;(2)基于形态和DNA条形码的等级多度分布曲线趋势一致,通过K-S检测发现二者之间没有显著性差异(P>0.05)。结果显示,基于DNA条形码的物种丰富度估计能够在一定程度上补充基于形态学的方法,可以尝试将其应用于蛾类群落生态学调查研究中。
To explore the feasibility of assessing species diversity using DNA barcoding, we investigated this approach by focusing on moths species(Lepidoptera) in Suqian, China. The study evaluated community species richness and rank-abundance curves using the DNA barcoding method, and compared it with the traditional morphology method. Results indicated that there was no significant difference between the DNA barcode-based approach and the morphology-based approach. All DNA barcode-based rank-abundance curves gave similar and clear patterns when compared with morphology-based curves(Kolmogorov-Smirnov two sample test, P > 0.05). Our results indicate that the DNA barcode-based approach is able to be used to estimate species richness.
To explore the feasibility of assessing species diversity using DNA barcoding, we investigated this approach by focusing on moths species(Lepidoptera) in Suqian, China. The study evaluated community species richness and rank-abundance curves using the DNA barcoding method, and compared it with the traditional morphology method. Results indicated that there was no significant difference between the DNA barcode-based approach and the morphology-based approach. All DNA barcode-based rank-abundance curves gave similar and clear patterns when compared with morphology-based curves(Kolmogorov-Smirnov two sample test, P > 0.05). Our results indicate that the DNA barcode-based approach is able to be used to estimate species richness.
引文
Austerlitz F,David O,Schaeffer B,Bleakley K,Olteanu MLeblois R,Veuille M,Laredo C(2009)DNA barcode analysis:a comparison of phylogenetic and statistical classification methods.BMC Bioinformatics,10(Suppl.14),1-13.
Blaxter M,Floyd R(2003)Molecular taxonomics for biodiversity surveys:already a reality.Trends in Ecology and Evolution,18,268-269.
Boykin LM,Armstrong KF,Kubatko L,Barro PD(2012)Species delimitation and global biosecurity.Evolutionary Bioinformatics,8,1-37.
Burnham KP,Anderson DR(2002)Model Selection and Multimodel Inference:A Practical Information-Theoretic Approach.Springer-Verlag,New York.
Chao A(1984)Nonparametric estimation of the number of classes in a population.Scandinavian Journal of Statistics11,265-270.
Chao A,Hwang WH,Chen YC,Kuo CY(2000)Estimating the number of shared species in two communities.Statistica Sinica,10,227-246.
Colwell RK,Coddington JA(1994)Estimating terrestrial biodiversity through extrapolation.Philosophical Transactions of the Royal Society B:Biological Sciences,345,101-118.
Darriba D,Taboada GL,Doallo R,Posada D(2012)j ModelTest 2:more models,new heuristics and parallel computing Nature Methods,9,772.
Deca?ns T,Porco D,James SW,Brown G,Da SE,Dupont LLapied E,Rougerie R,Taberlet P,Roy V(2015)Dissecting tropical earthworm biodiversity patterns in tropical rainforests through the use of DNA barcoding.Genome,58,210.
Dinc?V,Zakharov EV,Hebert PDN,Vila R(2011)Complete DNA barcode reference library for a country’s butterfly fauna reveals high performance for temperate Europe.Proceedings of the Royal Society B:Biological Sciences,278,347-355.
Drummond AJ,Ho SYW,Phillips MJ,Rambaut A(2006)Relaxed phylogenetics and dating with confidence.PLo S Biology,4,e88.
Drummond AJ,Rambaut A(2007)BEAST:Bayesian evolutionary analysis by sampling trees.BMC Evolutionary Biology,7,214.
Ebach MC,Holdrege C(2005)DNA barcoding is no substitute for taxonomy.Nature,434,697.
Ekrem T,Willassen E,Stur E(2007)A comprehensive DNAsequence library is essential for identification with DNAbarcodes.Molecular Phylogenetics and Evolution,43,530-542.
Fujisawa T,Barraclough TG(2013)Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent(GMYC)approach:a revised method and evaluation on simulated datasets.Systematic Biology,62,707-724.
Gomez-Alvarez V,King GM,Nüsslein K(2007)Comparative bacterial diversity in recent Hawaiian volcanic deposits of different ages.FEMS Microbiology Ecology,60,60-73.
Hebert PDN,Cywinska A,Ball SL,de Waard JR(2003)Biological identifications through DNA barcodes.Proceedings of the Royal Society of London B:Biological Sciences,270,313-321.
Hebert PDN,Humble LM(2011)A comprehensive DNA barcode library for the looper moths(Lepidoptera:Geometridae)of British Columbia,Canada.PLo S ONE,6,e18290.
Hebert PDN,Penton EH,Burns JM,Janzen DH,Hallwachs W(2004)Ten species in one:DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator.Proceedings of the National Academy of Sciences,USA,101,14812-14817.
Herrera A,Héry M,Stach JEM,JaffréT,Normand P,Navarro E(2007)Species richness and phylogenetic diversity comparisons of soil microbial communities affected by nickel-mining and revegetation efforts in New Caledonia.European Journal of Soil Biology,43,130-139.
Hickerson MJ,Meyer CP,Moritz C(2006)DNA barcoding will often fail to discover new animal species over broad parameter space.Systematic Biology,55,729-739.
Jin Q,He LJ,Zhang AB(2012)A simple 2D non-parametric resampling statistical approach to assess confidence in species identification in DNA barcoding-an alternative to Likelihood and Bayesian approaches.PLo S ONE,7,e50831.
Jin Q,Han HL,Hu XM,Li XH,Zhu CD,Ho SYW,Ward RD,Zhang AB(2013)Quantifying species diversity with a DNAbarcoding-based method:Tibetan moth species(Noctuidae)on the Qinghai-Tibetan Plateau.PLo S ONE,8,e64428.
Jin Q,Zhang AB(2013)Distance-based DNA barcoding methods for insects.Chinese Journal of Applied Entomology,50,283-287.(in Chinese)[金倩,张爱兵(2013)昆虫DNA条形码分析中的距离方法.应用昆虫学报,50,283-287.]
Kempton RA,Taylor LR(1974)Log-series and log-normal parameters as diversity discriminants for the Lepidoptera.The Journal of Animal Ecology,43,381-399.
Leray M,Knowlton N(2015)DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity.Proceedings of the National Academy of Sciences,USA,112,2076-2081.
Li X,Yang Y,Henry RJ,Rossetto M,Wang Y,Chen S(2015)Plant DNA barcoding:from gene to genome.Biological Reviews,90,157-166.
Mac Arthur RH(1957)On the relative abundance of bird species.Proceedings of the National Academy of Sciences,USA,43,293-295.
Mandelbrot BB(1983)The Fractal Geometry of Nature.W.H.Freeman and Company,San Francisco.
May RM(1988)How many species are there on earth?Science,241,1441-1449.
Meyer CP,Paulay G(2005)DNA barcoding:error rates based on comprehensive sampling.PLo S Biology,3,e422.
O’hara RB(2005)Species richness estimators:how many species can dance on the head of a pin?Journal of Animal Ecology,74,375-386.
Oline DK(2006)Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils.Applied and Environmental Microbiology,72,6965-6971.
Ovreas L(2000)Population and community level approaches for analyzing microbial diversity in natural environments.Ecology Letters,3,236-251.
Pons J,Barraclough TG,Gomez-Zurita J,Cardoso A,Duran DP,Hazell S,Kamoun S,Sumlin WD,Vogler AP(2006)Sequence-based species delimitation for the DNA taxonomy of undescribed insects.Systematic Biology,55,595-609.
Preston FW(1948)The commonness,and rarity,of species.Ecology,29,254-283.
Puillandre N,Lambert A,Brouillet S,Achaz G(2012)ABGD,Automatic Barcode Gap Discovery for primary species delimitation.Molecular Ecology,21,1864-1877.
Qin J,Zhang YZ,Zhou X,Kong XB,Wei SJ,Ward RD,Zhang AB(2015)Mitochondrial phylogenomics and genetic relationships of closely related pine moth(Lasiocampidae:Dendrolimus)species in China,using whole mitochondrial genomes.BMC Genomics,16,428.
Quicke DLJ,Smith MA,Janzen DH,Hallwachs W,Fernandez-Triana J,Laurenne NM,Zaldivar-Riveron A,Shaw MR,Broad GR,Klopfstein S,Shaw SR,Hrcek J,Hebert PDN,Miller SE,Rodriguez JJ,Whitfield JB,Sharkey MJ,Sharanowski BJ,Jussila R,Gauld ID,Chesters D,Vogler AP(2012)Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny(Hymenoptera:Ichneumonoidea):data release and new measure of taxonomic congruence Molecular Ecology Resources,12,676-685.
Rambaut A,Drummond AJ(2007)Tracer v1.4:MCMC Trace Analyses Tool.http://tree.bio.ed.ac.uk/software/tracer/(accessed on 2014-10-08).
Ratnasingham S,Hebert PD(2013)A DNA-based registry for all animal species:the Barcode Index Number(BIN)system.PLo S ONE,8,e66213.
Rubinoff D(2006)DNA barcoding evolves into the familiar Conservation Biology,20,1548-1549.
Saitou N,Nei M(1987)The neighbor-joining method:a new method for reconstructing phylogenetic trees.Molecular Biology and Evolution,4,406-425.
Schindel DE,Miller SE(2005)DNA barcoding a useful tool for taxonomists.Nature,435,17.
Smith MA,Fisher BL,Hebert PDN(2005)DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group:the ants of Madagascar.Philosophical Transactions of the Royal Society B:Biological Sciences,3601825-1834.
Tokeshi M(1990)Niche apportionment or random assortment:species abundance patterns revisited.The Journal of Animal Ecology,10,1129-1146.
Vrijenhoek R(1994)DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates.Molecular Marine Biology and Biotechnology,3,294-299.
Ward RD,Hanner R,Hebert PDN(2009)The campaign to DNA barcode all fishes,FISH-BOL.Journal of Fish Biology,74,329-356.
Wiemers M,Fiedler K(2007)Does the DNA barcoding gap exist?-a case study in blue butterflies(Lepidoptera:Lycaenidae).Frontiers in Zoology,4,8.
Wilson JB(1991)Methods for fitting dominance/diversity curves.Journal of Vegetation Science,2,35-46.
Zhang AB,Feng J,Ward RD,Wan P,Gao Q,Wu J,Zhao WZ(2012a)A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.PLo S ONE7,e30986.
Zhang AB,Muster C,Liang HB,Zhu CD,Crozier R,Wan PFeng J,Ward RD(2012b)A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding Molecular Ecology,21,1848-1863.
Zhang AB,Sikes DS,Muster C,Li SQ(2008)Inferring species membership using DNA sequences with back-propagation neural networks.Systematic Biology,57,202-215.
Zipf GK(1949)Human Behavior and the Principle of Least Effort.Hafner,New York.
Blaxter M,Floyd R(2003)Molecular taxonomics for biodiversity surveys:already a reality.Trends in Ecology and Evolution,18,268-269.
Boykin LM,Armstrong KF,Kubatko L,Barro PD(2012)Species delimitation and global biosecurity.Evolutionary Bioinformatics,8,1-37.
Burnham KP,Anderson DR(2002)Model Selection and Multimodel Inference:A Practical Information-Theoretic Approach.Springer-Verlag,New York.
Chao A(1984)Nonparametric estimation of the number of classes in a population.Scandinavian Journal of Statistics11,265-270.
Chao A,Hwang WH,Chen YC,Kuo CY(2000)Estimating the number of shared species in two communities.Statistica Sinica,10,227-246.
Colwell RK,Coddington JA(1994)Estimating terrestrial biodiversity through extrapolation.Philosophical Transactions of the Royal Society B:Biological Sciences,345,101-118.
Darriba D,Taboada GL,Doallo R,Posada D(2012)j ModelTest 2:more models,new heuristics and parallel computing Nature Methods,9,772.
Deca?ns T,Porco D,James SW,Brown G,Da SE,Dupont LLapied E,Rougerie R,Taberlet P,Roy V(2015)Dissecting tropical earthworm biodiversity patterns in tropical rainforests through the use of DNA barcoding.Genome,58,210.
Dinc?V,Zakharov EV,Hebert PDN,Vila R(2011)Complete DNA barcode reference library for a country’s butterfly fauna reveals high performance for temperate Europe.Proceedings of the Royal Society B:Biological Sciences,278,347-355.
Drummond AJ,Ho SYW,Phillips MJ,Rambaut A(2006)Relaxed phylogenetics and dating with confidence.PLo S Biology,4,e88.
Drummond AJ,Rambaut A(2007)BEAST:Bayesian evolutionary analysis by sampling trees.BMC Evolutionary Biology,7,214.
Ebach MC,Holdrege C(2005)DNA barcoding is no substitute for taxonomy.Nature,434,697.
Ekrem T,Willassen E,Stur E(2007)A comprehensive DNAsequence library is essential for identification with DNAbarcodes.Molecular Phylogenetics and Evolution,43,530-542.
Fujisawa T,Barraclough TG(2013)Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent(GMYC)approach:a revised method and evaluation on simulated datasets.Systematic Biology,62,707-724.
Gomez-Alvarez V,King GM,Nüsslein K(2007)Comparative bacterial diversity in recent Hawaiian volcanic deposits of different ages.FEMS Microbiology Ecology,60,60-73.
Hebert PDN,Cywinska A,Ball SL,de Waard JR(2003)Biological identifications through DNA barcodes.Proceedings of the Royal Society of London B:Biological Sciences,270,313-321.
Hebert PDN,Humble LM(2011)A comprehensive DNA barcode library for the looper moths(Lepidoptera:Geometridae)of British Columbia,Canada.PLo S ONE,6,e18290.
Hebert PDN,Penton EH,Burns JM,Janzen DH,Hallwachs W(2004)Ten species in one:DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator.Proceedings of the National Academy of Sciences,USA,101,14812-14817.
Herrera A,Héry M,Stach JEM,JaffréT,Normand P,Navarro E(2007)Species richness and phylogenetic diversity comparisons of soil microbial communities affected by nickel-mining and revegetation efforts in New Caledonia.European Journal of Soil Biology,43,130-139.
Hickerson MJ,Meyer CP,Moritz C(2006)DNA barcoding will often fail to discover new animal species over broad parameter space.Systematic Biology,55,729-739.
Jin Q,He LJ,Zhang AB(2012)A simple 2D non-parametric resampling statistical approach to assess confidence in species identification in DNA barcoding-an alternative to Likelihood and Bayesian approaches.PLo S ONE,7,e50831.
Jin Q,Han HL,Hu XM,Li XH,Zhu CD,Ho SYW,Ward RD,Zhang AB(2013)Quantifying species diversity with a DNAbarcoding-based method:Tibetan moth species(Noctuidae)on the Qinghai-Tibetan Plateau.PLo S ONE,8,e64428.
Jin Q,Zhang AB(2013)Distance-based DNA barcoding methods for insects.Chinese Journal of Applied Entomology,50,283-287.(in Chinese)[金倩,张爱兵(2013)昆虫DNA条形码分析中的距离方法.应用昆虫学报,50,283-287.]
Kempton RA,Taylor LR(1974)Log-series and log-normal parameters as diversity discriminants for the Lepidoptera.The Journal of Animal Ecology,43,381-399.
Leray M,Knowlton N(2015)DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity.Proceedings of the National Academy of Sciences,USA,112,2076-2081.
Li X,Yang Y,Henry RJ,Rossetto M,Wang Y,Chen S(2015)Plant DNA barcoding:from gene to genome.Biological Reviews,90,157-166.
Mac Arthur RH(1957)On the relative abundance of bird species.Proceedings of the National Academy of Sciences,USA,43,293-295.
Mandelbrot BB(1983)The Fractal Geometry of Nature.W.H.Freeman and Company,San Francisco.
May RM(1988)How many species are there on earth?Science,241,1441-1449.
Meyer CP,Paulay G(2005)DNA barcoding:error rates based on comprehensive sampling.PLo S Biology,3,e422.
O’hara RB(2005)Species richness estimators:how many species can dance on the head of a pin?Journal of Animal Ecology,74,375-386.
Oline DK(2006)Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils.Applied and Environmental Microbiology,72,6965-6971.
Ovreas L(2000)Population and community level approaches for analyzing microbial diversity in natural environments.Ecology Letters,3,236-251.
Pons J,Barraclough TG,Gomez-Zurita J,Cardoso A,Duran DP,Hazell S,Kamoun S,Sumlin WD,Vogler AP(2006)Sequence-based species delimitation for the DNA taxonomy of undescribed insects.Systematic Biology,55,595-609.
Preston FW(1948)The commonness,and rarity,of species.Ecology,29,254-283.
Puillandre N,Lambert A,Brouillet S,Achaz G(2012)ABGD,Automatic Barcode Gap Discovery for primary species delimitation.Molecular Ecology,21,1864-1877.
Qin J,Zhang YZ,Zhou X,Kong XB,Wei SJ,Ward RD,Zhang AB(2015)Mitochondrial phylogenomics and genetic relationships of closely related pine moth(Lasiocampidae:Dendrolimus)species in China,using whole mitochondrial genomes.BMC Genomics,16,428.
Quicke DLJ,Smith MA,Janzen DH,Hallwachs W,Fernandez-Triana J,Laurenne NM,Zaldivar-Riveron A,Shaw MR,Broad GR,Klopfstein S,Shaw SR,Hrcek J,Hebert PDN,Miller SE,Rodriguez JJ,Whitfield JB,Sharkey MJ,Sharanowski BJ,Jussila R,Gauld ID,Chesters D,Vogler AP(2012)Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny(Hymenoptera:Ichneumonoidea):data release and new measure of taxonomic congruence Molecular Ecology Resources,12,676-685.
Rambaut A,Drummond AJ(2007)Tracer v1.4:MCMC Trace Analyses Tool.http://tree.bio.ed.ac.uk/software/tracer/(accessed on 2014-10-08).
Ratnasingham S,Hebert PD(2013)A DNA-based registry for all animal species:the Barcode Index Number(BIN)system.PLo S ONE,8,e66213.
Rubinoff D(2006)DNA barcoding evolves into the familiar Conservation Biology,20,1548-1549.
Saitou N,Nei M(1987)The neighbor-joining method:a new method for reconstructing phylogenetic trees.Molecular Biology and Evolution,4,406-425.
Schindel DE,Miller SE(2005)DNA barcoding a useful tool for taxonomists.Nature,435,17.
Smith MA,Fisher BL,Hebert PDN(2005)DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group:the ants of Madagascar.Philosophical Transactions of the Royal Society B:Biological Sciences,3601825-1834.
Tokeshi M(1990)Niche apportionment or random assortment:species abundance patterns revisited.The Journal of Animal Ecology,10,1129-1146.
Vrijenhoek R(1994)DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates.Molecular Marine Biology and Biotechnology,3,294-299.
Ward RD,Hanner R,Hebert PDN(2009)The campaign to DNA barcode all fishes,FISH-BOL.Journal of Fish Biology,74,329-356.
Wiemers M,Fiedler K(2007)Does the DNA barcoding gap exist?-a case study in blue butterflies(Lepidoptera:Lycaenidae).Frontiers in Zoology,4,8.
Wilson JB(1991)Methods for fitting dominance/diversity curves.Journal of Vegetation Science,2,35-46.
Zhang AB,Feng J,Ward RD,Wan P,Gao Q,Wu J,Zhao WZ(2012a)A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.PLo S ONE7,e30986.
Zhang AB,Muster C,Liang HB,Zhu CD,Crozier R,Wan PFeng J,Ward RD(2012b)A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding Molecular Ecology,21,1848-1863.
Zhang AB,Sikes DS,Muster C,Li SQ(2008)Inferring species membership using DNA sequences with back-propagation neural networks.Systematic Biology,57,202-215.
Zipf GK(1949)Human Behavior and the Principle of Least Effort.Hafner,New York.