生物多样性 ›› 2016, Vol. 24 ›› Issue (11): 1296-1305.doi: 10.17520/biods.2016202

• • 上一篇    下一篇

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

金倩1, 2, 陈芬1, 罗桂杰1, 蔡卫佳1, 刘旭1, 王昊1, 杨采青2, 郝梦迪2, 张爱兵2, *()   

  1. 1.江苏省农业科学院宿迁农科所, 江苏宿迁 223800
    2.首都师范大学生命科学学院, 北京 100048
  • 收稿日期:2016-07-22 接受日期:2016-11-02 出版日期:2016-11-20
  • 通讯作者: 张爱兵 E-mail:zhangab2008@mail.cnu.edu.cn
  • 基金项目:
    国家杰出青年基金(31425023)、国家自然科学基金(31272340)、国家自然科学基金委青年科学基金项目(31601877)和宿迁市自主创新项目(SQCX2015-06)

Estimation of species richness of moths (Insecta: Lepidoptera) based on DNA barcoding in Suqian, China

Qian Jin1, 2, Fen Chen1, Guijie Luo1, Weijia Cai1, Xu Liu1, Hao Wang1, Caiqing Yang2, Mengdi Hao2, Aibing Zhang2, *()   

  1. 1 Suqian Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Suqian, Jiangsu 223800
    2 College of Life Sciences, Capital Normal University, Beijing 100048
  • Received:2016-07-22 Accepted:2016-11-02 Online:2016-11-20
  • Contact: Zhang Aibing E-mail:zhangab2008@mail.cnu.edu.cn

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。

关键词: 鳞翅目, DNA条形码, 物种丰富度, 等级多度分布曲线

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.

Key words: Lepidoptera, DNA barcoding, species richness, rank-abundance curves

图1

ABGD方法划分MOTU结果"

表1

ABGD方法MOTU分组结果与形态种类对照"

MOTU 种名 Species MOTU 种名 Species
MOTU01 Lacanobia contigua MOTU34 Parapoynx vittalis
MOTU02 Agrotis segetum 黄地老虎 MOTU35 Heliothis assulta 烟青虫
MOTU03 Conogethes punctiferalis 桃蛀螟 MOTU36 Herminia grisealis
MOTU04 Nola cicatricalis MOTU37 Spodoptera depravata
MOTU05 Hipoepa fractalis 中影单跗夜蛾 MOTU38 Scopula subpunctaria
MOTU06 Oraesia lata 平嘴壶夜蛾 MOTU39 Diaphania indica 瓜绢野螟
MOTU07 Spodoptera litura 斜纹夜蛾 MOTU40 Botyodes diniasalis 黄翅缀叶野螟
MOTU08 Uropyia meticulodina 核桃美舟蛾 MOTU41 Emmelia trabealis 谐夜蛾
MOTU09 Evergestis extimalis MOTU42 Termioptycha nigrescens
MOTU10 Mythimna separate MOTU43 Ipimorpha subtusa 杨逸色夜蛾
MOTU11 Ctenoplusia albostriata MOTU44 Spilosoma lubricipeda
MOTU12 Peridea lativitta 侧带内斑舟蛾 MOTU45 Parapediasia teterrellus
MOTU13 Thyas juno 肖毛翅夜蛾 MOTU46 Adoxophyes orana
MOTU14 Nephopterix fumella MOTU47 Simplicia rectalis 黑点贫夜蛾
MOTU15 Spodoptera exigua 甜菜夜蛾 MOTU48 Glyptoteles leucacrinella 亮雕斑螟
MOTU16 Oglasa consanguis MOTU49 Somena scintillans
MOTU17 Diaphania perspectalis 黄杨绢野螟 MOTU50 Anadevidia peponis 葫芦夜蛾
MOTU18 Athetis lepigone MOTU51 Hypocala subsatura 苹梢鹰夜蛾
MOTU19 Miyakea raddeella MOTU52 Choristoneura diversana 异色卷蛾
MOTU20 Herpetogramma pseudomagna 狭翅切叶野螟 MOTU53 Choristoneura luticostana 棕色卷蛾
MOTU21 Axylia putris 朽木夜蛾 MOTU54 Archips betulana; Archips podana
MOTU22 Mocis ancilla MOTU55 Palpita nigropunctalis 白蜡绢须野螟
MOTU23 Mecyna tricolor MOTU56 Epiblema foenella 白钩小卷蛾
MOTU24 Mamestra brassicae 甘蓝夜蛾 MOTU57 Grammodes geometrica 象夜蛾
MOTU25 Xanthorhoe quadrifasiata MOTU58;
MOTU60
Plusia nadeja
MOTU26 Euproctis similis MOTU59 Sphinx caligineus
MOTU27 Zanclognatha lunalis 朽镰须夜蛾 MOTU61 Acronicta rumicis 梨剑纹夜蛾
MOTU28 Theretra japonica MOTU62 Herminia tarsipennalis
MOTU29 Herminia tarsicrinalis MOTU63 Pangrapta trimantesalis
MOTU30 Eremodrina morosa MOTU64 Eutelia hamulatrix 沟尾夜蛾
MOTU31 Helicoverpa armigera 棉铃虫 MOTU65 Plusilla rosalia
MOTU32 Nomophila noctuella MOTU66 Bertula bistrigata
MOTU33 Dysgonia mandschuriana MOTU67 Gastropacha populifolia 杨枯叶蛾

图2

121条单倍型基于超度量树绘制的时间-谱系数量关系图。曲线表示支长速率, 支长速率急剧上升的变化转折点对应物种界定的数量。"

图3

基于不同方法的物种丰富度估计结果。粉红色表示基于ABGD方法的结果, 绿色表示基于GMYC方法的结果, 蓝色表示形态学结果, 黑色误差线表示置信区间。"

图4

等级多度分布曲线及模型拟合。a-1) 基于形态的等级多度分布曲线, a-2) 基于ABGD方法的等级多度分布曲线, a-3) 基于GMYC方法的等级多度分布曲线; b-1) 基于形态学的物种多度模型, b-2) 基于ABGD方法的物种多度模型, b-3) 基于GMYC方法的物种多度模型。黑点表示实际观测数据, 黑色曲线是零模型断棍模型, 红色曲线是生态位优先占领模型, 绿色曲线是正态分布模型, 深蓝色曲线是Zipf模型, 淡蓝色曲线是Zipf-Mandelbrot模型。"

1 Austerlitz F, David O, Schaeffer B, Bleakley K, Olteanu M, Leblois R, Veuille M, Laredo C (2009) DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. BMC Bioinformatics, 10(Suppl. 14), 1-13.
2 Blaxter M, Floyd R (2003) Molecular taxonomics for biodiversity surveys: already a reality. Trends in Ecology and Evolution, 18, 268-269.
3 Boykin LM, Armstrong KF, Kubatko L, Barro PD (2012) Species delimitation and global biosecurity. Evolutionary Bioinformatics, 8, 1-37.
4 Burnham KP, Anderson DR (2002) Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach. Springer-Verlag, New York.
5 Chao A (1984) Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics, 11, 265-270.
6 Chao A, Hwang WH, Chen YC, Kuo CY (2000) Estimating the number of shared species in two communities. Statistica Sinica, 10, 227-246.
7 Colwell RK, Coddington JA (1994) Estimating terrestrial biodiversity through extrapolation. Philosophical Transactions of the Royal Society B: Biological Sciences, 345, 101-118.
8 Darriba D, Taboada GL, Doallo R, Posada D (2012) jModel- Test 2: more models, new heuristics and parallel computing. Nature Methods, 9, 772.
9 Decaëns T, Porco D, James SW, Brown G, Da SE, Dupont L, Lapied 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.
10 Dincă 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.
11 Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biology, 4, e88.
12 Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
13 Ebach MC, Holdrege C (2005) DNA barcoding is no substitute for taxonomy. Nature, 434, 697.
14 Ekrem T, Willassen E, Stur E (2007) A comprehensive DNA sequence library is essential for identification with DNA barcodes. Molecular Phylogenetics and Evolution, 43, 530-542.
15 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.
16 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.
17 Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences, 270, 313-321.
18 Hebert PDN, Humble LM (2011) A comprehensive DNA barcode library for the looper moths (Lepidoptera: Geometridae) of British Columbia, Canada. PLoS ONE, 6, e18290.
19 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.
20 Herrera A, Héry M, Stach JEM, Jaffré T, 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.
21 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.
22 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. PLoS ONE, 7, e50831.
23 Jin Q, Han HL, Hu XM, Li XH, Zhu CD, Ho SYW, Ward RD, Zhang AB (2013) Quantifying species diversity with a DNA barcoding-based method: Tibetan moth species (Noctuidae) on the Qinghai-Tibetan Plateau. PLoS ONE, 8, e64428.
24 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.]
25 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.
26 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.
27 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.
28 MacArthur RH (1957) On the relative abundance of bird species. Proceedings of the National Academy of Sciences, USA, 43, 293-295.
29 Mandelbrot BB (1983) The Fractal Geometry of Nature. W.H. Freeman and Company, San Francisco.
30 May RM (1988) How many species are there on earth? Science, 241, 1441-1449.
31 Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biology, 3, e422.
32 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.
33 Oline DK (2006) Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils. Applied and Environmental Microbiology, 72, 6965-6971.
34 Ovreas L (2000) Population and community level approaches for analyzing microbial diversity in natural environments. Ecology Letters, 3, 236-251.
35 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.
36 Preston FW (1948) The commonness, and rarity, of species. Ecology, 29, 254-283.
37 Puillandre N, Lambert A, Brouillet S, Achaz G (2012) ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology, 21, 1864-1877.
38 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.
39 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.
40 Rambaut A, Drummond AJ (2007) Tracer v1.4: MCMC Trace Analyses Tool. .
41 Ratnasingham S, Hebert PD (2013) A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS ONE, 8, e66213.
42 Rubinoff D (2006) DNA barcoding evolves into the familiar. Conservation Biology, 20, 1548-1549.
43 Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
44 Schindel DE, Miller SE (2005) DNA barcoding a useful tool for taxonomists. Nature, 435, 17.
45 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, 360, 1825-1834.
46 Tokeshi M (1990) Niche apportionment or random assortment: species abundance patterns revisited. The Journal of Animal Ecology, 10, 1129-1146.
47 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.
48 Ward RD, Hanner R, Hebert PDN (2009) The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology, 74, 329-356.
49 Wiemers M, Fiedler K (2007) Does the DNA barcoding gap exist? — a case study in blue butterflies (Lepidoptera: Lycaenidae). Frontiers in Zoology, 4, 8.
50 Wilson JB (1991) Methods for fitting dominance/diversity curves. Journal of Vegetation Science, 2, 35-46.
51 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. PLoS ONE, 7, e30986.
52 Zhang AB, Muster C, Liang HB, Zhu CD, Crozier R, Wan P, Feng J, Ward RD (2012b) A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding. Molecular Ecology, 21, 1848-1863.
53 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.
54 Zipf GK (1949) Human Behavior and the Principle of Least Effort. Hafner, New York.
[1] 邹安龙, 马素辉, 倪晓凤, 蔡琼, 李修平, 吉成均. 模拟氮沉降对北京东灵山辽东栎群落林下植物物种多样性的影响[J]. 生物多样性, 2019, 27(6): 607-618.
[2] 刘艳, 杨钰爽. 生物多样性保护优先区对重庆苔藓植物多样性保护的重要性[J]. 生物多样性, 2019, 27(6): 677-682.
[3] 邵昕宁, 宋大昭, 黄巧雯, 李晟, 姚蒙. 基于粪便DNA及宏条形码技术的食肉动物快速调查及食性分析[J]. 生物多样性, 2019, 27(5): 543-556.
[4] 刘山林. DNA条形码参考数据集构建和序列分析相关的新兴技术[J]. 生物多样性, 2019, 27(5): 526-533.
[5] 胡建霖,刘志芳,慈秀芹,李捷. DNA条形码在热带龙脑香科树种鉴定中的应用[J]. 植物学报, 2019, 54(3): 350-359.
[6] 刘安榕, 杨腾, 徐炜, 上官子健, 王金洲, 刘慧颖, 时玉, 褚海燕, 贺金生. 青藏高原高寒草地地下生物多样性: 进展、问题与展望[J]. 生物多样性, 2018, 26(9): 972-987.
[7] 徐翔, 张化永, 谢婷, 孙青青, 田永兰. 西双版纳种子植物物种多样性的垂直格局及机制[J]. 生物多样性, 2018, 26(7): 678-689.
[8] 舒江平, 罗俊杰, 韦宏金, 严岳鸿. 基于模式产地的分子证据澄清南平鳞毛蕨的分类学地位[J]. 植物学报, 2018, 53(6): 793-800.
[9] 张则瑾, 郭焱培, 贺金生, 唐志尧. 中国极小种群野生植物的保护现状评估[J]. 生物多样性, 2018, 26(6): 572-577.
[10] 杨倩, 王娓, 曾辉. 氮添加对内蒙古退化草地植物群落多样性和生物量的影响[J]. 植物生态学报, 2018, 42(4): 430-441.
[11] 侯勤曦, 慈秀芹, 刘志芳, 徐武美, 李捷. 基于DNA条形码评估西双版纳国家级自然保护区对樟科植物进化历史的保护[J]. 生物多样性, 2018, 26(3): 217-228.
[12] 李斌强, 李鹏映, 杨家伟, 字红军, 李兴权, 段锡焕, 罗旭. 运用红外相机调查云南巍山青华绿孔雀自然保护区的鸟兽多样性[J]. 生物多样性, 2018, 26(12): 1343-1347.
[13] 刘青青, 董志军. 基于线粒体COI基因分析钩手水母的群体遗传结构[J]. 生物多样性, 2018, 26(11): 1204-1211.
[14] 宋慧芳, 刘海双, 杨义明, 范书田, 李昌禹, 艾军. 山葡萄种质资源DNA条形码通用序列的筛选[J]. 植物学报, 2017, 52(6): 723-732.
[15] 郝金凤, 张晓红, 王昱淞, 刘金林, 智永超, 李新江. 白洋淀湿地蝗虫多样性调查及DNA条形码应用研究[J]. 生物多样性, 2017, 25(4): 409-417.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed