植物DNA条形码促进系统发育群落生态学发展

doi:10.3724/SP.J.1003.2011.11250

生物多样性 ›› 2011, Vol. 19 ›› Issue (3): 284-294. DOI: 10.3724/SP.J.1003.2011.11250

所属专题：物种形成与系统进化

植物DNA条形码促进系统发育群落生态学发展

裴男才¹^,³^,^*(), 张金龙²^,³, 米湘成², 葛学军¹

1 (中国科学院华南植物园, 中国科学院植物资源保护与可持续利用重点实验室, 广州 510650)
2 (中国科学院植物研究所植被与环境变化国家重点实验室, 北京 100093)
3 (中国科学院研究生院, 北京 100049)

收稿日期:2010-10-14 接受日期:2011-03-08 出版日期:2011-05-20 发布日期:2013-12-10
通讯作者: 裴男才
作者简介:*E-mail: nancai.pei@gmail.com
基金资助:
国家重点基础研究发展计划(9732007CB411600);中国科学院知识创新工程重要方向项目(KSCX2-YW-N-0807)

Plant DNA barcodes promote the development of phylogenetic commu- nity ecology

Nancai Pei¹^,³^,^*(), Jinlong Zhang²^,³, Xiangcheng Mi², Xuejun Ge¹

1 Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650
2 State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093
3 Graduate University of the Chinese Academy of Sciences, Beijing 100049

Received:2010-10-14 Accepted:2011-03-08 Online:2011-05-20 Published:2013-12-10
Contact: Nancai Pei

摘要/Abstract

摘要：

系统发育群落生态学是近年兴起的一个重要生态学研究分支, 它以群落生态学为基础并引入了系统发育的分析方法, 全面动态地反映了群落中物种内和物种间的相互作用关系, 揭示了群落格局形成的生态学过程, 研究了生物多样性的形成及维持机制。巴拿马BCI (Barro Colorado Island)样地的成功例子说明, 在固定样地进行长期的群落生态与系统发育研究切实可行且极具意义; DNA条形码的快速兴起对这一研究发挥着重要作用。本文先列举了群落生态与系统发育综合分析能解决的群落系统发育结构、群落生态位结构、生物地理学和性状进化等生态学问题; 接着介绍了标准植物DNA条形码以及利用片段组合(rbcL+matK+trnH-psbA)进行快速物种识别和近缘种区分、精确群落系统发育关系的构建以及群落生态学研究; 随后提出DNA条形码研究在类群水平上需注意两片段的条形码组合(matK+rbcL)在同属种鉴别能力上的不足, 而在较大尺度群落水平上需对实验设计进行优化。DNA条形码将为探讨物种多样性及其维持机理、系统发育beta多样性以及群落水平上功能性状进化研究提供新的思路。

关键词: 群落系统发育重建, 群落生态学, rbcL,matK,trnH-psbA, 大型固定样地, APG分类系统

Abstract

There is a dynamic interplay between ecology and evolution within community ecology. Phylogenetic community ecology describes the intraspecific and interspecific relationships within a community, aiming to reveal the processes driving community assembly at multiple scales. Previous research has highlighted the role of phylogenetic and historical biogeographical data in explaining current patterns of global biodiversity. The success of using DNA barcoding in the construction of tropical forest community phylogenies highlights the usefulness and challenges of long-term research on community ecology and phylogenetics based on forest dynamic plots. In this paper, we illustrate the feasibility of a synthesis between community ecology and evolutionary biology in order to resolve particular ecological issues on community phylogenetic structure, community niche structure, biogeography, and trait evolution. We summarize progress on the development of a plant DNA barcoding system, and introduce the usage of a combination of DNA markers (rbcL+matK+trnH-psbA) for fast species discrimination and community phylogenetic reconstruction. We also explore the utilization of well-resolved phylogenies to understand community ecology. We discuss the limitations of core plant DNA barcodes (rbcL+matK) when identifying congeners, and propose an improved sequencing strategy suitable for studies at the community level. We expect that plant DNA barcodes will prove very useful for the study of species diversity, mechanisms of biodiversity maintenance, phylogenetic beta diversity and functional trait evolution.

Key words: community phylogenetic reconstruction, community ecology, rbcL,matK,trnH-psbA, large scale permanent plot, APG

裴男才, 张金龙, 米湘成, 葛学军 (2011) 植物DNA条形码促进系统发育群落生态学发展. 生物多样性, 19, 284-294. DOI: 10.3724/SP.J.1003.2011.11250.

Nancai Pei, Jinlong Zhang, Xiangcheng Mi, Xuejun Ge (2011) Plant DNA barcodes promote the development of phylogenetic commu- nity ecology. Biodiversity Science, 19, 284-294. DOI: 10.3724/SP.J.1003.2011.11250.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2011.11250

https://www.biodiversity-science.net/CN/Y2011/V19/I3/284

图/表 3

图1 rbcL+matK+trnH-psbA的3位点组合片段的超级矩阵示意图(改自Kress et al., 2009)。第一列为物种名称, 第二列之后的为各片段的序列排列情况, 其中trnH-psbA (也即trnH-psbA I, trnH-psbA II, trnH-psbA III等)片段以目为单位进行归类。3个片段共同组成一个矩阵。

Fig. 1 Illustration of supermatrix approach in sequence alignment for phylogenetic analysis (adopted from Kress et al., 2009). The first column represents species name, while others represent sequence alignments of rbcL, matK, and trnH-psbA. In trnH-psbA, each order consists of a dataset.

图2 10个物种的系统发育关系示意图。图A用Phylomatic的方法获得, 图B和C用条形码(Barcode)的方法获得。Sp 1-10表示物种1-10, 以此类推。图A表示当使用在线软件Phylomatic获取该10个物种的系统发育关系时, 物种2-10的位置未得到解决, 也就是常说的多分枝结构。图B表示, 当使用2个DNA条形码片段(如rbcL+matK)时, 物种3-5和物种6-8的系统发育关系尚不明确, 而其他物种的位置得到了较好解决。图C表示, 当使用3个DNA条形码片段构成的超级矩阵(如rbcL+matK+trnH-psbA)时, 全部物种的系统发育关系都得到了解决。

Fig. 2 A graphic representation of phylogenetic trees of ten species using Phylomatic (A) and Barcode (B, C) approaches. Sp 1-10 means species 1-10. (A) Phylogenetic relationships of Sp 2-10 are not well-resolved, i.e., there are polytomies among these taxa when using an online query tool Phylomatic; (B) Phylogenetic relationships of Sp 3-5, and Sp 6-8 are not well-resolved using a two-locus DNA barcode (rbcL+matK); (C) Phylogenetic relationships of Sp 1-10 are well-resolved using a supermatrix of three DNA barcodes (rbcL+matK+trnH-psbA).

附录I 本研究所使用的条形码片段引物对

Appendix 1 Primer pairs for barcode loci rbcL, matK, and trnH-psbA

标记 Marker	引物 Primer	序列 Sequence (5′- 3′)	长度 Size (bp)	参考文献 Reference
rbcL	SI_F	ATGTCACCACAAACAGAGACTAAAGC	554	Kress & Erickson (2007)
rbcL	SI_R	GTYAAATCAAGTCCACCYCG	554	Kress & Erickson (2007)
matK	KIM_3F	CGTACAGTACTTTTGTGTTTACGAG	Average 850	Kim KJ, unpublished primers
	KIM_1R	ACCCAGTCCATCTGGAAATCTTGGTTC	Average 850	Kim KJ, unpublished primers
	KIM_1F	AATATCCAAATACCAAATCC	Average 850	Kim KJ, unpublished primers
	KIM_1R	ACCCAGTCCATCTGGAAATCTTGGTTC	Average 850	Kim KJ, unpublished primers
	2.1a-f	ATCCATCTGGAAATCTTAGTTC	Average 890	www.kew.org/barcoding/protocols.html
	5r	GTTCTAGCACAAGAAAGTCG	Average 890	www.kew.org/barcoding/protocols.html
trnH-psbA	psbA	GTTATGCATGAACGTAATGCTC	280-750, average 470	Sang et al., 1997
trnH-psbA	trnH	CGCGCATGGTGGATTCACAATCC	280-750, average 470	Tate & Simpson (2003)

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植物DNA条形码促进系统发育群落生态学发展

Plant DNA barcodes promote the development of phylogenetic commu- nity ecology

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