生物多样性 ›› 2014, Vol. 22 ›› Issue (1): 3-20.DOI: 10.3724/SP.J.1003.2014.13170

所属专题: 基因组和生物多样性

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生命之树及其应用

鲁丽敏1,2, 孙苗1,2, 张景博1,2, 李洪雷1,2, 林立1,2, 杨拓1,2, 陈闽1,2, 陈之端1,,A;*()   

  1. 1 .中国科学院植物研究所系统与进化植物学国家重点实验室, 北京 100093
    2 .中国科学院大学, 北京 100049
  • 收稿日期:2013-07-22 接受日期:2014-01-06 出版日期:2014-01-20 发布日期:2014-02-10
  • 通讯作者: 陈之端
  • 基金资助:
    国家自然科学基金国际(地区)合作交流项目(31061160184)和面上项目(31270268)

Tree of life and its applications

Limin Lu1,2, Miao Sun1,2, Jingbo Zhang1,2, Honglei Li1,2, Li Lin1,2, Tuo Yang1,2, Min Chen1,2, Zhiduan Chen1,*()   

  1. 1. State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093
    2. Graduate University of the Chinese Academy of Sciences, Beijing 100049
  • Received:2013-07-22 Accepted:2014-01-06 Online:2014-01-20 Published:2014-02-10
  • Contact: Chen Zhiduan

摘要:

生命之树的概念由达尔文在1859年提出, 用以反映分类群的亲缘关系和进化历史。近30年来, 随着建树性状种类的多样化、数据量的快速增长以及建树方法的不断发展和完善, 生命之树的规模越来越大, 可信度也越来越高。分子生物学、生态学、基因组学、生物信息学及计算机科学等的快速发展, 使得生命之树成为开展学科间交叉研究的桥梁, 其用途日益广泛。本文综述了生命之树研究的历史和现状, 介绍了生命之树在以下几个方面的应用: (1)通过构建不同尺度的生命之树, 理解生物类群间的系统发育关系; (2)通过时间估算和地理分布区重建, 推测现存生物的起源和地理分布格局及其成因; (3)基于时间树, 结合生态、环境因子及关键创新性状, 探讨生物的多样化进程和成因; (4)揭示生物多样性的来源和格局, 预测生物多样性动态变化, 并提出相应的保护策略。最后, 本文评估了生命之树在目前海量数据情况下遇到的序列比对困难、基因树冲突、“流浪类群”干扰等建树难题, 并指出了构建“超大树”的发展趋势。

关键词: 生命之树, 系统发育, 基因树冲突, 生物地理, 生物多样性, 系统发育多样性

Abstract:

The term “Tree of Life” was first used by Charles Darwin in 1859 as a metaphor for describing phylogenetic relationships among organisms. Over the past three decades, the recognized tree of life has improved considerably in overall size and reliability due to an increase in diversity of character resources, a dramatic growth in useable data, and the development of tree-reconstruction methods. As a bridge connecting phylogeny, evolution and related disciplines, such as molecular biology, ecology, genomics, bioinformatics and computer science, the tree of life is increasingly widely used. In this paper, we review the history and progress of tree of life studies and focus on its application in the following fields: (1) the reconstruction of phylogenetic trees at different taxonomic hierarchies to understand phylogenetic relationships among taxa; (2) investigation of the origins of taxa and biogeographic patterns based on dating estimation and biogeographic reconstruction; (3) examination of species’ diversification and its causes by integrating dated trees, ecological factors, environmental variation and key innovations; (4) the study of the origin and patterns of biodiversity, predating biodiversity dynamics, and development of conservation strategies. Finally, we evaluate the difficulties from matrix alignment, gene tree incongruence and “rogue taxa” distraction in tree reconstruction due to massive increases of useable data and in the context consider “supertree” building in the future.

Key words: tree of life, phylogeny, gene tree incongruence, biogeography, biodiversity, phylogenetic diversity