生命之树及其应用

doi:10.3724/SP.J.1003.2014.13170

摘要/Abstract

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

鲁丽敏, 孙苗, 张景博, 李洪雷, 林立, 杨拓, 陈闽, 陈之端 (2014) 生命之树及其应用. 生物多样性, 22, 3-20. DOI: 10.3724/SP.J.1003.2014.13170.

Limin Lu,Miao Sun,Jingbo Zhang,Honglei Li,Li Lin,Tuo Yang,Min Chen,Zhiduan Chen (2014) Tree of life and its applications. Biodiversity Science, 22, 3-20. DOI: 10.3724/SP.J.1003.2014.13170.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2014.13170

https://www.biodiversity-science.net/CN/Y2014/V22/I1/3

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	冲突原因阐述 Description	解决方案 Solutions
软冲突(假冲突) Soft incongruence
人为因素 Artificial factors	数据不足 Insufficient data	下一代测序技术; 系统发育基因组学; 取样代表性; 基因选择; 进化模型的选择 Next-generation sequencing technologies; phylogenomics; Taxon sampling; DNA regions selection; selection of substitution models
	取样偏差 Biased sampling
	基因选择不当 Sub-optimized gene selection
	测序错误 Sequencing errors
序列因素 Sequencing factors	碱基组成成分偏差 Compositional bias	第三密码子排除; 氨基酸序列建树; RY编码; 快速进化位点移除; 一致网络分析法 3rd codon position exclusion; amino acid tree; RY coding; removing fast-evolving nucleotide sites; consensus networks
	长枝吸引 Long-branch attraction
	进化速率异质性 Evolutionary rate heterogeneity
	进化饱和 Evolutionary saturation
硬冲突 Hard incongruence
生物过程 Biological factors	快速辐射分化 Rapid diversification	最小遗传距离法; 融合法; 基因树简约法; 网状进化网络分析法 Minimum genetic distance method; coalescence-based methods; gene tree parsimony; reticulation networks
	杂交/渐渗 Hybridization/Introgression
	不完全谱系筛选 Incomplete lineage sorting
	基因水平转移 Horizontal gene transfer
	并系基因 Paralogous genes
	基因重复和/或丢失 Gene duplication and/or gene loss
	基因重组 Gene recombination

	冲突原因阐述 Description	解决方案 Solutions
软冲突(假冲突) Soft incongruence
人为因素 Artificial factors	数据不足 Insufficient data	下一代测序技术; 系统发育基因组学; 取样代表性; 基因选择; 进化模型的选择 Next-generation sequencing technologies; phylogenomics; Taxon sampling; DNA regions selection; selection of substitution models
	取样偏差 Biased sampling
	基因选择不当 Sub-optimized gene selection
	测序错误 Sequencing errors
序列因素 Sequencing factors	碱基组成成分偏差 Compositional bias	第三密码子排除; 氨基酸序列建树; RY编码; 快速进化位点移除; 一致网络分析法 3rd codon position exclusion; amino acid tree; RY coding; removing fast-evolving nucleotide sites; consensus networks
	长枝吸引 Long-branch attraction
	进化速率异质性 Evolutionary rate heterogeneity
	进化饱和 Evolutionary saturation
硬冲突 Hard incongruence
生物过程 Biological factors	快速辐射分化 Rapid diversification	最小遗传距离法; 融合法; 基因树简约法; 网状进化网络分析法 Minimum genetic distance method; coalescence-based methods; gene tree parsimony; reticulation networks
	杂交/渐渗 Hybridization/Introgression
	不完全谱系筛选 Incomplete lineage sorting
	基因水平转移 Horizontal gene transfer
	并系基因 Paralogous genes
	基因重复和/或丢失 Gene duplication and/or gene loss
	基因重组 Gene recombination