Biodiversity Science ›› 2014, Vol. 22 ›› Issue (1): 3-20.doi: 10.3724/SP.J.1003.2014.13170

Special Issue: From Genome to Diversity

• Orginal Article • Previous Article     Next Article

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:2014-02-10
  • Chen Zhiduan

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

Fig. 1

Phylogenetic relationships of the angiosperms at the ordinal level (based on Soltis et al., 2011). Names of the families, orders and other major clades follow APG III (2009) and Cantino et al. (2007). Numbers above branches are Maximum Likelihood bootstrap values."

Table 1

Causes and resolutions for phylogenetic incongruences"

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
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