Biodiv Sci ›› 2014, Vol. 22 ›› Issue (1): 3-20.  DOI: 10.3724/SP.J.1003.2014.13170

Special Issue: 基因组和生物多样性 物种形成与系统进化

• Orginal Article • Previous Articles     Next Articles

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


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