Biodiv Sci ›› 2019, Vol. 27 ›› Issue (2): 219-234.  DOI: 10.17520/biods.2018319

Special Issue: 物种形成与系统进化

• Review • Previous Articles    

Advancing phylogeography with chloroplast DNA markers

Hu Ying1,2,Wang Xi1,2,Zhang Xinxin1,2,Zhou Wei1,2,Chen Xiaoyang1,2,Hu Xinsheng1,2,*()   

  1. 1 Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642
    2 College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642
  • Received:2018-12-02 Accepted:2019-02-12 Online:2019-02-20 Published:2019-04-16
  • Contact: Hu Xinsheng


Phylogeography seeks to identify the historical ecological and evolutionary processes underlying modern-day phylogenetic relationships across a spatial gradient. Owing to the characteristics of uniparental inheritance, low mutation rates and haploid, chloroplast DNA (cpDNA) markers record the events occurring in historical long-term evolutionary processes to different extents, and hence aid in understanding the mechanisms for phylogeographic variation. Here we discuss how these characteristics affect cpDNA marker selection, how they increase or reduce population genetic differentiation, how they lengthen or shorten the average gene coalescent times, how they promote or impede gene introgression among species and how the process of lineage sorting functions from polyphyly to paraphyly to monophyly. We reviewed the theoretical bases of these mechanisms, as well as the progress made in empirical studies regarding the theories of phylogeographic variation. Because of the heterogeneity of DNA sites in mutation rate, selection strength and interactions with genetic drift effects, one study to examine the genome-wide pattern of phylogeography will be necessary in the future. This must include the analysis of differential gene introgression and gene flow among sites, as well as the distribution of the differential phases of lineage sorting along the chloroplast genome.

Key words: chloroplast, phylogeography, hybrid zone, gene coalescent theory, speciation