Biodiversity Science ›› 2019, Vol. 27 ›› Issue (2): 219-234.doi: 10.17520/biods.2018319

• Review • Previous Article    

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:2019-04-16
  • 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

Table 1

Testing phylogeographic structure based on the variation of cpDNA haplotypes within and among populations"

物种 Species 主要谱系分析
Main phylogeographic
Mechanisms of forming phylogeographic structure
海仙报春 Primula poissonii Nst > Gst 异域片断化 Allopatric fragmentation Song et al, 2011
绵参 Eriophyton wallichii Nst = Gst 无谱系结构、地形和环境及“孤岛效应”形成
No phylogeographic structure due to the effects of
topography, environments and “isolated islands” of habitats
Wang YZ et al, 2011
Spiraea mongolica
Nst > Gst, NCA 第四纪冰期-间冰期气候动荡, 青藏高原隆升的共同作用
Joint effects of climate oscillation in Quaternary
glacial-interglacial periods and the rise of the Qinghai-Tibetan Plateau
Wang JL et al, 2014;
Zhang FQ et al, 2012
手参 Gymnadenia conopsea Nst < Gst 无谱系地理分化、群体未经历扩张
Insignificant phylogeographic structure and no population expansion
Bao et al, 2016
Hippophae neurocarpa
Nst > Gst, NCA 避难所隔离分化及邻域扩张
Allopatric isolation of refugia and contiguous range expansion
Meng et al, 2008
远志 Polygala tenuifolia Nst > Gst 地理隔离 Geographic isolation Han et al, 2014
Juniperus przewalskii
Gst 多个避难所、瓶颈效应和奠基者效应
Multiple refugia, bottleneck and founder effects
Zhang et al, 2005
虎耳草 Saxifraga stolonifera Nst = Gst 无谱系地理结构、多个微型避难所、群体片断化
No phylogeographic structure, multiple small refugia,
and population fragmentation
Gengji et al, 2018
Helianthemum soongoricum
Nst > Gst 地理隔离 Geographic isolation Han et al, 2017
伯乐树 Bretschneidera sinensis Gst 生境破碎化、地理隔离
Habitat fragmentation and geographic isolation
Wang MN, et al, 2011
Taxus wallichiana var. Mairei
Gst, NCA 弱谱系地理结构、片断化和隔离
Weak phylogeographic structure, fragmentation and isolation
Zhang XM, et al, 2012

Table 2

Models and methods for indirect estimation of gene flow"

Gene frequency
Fst (岛屿模型)
Fst (Island model)
Wright, 1969
Private allele
Barton & Slatkin, 1986
Maximum likelihood estimate
Slatkin & Barton, 1989
DNA sequence
Fst (gene tree approach)
Hudson et al, 1992
Isolation-with-migration (IM) model
Hey & Nielsen, 2007;
Wang & Hey, 2010
Initial-isolation-with-migration (IIM) model
Costa& Wilkinson-
Herbots, 2017

Table 3

Comparison of lineage sorting phases between cpDNA and nDNA and the possible evolutionary processes"

nDNA/表型性状 nDNA/ Phenotypic traits cpDNA 可能的进化过程
Possible evolutionary processes
nDNA markers
cpDNA markers
Taxonomic groups
物种形成初期, nDNA和cpDNA均以漂变过程为主
Lineage sorting is mainly driven by drift process for both nDNA and cpDNA in the incipient stage of speciation.
LBD6 matK, trnD-T 葛藤属(豆科)
Pueraria (Leguminosae)
Egan et al, 2016
trnK intron, trnL-F 姜味草属(唇形科)
Micromeria (Lamiaceae)
Brauchler et al, 2005
ITS1-5.8S-ITS2 trnL-F, trnD-T 长喙藓属(青藓科)
Rhynchostegium (Brachytheciaceae)
Huttunen &
Ignatov, 2010
ITS atpB-rbcL 丁香蓼属(柳叶菜科)
Ludwigia (Onagraceae)
Hung et al, 2009
ITS, 表型
trnL-F 唇柱苣苔属 Chirita Wang YZ, et al, 2011
ITS trnT-L 火把莲属(独尾草科)
Kniphofia (Asphodelaceae)
Ramdhani et al, 2009
ITS trnL-F, psbA-trnH 瓦苇属(独尾草科)
Haworthia (Asphodelaceae)
Ramdhani et al, 2011
cpDNA以漂变或自然选择过程为主; nDNA存在杂交或渐渗过程
Lineage sorting is mainly driven by drift or selection process for cpDNA but by hybridization or introgression process for nDNA.
- - - -
cpDNA以漂变或自然选择为主; nDNA存在杂交或渐渗过程
Lineage sorting is mainly driven by drift or selection process for cpDNA but by hybridization or introgression process for nDNA.
- - - -
Phenotypic traits
cpDNA 可能的进化过程
Possible evolutionary processes
nDNA markers
cpDNA markers
Taxonomic groups
nDNA以自然选择过程为主; cpDNA存在渐渗过程
Lineage sorting is mainly driven by selection process for nDNA but by introgression process for cpDNA.
- - - -
nDNA和cpDNA均以漂变过程为主, 或存在渐渗/基因流过程
Lineage sorting is mainly driven by drift process or introgression/gene flow process for both nDNA and cpDNA.
ITS, ETS trnQ-rps16,
32-trnL, rps16,
S-G, trnH-psbA
Columnea kucyniakii
Smith et al, 2018
Microsatellites DNA
atpL-H, rps16-trnK 穗花杉(红豆杉科)
Amentotaxus argotaenia (Taxaceae)
Ge et al, 2015
ITS matK, rbcL 松属单维管束松亚属(松科)
Pinus subgenus Strobus (Pinaceae)
Sying et al, 2007;
Gernandt et al, 2005
cpDNA以漂变或自然选择过程为主Lineage sorting for cpDNA is mainly driven by drift or selection process. - -
nDNA以自然选择过程为主; cpDNA以漂变过程为主或存在渐渗过程
Lineage sorting is mainly driven by selection process for nDNA but by drift or introgression process for cpDNA.
ITS trnL-F, rpl16 克非亚草属(千屈菜科)
Cuphea (Lythraceae)
Barber et al, 2010
nDNA以自然选择过程为主; cpDNA以漂变过程为主, 或存在渐渗过程
Lineage sorting is mainly driven by selection process for nDNA but by drift or introgression process for cpDNA.
- - -
nDNA和cpDNA均以漂变过程为主, 或均存在自然选择过程
Lineage sorting for both nDNA and cpDNA is mainly driven by drift or selection process.
ITS, 表型
ITS, phenotype
trnT-L 常春藤(五加科)
Hedera (Araliaceae)
Valcarcel et al, 2003
表型 Phenotype rbcL, ndhF 柳叶菜科 Onagraceae Levin et al, 2003
ITS matK, trnL, trnL-F,
S-G, trnD-T,
花荵科 Polemoniaceae Johnson et al, 2008
表型 Phenotype rbcL, rps16,
Kelloggiatorrey (Rubiaceae)
Nie et al, 2005
ITS rbcL, trnL-F,
Persicaria (Polygonaceae)
Kim & Donoghue,
ITS1-5.8S-ITS2 trnL-F 红杉花属(花荵科)
Ipomopsis (Polemoniaceae)
Porter et al,
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