生物多样性 ›› 2019, Vol. 27 ›› Issue (2): 219-234.doi: 10.17520/biods.2018319

• 综述 • 上一篇    

叶绿体DNA标记在谱系地理学中的应用研究进展

胡颖1, 2, 王茜1, 2, 张新新1, 2, 周玮1, 2, 陈晓阳1, 2, 胡新生1, 2, *()   

  1. 1 广东省植物种质资源与利用重点实验室, 广州 510642
    2 华南农业大学林学与风景园林学院, 广州 510642
  • 收稿日期:2018-12-02 接受日期:2019-02-12 出版日期:2019-02-20
  • 通讯作者: 胡新生 E-mail:xinsheng@scau.edu.cn
  • 基金项目:
    华南农业大学人才引进启动项目(4400-K16013)

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
  • Contact: Hu Xinsheng E-mail:xinsheng@scau.edu.cn

谱系地理学研究旨在探究历史上发生的影响目前遗传谱系系统发育和空间分布格局关系的生态与进化过程。叶绿体DNA具有单亲遗传、低突变率、单倍体等特征, 其分子标记不同程度地保留着植物长期进化的历史遗传痕迹, 有助于深度解析谱系地理变异的形成机制。本文探讨了上述特征是怎样影响分子标记的选择、扩大或缩小群体遗传结构分化、延长或缩短空间基因溯祖时间、促进或阻碍种间基因渐渗及谱系分选(复系、并系和单系形成)进程, 重点阐述了这些影响过程的理论基础, 并结合实际例子阐述谱系地理研究进展。由于位点间在突变率、选择强度及它们与漂变互作等方面存在异质性, 今后一个研究重点就是基于叶绿体全基因组序列分析谱系地理变化格局, 包括分析DNA位点间的基因渐渗或基因流动程度差异分布及沿着叶绿体DNA序列上谱系分选差异分布。

关键词: 叶绿体, 谱系地理学, 杂交带, 基因溯祖理论, 物种形成

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

表1

基于cpDNA单倍型在群体内与群体间的变异检测谱系地理结构"

物种 Species 主要谱系分析
Main phylogeographic
analysis
谱系地理形成机制
Mechanisms of forming phylogeographic structure
参考文献
References
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
蒙古绣线菊
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
肋果沙棘
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
祁连圆柏
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
半日花
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
南方红豆杉
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

表2

基因流间接估算模型与方法"

模型
Models
参考文献
References
基因频率
Gene frequency
Fst (岛屿模型)
Fst (Island model)
Wright, 1969
基于私有基因途径
Private allele
Barton & Slatkin, 1986
极大似然估计
Maximum likelihood estimate
Slatkin & Barton, 1989
DNA序列
DNA sequence
Fst(基因树途径)
Fst (gene tree approach)
Hudson et al, 1992
隔离-迁移模型
Isolation-with-migration (IM) model
Hey & Nielsen, 2007;
Wang & Hey, 2010
起始隔离-迁移模型
Initial-isolation-with-migration (IIM) model
Costa& Wilkinson-
Herbots, 2017

表3

cpDNA和nDNA谱系分选进程比较及可能的进化过程"

nDNA/表型性状 nDNA/ Phenotypic traits cpDNA 可能的进化过程
Possible evolutionary processes
nDNA标记
nDNA markers
cpDNA标记
cpDNA markers
分类群
Taxonomic groups
参考文献
References
复系
Polyphyly
复系
Polyphyly
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
Phenotype
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
并系
Paraphyly
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.
- - - -
单系
Monophyly
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.
- - - -
nDNA/表型性状
nDNA/
Phenotypic traits
cpDNA 可能的进化过程
Possible evolutionary processes
nDNA标记
nDNA markers
cpDNA标记
cpDNA markers
分类群
Taxonomic groups
参考文献
References
并系
Paraphyly
复系
Polyphyly
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.
- - - -
并系
Paraphyly
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,
rpl
32-trnL, rps16,
trn
S-G, trnH-psbA
可草拟库氏金鱼花
(苦苣苔科)
Columnea kucyniakii
(Gesneriaceae)
Smith et al, 2018
卫星DNA
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
单系
Monophyly
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. - -
单系
Monophyly
复系
Polyphyly
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
并系
Paraphyly
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.
- - -
单系
Monophyly
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,
trn
S-G, trnD-T,
psb
M-trnD
花荵科 Polemoniaceae Johnson et al, 2008
表型 Phenotype rbcL, rps16,
atp
B-rbcL
茜草属(茜草科)
Kelloggiatorrey (Rubiaceae)
Nie et al, 2005
ITS rbcL, trnL-F,
trn
K-matK,
psb
A-trnH
春蓼属(蓼科)
Persicaria (Polygonaceae)
Kim & Donoghue,
2008
ITS1-5.8S-ITS2 trnL-F 红杉花属(花荵科)
Ipomopsis (Polemoniaceae)
Porter et al,
2010
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