叶绿体DNA标记在谱系地理学中的应用研究进展

doi:10.17520/biods.2018319

摘要/Abstract

摘要：

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

Abstract

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

胡颖, 王茜, 张新新, 周玮, 陈晓阳, 胡新生 (2019) 叶绿体DNA标记在谱系地理学中的应用研究进展. 生物多样性, 27, 219-234. DOI: 10.17520/biods.2018319.

Hu Ying, Wang Xi, Zhang Xinxin, Zhou Wei, Chen Xiaoyang, Hu Xinsheng (2019) Advancing phylogeography with chloroplast DNA markers. Biodiversity Science, 27, 219-234. DOI: 10.17520/biods.2018319.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2018319

https://www.biodiversity-science.net/CN/Y2019/V27/I2/219

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参考文献 122

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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	N_st > G_st	异域片断化 Allopatric fragmentation	Song et al, 2011
绵参 Eriophyton wallichii	N_st = G_st	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	N_st > G_st, 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	N_st < G_st	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	N_st > G_st, 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	N_st > G_st	地理隔离 Geographic isolation	Han et al, 2014
祁连圆柏 Juniperus przewalskii	G_st	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	N_st = G_st	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	N_st > G_st	地理隔离 Geographic isolation	Han et al, 2017
伯乐树 Bretschneidera sinensis	G_st	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	G_st, 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

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	N_st > G_st	异域片断化 Allopatric fragmentation	Song et al, 2011
绵参 Eriophyton wallichii	N_st = G_st	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	N_st > G_st, 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	N_st < G_st	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	N_st > G_st, 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	N_st > G_st	地理隔离 Geographic isolation	Han et al, 2014
祁连圆柏 Juniperus przewalskii	G_st	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	N_st = G_st	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	N_st > G_st	地理隔离 Geographic isolation	Han et al, 2017
伯乐树 Bretschneidera sinensis	G_st	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	G_st, 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

模型 Models	参考文献 References
基因频率 Gene frequency
F_st (岛屿模型) F_st(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
F_st(基因树途径) F_st(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

模型 Models	参考文献 References
基因频率 Gene frequency
F_st (岛屿模型) F_st(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
F_st(基因树途径) F_st(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

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, rpl32-trnL, rps16, trnS-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, trnS-G, trnD-T, psbM-trnD	花荵科 Polemoniaceae	Johnson et al, 2008
			表型 Phenotype		rbcL, rps16, atpB-rbcL	茜草属(茜草科) Kelloggiatorrey (Rubiaceae)	Nie et al, 2005
			ITS		rbcL, trnL-F, trnK-matK, psbA-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