Biodiv Sci ›› 2019, Vol. 27 ›› Issue (2): 219-234. DOI: 10.17520/biods.2018319
• Review • Previous Articles
Hu Ying1,2,Wang Xi1,2,Zhang Xinxin1,2,Zhou Wei1,2,Chen Xiaoyang1,2,Hu Xinsheng1,2,*()
Received:
2018-12-02
Accepted:
2019-02-12
Online:
2019-02-20
Published:
2019-04-16
Contact:
Hu Xinsheng
Hu Ying, Wang Xi, Zhang Xinxin, Zhou Wei, Chen Xiaoyang, Hu Xinsheng. Advancing phylogeography with chloroplast DNA markers[J]. Biodiv Sci, 2019, 27(2): 219-234.
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 | |
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 | |
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 | |
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 | |
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 | |
远志 Polygala tenuifolia | Nst > Gst | 地理隔离 Geographic isolation | |
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 | |
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 | |
半日花 Helianthemum soongoricum | Nst > Gst | 地理隔离 Geographic isolation | |
伯乐树 Bretschneidera sinensis | Gst | 生境破碎化、地理隔离 Habitat fragmentation and geographic isolation | |
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 |
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 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 | |
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 | |
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 | |
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 | |
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 | |
远志 Polygala tenuifolia | Nst > Gst | 地理隔离 Geographic isolation | |
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 | |
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 | |
半日花 Helianthemum soongoricum | Nst > Gst | 地理隔离 Geographic isolation | |
伯乐树 Bretschneidera sinensis | Gst | 生境破碎化、地理隔离 Habitat fragmentation and geographic isolation | |
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 |
模型 Models | 参考文献 References |
---|---|
基因频率 Gene frequency | |
Fst (岛屿模型) Fst (Island model) | |
基于私有基因途径 Private allele | |
极大似然估计 Maximum likelihood estimate | |
DNA序列 DNA sequence | |
Fst(基因树途径) Fst (gene tree approach) | |
隔离-迁移模型 Isolation-with-migration (IM) model | |
起始隔离-迁移模型 Initial-isolation-with-migration (IIM) model | Herbots, 2017 |
Table 2 Models and methods for indirect estimation of gene flow
模型 Models | 参考文献 References |
---|---|
基因频率 Gene frequency | |
Fst (岛屿模型) Fst (Island model) | |
基于私有基因途径 Private allele | |
极大似然估计 Maximum likelihood estimate | |
DNA序列 DNA sequence | |
Fst(基因树途径) Fst (gene tree approach) | |
隔离-迁移模型 Isolation-with-migration (IM) model | |
起始隔离-迁移模型 Initial-isolation-with-migration (IIM) model | 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) | ||||||||
trnK intron, trnL-F | 姜味草属(唇形科) Micromeria (Lamiaceae) | ||||||||||||
ITS1-5.8S-ITS2 | trnL-F, trnD-T | 长喙藓属(青藓科) Rhynchostegium (Brachytheciaceae) | Huttunen & | ||||||||||
ITS | atpB-rbcL | 丁香蓼属(柳叶菜科) Ludwigia (Onagraceae) | |||||||||||
ITS, 表型 Phenotype | trnL-F | 唇柱苣苔属 Chirita | |||||||||||
ITS | trnT-L | 火把莲属(独尾草科) Kniphofia (Asphodelaceae) | |||||||||||
ITS | trnL-F, psbA-trnH | 瓦苇属(独尾草科) Haworthia (Asphodelaceae) | |||||||||||
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) | |||||||||
卫星DNA Microsatellites DNA | atpL-H, rps16-trnK | 穗花杉(红豆杉科) Amentotaxus argotaenia (Taxaceae) | |||||||||||
ITS | matK, rbcL | 松属单维管束松亚属(松科) Pinus subgenus Strobus (Pinaceae) | |||||||||||
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) | ||||||||
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) | |||||||||
表型 Phenotype | rbcL, ndhF | 柳叶菜科 Onagraceae | |||||||||||
ITS | matK, trnL, trnL-F, trnS-G, trnD-T, psbM-trnD | 花荵科 Polemoniaceae | |||||||||||
表型 Phenotype | rbcL, rps16, atpB-rbcL | 茜草属(茜草科) Kelloggiatorrey (Rubiaceae) | |||||||||||
ITS | rbcL, trnL-F, trnK-matK, psbA-trnH | 春蓼属(蓼科) Persicaria (Polygonaceae) | 2008 | ||||||||||
ITS1-5.8S-ITS2 | trnL-F | 红杉花属(花荵科) Ipomopsis (Polemoniaceae) | 2010 |
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) | ||||||||
trnK intron, trnL-F | 姜味草属(唇形科) Micromeria (Lamiaceae) | ||||||||||||
ITS1-5.8S-ITS2 | trnL-F, trnD-T | 长喙藓属(青藓科) Rhynchostegium (Brachytheciaceae) | Huttunen & | ||||||||||
ITS | atpB-rbcL | 丁香蓼属(柳叶菜科) Ludwigia (Onagraceae) | |||||||||||
ITS, 表型 Phenotype | trnL-F | 唇柱苣苔属 Chirita | |||||||||||
ITS | trnT-L | 火把莲属(独尾草科) Kniphofia (Asphodelaceae) | |||||||||||
ITS | trnL-F, psbA-trnH | 瓦苇属(独尾草科) Haworthia (Asphodelaceae) | |||||||||||
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) | |||||||||
卫星DNA Microsatellites DNA | atpL-H, rps16-trnK | 穗花杉(红豆杉科) Amentotaxus argotaenia (Taxaceae) | |||||||||||
ITS | matK, rbcL | 松属单维管束松亚属(松科) Pinus subgenus Strobus (Pinaceae) | |||||||||||
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) | ||||||||
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) | |||||||||
表型 Phenotype | rbcL, ndhF | 柳叶菜科 Onagraceae | |||||||||||
ITS | matK, trnL, trnL-F, trnS-G, trnD-T, psbM-trnD | 花荵科 Polemoniaceae | |||||||||||
表型 Phenotype | rbcL, rps16, atpB-rbcL | 茜草属(茜草科) Kelloggiatorrey (Rubiaceae) | |||||||||||
ITS | rbcL, trnL-F, trnK-matK, psbA-trnH | 春蓼属(蓼科) Persicaria (Polygonaceae) | 2008 | ||||||||||
ITS1-5.8S-ITS2 | trnL-F | 红杉花属(花荵科) Ipomopsis (Polemoniaceae) | 2010 |
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