基于nrITS及cpDNA序列变异的菝葜复合种（Smilax china complex）系统发育及谱系地理学研究
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摘要
菝葜复合种(Smilax china complex)隶属于菝葜科(Smilacaceae),菝葜属(Smilax),是以菝葜(S. china)为核心,与近缘种小果菝葜(S. davidiana)、三脉菝葜(S. trinervula)、南投菝葜(S. nantoensis)和双花菝葜(S. biflora)共同构成的一个复合群。该复合种广泛分布于东亚：在中国大陆分布北至胶东半岛,南至福建、广东沿海,东至舟山群岛和台湾,西至云、贵、川,并扩展到朝鲜半岛,日本全境,琉球群岛等东亚、东北亚地区,涵盖了中国-日本植物区系。为了探讨由多倍化引起的植物物种起源及进化,本研究采用nrITS片段及2个cpDNA片段对该复合种37个群体共358个个体的系统进化及谱系地理学进行了研究,获得如下主要结果：
(1)使用nrITS片段,对上述群体各1-3个个体的ITS序列分析重建了菝葜复合种的系统发育。结果显示菝葜复合种为一良好的单系类群(支持率=72%,后验概率=1),包括菝葜(S. china各倍性群体2X,4X,6X)、琉球菝葜(S. china var. kuru)、小果菝葜(S. davidiana)、三脉菝葜(S. trinervula)、南投菝葜(S. nantoensis)和双花菝葜(S. biflora)。
(2)利用2个cpDNA片段(matK, trnS-G)对该复合种进行群体遗传及谱系地理学研究,37个群体内共检测到25个cpDNA单倍型,17个群体(45.9%)具有单倍型多态性。菝葜复合种单倍型多态性丰富的地区位于日本本州和中国东部；单倍型系统系统树和TCS网状结构分析推测菝葜复合种曾具有一二倍体S. china祖先,具有原始单倍型(H18,H19)。而具有该单倍型的二倍体群体已经灭绝,但该单倍型在可能的避难所：日本本州中部大阪群体(h=0.5606,π×10﹣3=0.362,R=0.936)及中国东部庐山六倍体群体(h=0.6970,π=10﹣3=1.105, R=1.182)中获得保留。
(3)研究揭示该复合种内的多倍体群体为多次起源,至少具有3次独立的起源事件,分别发生于中国西南部,中国东部和日本本岛。推测该复合种具有2个谱系：中国中部-西南-南部谱系以及中国东部-韩国-日本谱系。中国中部-西南-南部谱系经历了群体扩张事件(SSD=0.02099, P=0.055, Fu's Fs=-10.0181, P=0.006, Tajima'D=-1.83349, P=0.005,τ=1.25391),是推测约在10万年前(0.094Mya)的一次由多倍化现象导致的快速群体扩张事件。中国东部-韩国-日本谱系中未检测到明显的群体扩张(SSD=0.50820, P=0, Fu'sFs=0.72222, P>0.05, Tajima'D=-0.65976, P>0.05)。
(4)结果显示日本多倍体群体的分布格局是由本州中部避难所向南扩张形成。中国台湾,日本琉球群岛,屋久岛保留了二倍体的S. china群体,反映了群体扩张中的遗传漂变和异域物种形成事件,特殊的岛屿生境使这些二倍体群体发生了部分分化,形成了S. china var. kuru, S. nantoensis, S. biflora等岛屿特有种。
Smilax china complex, a member of sect. China in Smilax (Smilacaceae), includes a key species, S. china, and several relatives, S. china var. kuru, S. davidiana, S. trinervula, S. biflora, and S. nantoensis. Such species complex, whose distribution area covers the Sino-Japan floral region, distributes widely in East Asia, including the mainland of China, Taiwan, the Ryukyu, Korea and Japan. To investigate speciation and evolution caused by plant polyploidization, I studied on the phylogeny and phylogeography of Smilax china complex using nrlTS and two cpDNA regions, involving 358 individual from 37 populations of the complex. The main results are summarized as follows:
(1) Select one to three individual from each population to reconstruct phylogeny tree of S. china complex based on nrlTS region. The result show that the Smilax china species complex forms a monophyletic group with strong support (bootstrap 72%, posterior probability) including S. china (2X,4X,6X), S. china var. kuru, S. davidiana, S. trinervula, and S. biflora, and S. nantoensis.
(2) Population genetic and phylogeographic analysis based on cpDNA (matK, trnS-G) identify 25 different cpDNA haplotypes,17 populations (45.9%) have haplotype diversity. Central Japan and East China have the highest level of haplotype diversity. Phylogeny MP tree and TCS network based on cpDNA data suggest infer that S.china complex have diploid progenitor with ancestral haplotypes (H18, H19). Although this diploid progenitor has already been extinct, the ancestral haplotypes (H18, H19) are remained in potential refuges:the scJDB population in central Japan (h=0.5606,π×10﹣3=0.362,R=0.936) and the scCJX population in East China (h=0.6970,π×10﹣3=1.105,R=1.182).
(3) Both phylogenetic reconstruction of nrITS and genealogical relationships of cpDNA sequences suggest the multiple origins of polyploid S. china. The polyploidization happened at least three times, which are located in South-west China, East China and Japan. Two major cpDNA lineages were identified in S. china complex, the Lineage A (Central-South-west-South China) and Grade B (East China-Korea-Japan). Demographic expansion could be detected in Lineage A (SSD=0.02099, P=0.055, Fu's Fs=-10.0181, P=0.006, Tajima'D=-1.83349, P=0.005,τ=1.25391), which might be a rapid expansion caused by polyploidization in around 0.094 Mya. Demographic expansion could not be detected in Grade B (SSD=0.50820, P=0, Fu's Fs=0.72222, P>0.05, Tajima'D=-0.65976, P>0.05).
(4) The results suggest that Japan population migrated from refuge in Central Japan to South Japan. S. china diploid populations are remained in Taiwan, the Ryukyu and Yaku-shima in Japan, which reflect the genetic drift and allopatric speciation during expansion. Unique habitats on island led diversification between such diploid species, involving S. china var. kuru, S. nantoensis and S. biflora.
(1)使用nrITS片段,对上述群体各1-3个个体的ITS序列分析重建了菝葜复合种的系统发育。结果显示菝葜复合种为一良好的单系类群(支持率=72%,后验概率=1),包括菝葜(S. china各倍性群体2X,4X,6X)、琉球菝葜(S. china var. kuru)、小果菝葜(S. davidiana)、三脉菝葜(S. trinervula)、南投菝葜(S. nantoensis)和双花菝葜(S. biflora)。
(2)利用2个cpDNA片段(matK, trnS-G)对该复合种进行群体遗传及谱系地理学研究,37个群体内共检测到25个cpDNA单倍型,17个群体(45.9%)具有单倍型多态性。菝葜复合种单倍型多态性丰富的地区位于日本本州和中国东部；单倍型系统系统树和TCS网状结构分析推测菝葜复合种曾具有一二倍体S. china祖先,具有原始单倍型(H18,H19)。而具有该单倍型的二倍体群体已经灭绝,但该单倍型在可能的避难所：日本本州中部大阪群体(h=0.5606,π×10﹣3=0.362,R=0.936)及中国东部庐山六倍体群体(h=0.6970,π=10﹣3=1.105, R=1.182)中获得保留。
(3)研究揭示该复合种内的多倍体群体为多次起源,至少具有3次独立的起源事件,分别发生于中国西南部,中国东部和日本本岛。推测该复合种具有2个谱系：中国中部-西南-南部谱系以及中国东部-韩国-日本谱系。中国中部-西南-南部谱系经历了群体扩张事件(SSD=0.02099, P=0.055, Fu's Fs=-10.0181, P=0.006, Tajima'D=-1.83349, P=0.005,τ=1.25391),是推测约在10万年前(0.094Mya)的一次由多倍化现象导致的快速群体扩张事件。中国东部-韩国-日本谱系中未检测到明显的群体扩张(SSD=0.50820, P=0, Fu'sFs=0.72222, P>0.05, Tajima'D=-0.65976, P>0.05)。
(4)结果显示日本多倍体群体的分布格局是由本州中部避难所向南扩张形成。中国台湾,日本琉球群岛,屋久岛保留了二倍体的S. china群体,反映了群体扩张中的遗传漂变和异域物种形成事件,特殊的岛屿生境使这些二倍体群体发生了部分分化,形成了S. china var. kuru, S. nantoensis, S. biflora等岛屿特有种。
Smilax china complex, a member of sect. China in Smilax (Smilacaceae), includes a key species, S. china, and several relatives, S. china var. kuru, S. davidiana, S. trinervula, S. biflora, and S. nantoensis. Such species complex, whose distribution area covers the Sino-Japan floral region, distributes widely in East Asia, including the mainland of China, Taiwan, the Ryukyu, Korea and Japan. To investigate speciation and evolution caused by plant polyploidization, I studied on the phylogeny and phylogeography of Smilax china complex using nrlTS and two cpDNA regions, involving 358 individual from 37 populations of the complex. The main results are summarized as follows:
(1) Select one to three individual from each population to reconstruct phylogeny tree of S. china complex based on nrlTS region. The result show that the Smilax china species complex forms a monophyletic group with strong support (bootstrap 72%, posterior probability) including S. china (2X,4X,6X), S. china var. kuru, S. davidiana, S. trinervula, and S. biflora, and S. nantoensis.
(2) Population genetic and phylogeographic analysis based on cpDNA (matK, trnS-G) identify 25 different cpDNA haplotypes,17 populations (45.9%) have haplotype diversity. Central Japan and East China have the highest level of haplotype diversity. Phylogeny MP tree and TCS network based on cpDNA data suggest infer that S.china complex have diploid progenitor with ancestral haplotypes (H18, H19). Although this diploid progenitor has already been extinct, the ancestral haplotypes (H18, H19) are remained in potential refuges:the scJDB population in central Japan (h=0.5606,π×10﹣3=0.362,R=0.936) and the scCJX population in East China (h=0.6970,π×10﹣3=1.105,R=1.182).
(3) Both phylogenetic reconstruction of nrITS and genealogical relationships of cpDNA sequences suggest the multiple origins of polyploid S. china. The polyploidization happened at least three times, which are located in South-west China, East China and Japan. Two major cpDNA lineages were identified in S. china complex, the Lineage A (Central-South-west-South China) and Grade B (East China-Korea-Japan). Demographic expansion could be detected in Lineage A (SSD=0.02099, P=0.055, Fu's Fs=-10.0181, P=0.006, Tajima'D=-1.83349, P=0.005,τ=1.25391), which might be a rapid expansion caused by polyploidization in around 0.094 Mya. Demographic expansion could not be detected in Grade B (SSD=0.50820, P=0, Fu's Fs=0.72222, P>0.05, Tajima'D=-0.65976, P>0.05).
(4) The results suggest that Japan population migrated from refuge in Central Japan to South Japan. S. china diploid populations are remained in Taiwan, the Ryukyu and Yaku-shima in Japan, which reflect the genetic drift and allopatric speciation during expansion. Unique habitats on island led diversification between such diploid species, involving S. china var. kuru, S. nantoensis and S. biflora.
引文
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