沙芥属（十字花科）物种界定及物种形成研究
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摘要
沙芥属(Pugionium)是十字花科(Brassicaceae)中的一个小属,也是亚洲中部蒙古高原的特有属,主要分布于中国西北部典型草原带的半固定或流动沙地上。该属物种的分类一直存在较大争议,曾报道有五个种和一个变种,现在普遍认为应合并为沙芥和斧形沙芥两个物种。由于沙芥属植物形态变异复杂多样,分类历史争议不断,可用DNA条形码技术来进行物种界定；同时也能反向验证各种不同类型的DNA条形码片段对近缘物种的界定能力。另外,沙芥和斧形沙芥虽为同属仅有的两个姊妹种,却具有明显的形态学差异和不同的栖息地偏好,是研究干旱沙漠生境下植物物种分化的理想材料。
本文主要包括沙芥属DNA条形码研究和物种形成两方面的研究：
一、本文以沙芥和斧形沙芥为研究对象,采用近年来兴起的DNA条形码技术,进一步确认沙芥属的物种划分情况,反之亦能比较不同类型基因片段对近缘种的界定能力。我们检测了三个建议的cpDNA片段(rbcL, trnH-psbA, matK),核基因ITS和五个随机选择的低拷贝核基因位点,藉以评估哪种片段是更适合区分近缘物种的理想条码。
研究结果表明,在叶绿体DNA片段rbcL和trnH-psbA上,10个沙芥属个体的序列均未出现任何种内或种间的变异,尽管我们在matK中发现了一处突变,但形成的两种单倍型却在物种间共享。ITS序列中发生了一处单碱基突变并可以严格的将这两个物种区分开来。低拷贝核基因片段上,两个物种的所有个体都出现了多处变异,但只有与花期调节有关的基因Det/可将两个物种完全区分开来。但该片段的通用性较差,在十字花科之外的其他物种中很难扩增。不同类型基因片段的物种鉴定能力差异,可能受不完全谱系筛选、基因流和种间特异性进化等多种因素影响。
我们的结果表明,cpDNA片段在界定近缘物种方面能力有限；低拷贝核基因做为植物条形码的局限性太大,有许多问题需要克服；而ITS可作为区分近期分化物种的一个关键条形码片段,至少是一个重要的补充片段。
二、第四纪全球气温波动较大、冰川期和间冰期交替,特别是更新世以来全球的气候环境发生了巨大的变化。目前已有许多研究证明,更新世的气候震荡对对许多动植物的进化历史和种群遗传结构分化具有重要的影响。但是该时期的气候活动对物种形成是否也有同样重要的作用,对这方面问题的研究工作较少,机制尚不明确。我们以沙芥和斧形沙芥为研究对象,对两物种自然分布区内各11个种群的样品进行了ITS,三套叶绿体DNA (cpDNA)片段和8个低拷贝核基因的扩增和测序并做了群体遗传学分析。
分析发现,这两个沙芥属物种在ITS序列上有固定性碱基差异,但在三个叶绿体DNA片段上尚无发现。在本文中研究的8个低拷贝核基因片段中,与光调节基因表达有关的核基因座位(Detl)表现出了最高的种间分化。我们对这些核基因位点的序列变异和ITS的序列分化进行了模拟分析,对低拷贝核基因片段数据集的分析结果显示沙芥和斧形沙芥的分化发生在大约3.2-3.8万年前,这一时间晚于根据ITS估算的结果(8-16万年前)。两组结果都显示沙芥的物种分化始于更新世(Pleistocene),历史上这段时期中国中西部发生了大规模的沙丘移动和沙漠扩张扩张。我们的结果表明,更新世的气候变化导致干旱问题加剧、中国西北部沙漠扩张,从而引发沙漠内生境多样化,在这些因素的共同影响下促进了沙芥属的物种分化。
Pugionium Gaertn (Brassicaceae) is a typical psammophytes endemic to Mongolian plateau of the central Asia. This genus occurs mainly in the arid or semi-arid desert regions with only two species acknowledges based on the recent taxonomic revision, i.e., P. dolabratum and P. cornutum. We used these two species as a model system to examine the accuracy and effectiveness of DNA fragments suggested for plant barcodes. The second part of this thesis was to trace speciation divergences of these two species. The only two species of this genus differ from each other in habitat, morphology and growth form.
1. Three kinds of DNA markers were tested, comprising three chloroplast (cp) DNA fragments(rbcL, matK, and trnH-psbA), nuclear ribosomal internal transcribed regions (ITS) and five low-copy nuclear loci. There is no any fixed interspecific variation for three cpDNA fragments and therefore none of them is useful to discriminate these two species. However, a single base mutation in the internal transcribed spacer (ITS) could discriminate between the two species consistently. We found more variations among all individuals of the two species using each of the other five low-copy nuclear loci. However, only alleles from one locus (Det1) of the five low-copy loci related to flowering regulation was able to distinguish the sampled individuals into two species. However, it is difficult to amplify the corresponding fragments of this locus out of Brassicaceae using the designed Det1primers. These results suggested that three cpDNA fragments are useless to discriminate these two closely-related species. In addition, it is still difficult to use any examined low-copy nuclear fragments as the candidate plant barcodes. In addition, these tests further suggested that ITS is a useful fragment as a core or complementary barcode to distinguish the recent diverged species.
2. Pleistocene climate change is known to have had an important effect in shaping intraspecific genetic variation in many species; however, its role in driving speciation is less clear. We examined the possibility of a Pleistocene origin of the only two representatives of the genus Pugionium (Brassicaceae), P. cornutum and P. dolabratum, which occupy different desert habitats in northwest China. We surveyed sequence variation for ITS, three chloroplast (cp) DNA fragments, and eight low copy nuclear genes among individuals sampled from eleven populations of each species across their geographic ranges. One ITS-mutation distinguished the two species whereas mutations in cpDNA and the eight low copy nuclear gene sequences were not species-specific. Although interspecific divergence varied greatly among nuclear gene sequences, in each case divergence was estimated to have occurred within the Pleistocene when deserts expanded in northwest China. Our findings point to the importance of Pleistocene climate change, in this case an increase in aridity, as a cause of speciation in Pugionium due to divergence in different desert habitats that formed in association with the expansion of deserts in China.
本文主要包括沙芥属DNA条形码研究和物种形成两方面的研究：
一、本文以沙芥和斧形沙芥为研究对象,采用近年来兴起的DNA条形码技术,进一步确认沙芥属的物种划分情况,反之亦能比较不同类型基因片段对近缘种的界定能力。我们检测了三个建议的cpDNA片段(rbcL, trnH-psbA, matK),核基因ITS和五个随机选择的低拷贝核基因位点,藉以评估哪种片段是更适合区分近缘物种的理想条码。
研究结果表明,在叶绿体DNA片段rbcL和trnH-psbA上,10个沙芥属个体的序列均未出现任何种内或种间的变异,尽管我们在matK中发现了一处突变,但形成的两种单倍型却在物种间共享。ITS序列中发生了一处单碱基突变并可以严格的将这两个物种区分开来。低拷贝核基因片段上,两个物种的所有个体都出现了多处变异,但只有与花期调节有关的基因Det/可将两个物种完全区分开来。但该片段的通用性较差,在十字花科之外的其他物种中很难扩增。不同类型基因片段的物种鉴定能力差异,可能受不完全谱系筛选、基因流和种间特异性进化等多种因素影响。
我们的结果表明,cpDNA片段在界定近缘物种方面能力有限；低拷贝核基因做为植物条形码的局限性太大,有许多问题需要克服；而ITS可作为区分近期分化物种的一个关键条形码片段,至少是一个重要的补充片段。
二、第四纪全球气温波动较大、冰川期和间冰期交替,特别是更新世以来全球的气候环境发生了巨大的变化。目前已有许多研究证明,更新世的气候震荡对对许多动植物的进化历史和种群遗传结构分化具有重要的影响。但是该时期的气候活动对物种形成是否也有同样重要的作用,对这方面问题的研究工作较少,机制尚不明确。我们以沙芥和斧形沙芥为研究对象,对两物种自然分布区内各11个种群的样品进行了ITS,三套叶绿体DNA (cpDNA)片段和8个低拷贝核基因的扩增和测序并做了群体遗传学分析。
分析发现,这两个沙芥属物种在ITS序列上有固定性碱基差异,但在三个叶绿体DNA片段上尚无发现。在本文中研究的8个低拷贝核基因片段中,与光调节基因表达有关的核基因座位(Detl)表现出了最高的种间分化。我们对这些核基因位点的序列变异和ITS的序列分化进行了模拟分析,对低拷贝核基因片段数据集的分析结果显示沙芥和斧形沙芥的分化发生在大约3.2-3.8万年前,这一时间晚于根据ITS估算的结果(8-16万年前)。两组结果都显示沙芥的物种分化始于更新世(Pleistocene),历史上这段时期中国中西部发生了大规模的沙丘移动和沙漠扩张扩张。我们的结果表明,更新世的气候变化导致干旱问题加剧、中国西北部沙漠扩张,从而引发沙漠内生境多样化,在这些因素的共同影响下促进了沙芥属的物种分化。
Pugionium Gaertn (Brassicaceae) is a typical psammophytes endemic to Mongolian plateau of the central Asia. This genus occurs mainly in the arid or semi-arid desert regions with only two species acknowledges based on the recent taxonomic revision, i.e., P. dolabratum and P. cornutum. We used these two species as a model system to examine the accuracy and effectiveness of DNA fragments suggested for plant barcodes. The second part of this thesis was to trace speciation divergences of these two species. The only two species of this genus differ from each other in habitat, morphology and growth form.
1. Three kinds of DNA markers were tested, comprising three chloroplast (cp) DNA fragments(rbcL, matK, and trnH-psbA), nuclear ribosomal internal transcribed regions (ITS) and five low-copy nuclear loci. There is no any fixed interspecific variation for three cpDNA fragments and therefore none of them is useful to discriminate these two species. However, a single base mutation in the internal transcribed spacer (ITS) could discriminate between the two species consistently. We found more variations among all individuals of the two species using each of the other five low-copy nuclear loci. However, only alleles from one locus (Det1) of the five low-copy loci related to flowering regulation was able to distinguish the sampled individuals into two species. However, it is difficult to amplify the corresponding fragments of this locus out of Brassicaceae using the designed Det1primers. These results suggested that three cpDNA fragments are useless to discriminate these two closely-related species. In addition, it is still difficult to use any examined low-copy nuclear fragments as the candidate plant barcodes. In addition, these tests further suggested that ITS is a useful fragment as a core or complementary barcode to distinguish the recent diverged species.
2. Pleistocene climate change is known to have had an important effect in shaping intraspecific genetic variation in many species; however, its role in driving speciation is less clear. We examined the possibility of a Pleistocene origin of the only two representatives of the genus Pugionium (Brassicaceae), P. cornutum and P. dolabratum, which occupy different desert habitats in northwest China. We surveyed sequence variation for ITS, three chloroplast (cp) DNA fragments, and eight low copy nuclear genes among individuals sampled from eleven populations of each species across their geographic ranges. One ITS-mutation distinguished the two species whereas mutations in cpDNA and the eight low copy nuclear gene sequences were not species-specific. Although interspecific divergence varied greatly among nuclear gene sequences, in each case divergence was estimated to have occurred within the Pleistocene when deserts expanded in northwest China. Our findings point to the importance of Pleistocene climate change, in this case an increase in aridity, as a cause of speciation in Pugionium due to divergence in different desert habitats that formed in association with the expansion of deserts in China.
引文
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