从种群遗传学、系统地理学和系统基因组学等方面研究Strepiocarpus ionanthus（苦苣苔科）种内复杂的演化
发布时间：2021-01-13 03:00
Streptocarpus ionanthus（苦苣苔科:海角苣苔属）是坦桑尼亚和肯尼亚特有的草本植物,分布在坦噶,莫罗戈罗和基利菲地区。该物种包括九个密切相关的亚种,亚种之间有着复杂的形态特征和尚不明晰的演化关系,导致该物种复合体一直以来在分类处理上未能达成一致。悬而未决的物种界定使得弄清其种下分类单元之间的亲缘关系变得复杂,这又严重影响了对这一濒危物种保育工作。同时Str.Ionanthus也为我们研究物种演化的时空动态变化提供一个理想的材料。此项工作综合多种方法,对整个分布区的23个居群取样,旨在重建Str.ionanthus的演化历史。运用叶绿体基因组和核基因组的SSR分子标记,我们对遗传多样性,居群结构和分化进行了讨论,同时还对叶绿体基因组四个片段进行了谱系地理学结构分析。基于以往对叶绿体替代率的研究结果,我们对叶绿体DNA的单倍型进行分析,以此来探讨Str.ionanthus的分化历史。生态位模型分析有助于我们理解Str.ionanthus的过去（末次间冰期和末次盛冰期）、现在和将来（未来五十年）。此外,对五个亚种的叶绿体基因组得到组装和注释,在基因组水平上对结构特征和DN...
【文章来源】：中国科学院大学(中国科学院武汉植物园)湖北省
【文章页数】：129 页
【学位级别】：博士
【文章目录】：
摘要
abstract
Chapter 1 Introduction
1.1 Background information
1.1.1 Taxonomy,distribution& ecology of section Saintpaulia
1.1.2 Conservation status of Streptocarpus section Saintpaulia
1.2 Literature review
1.2.1 Phylogenetic history of Str.sect.Saintpaulia
1.2.2 Evolutionary complexity of Streptocarpus ionanthus
1.2.3 Genetic diversity studies in Str.sect.Saintpaulia
1.3 Problem statement
1.4 Justification of the study
1.5 Research objectives
1.5.1 Main objective
1.5.2 Specific objectives
CHAPTER 2 Development of Molecular markers for Streptocarpus section Saintpaulia
2.1 Introduction
2.1.1 Molecular markers
2.1.2 Previous Molecular markers in Saintpaulia
2.2 Material and Methods
2.2.1 Sampling and DNA isolation
2.2.2 Development of Microsatellite markers for Streptocarpus teitensis
2.2.3 Development of Microsatellites for Str.ionanthus subsp.grandifolius
2.2.4 Chloroplast DNA（cpDNA）markers
2.3 Results and Conclusion
Chapter 3 Multiple Pleistocene refugia and recent diversification for Streptocarpus ionanthus（Gesneriaceae）complex:insights from multiple molecular sources
3.1 Introduction
3.2 Material& Methods
3.2.1 Study species& Sampling
3.2.2 Morphological representation
3.2.3 DNA Extraction
3.2.4 Microsatellite genotyping
3.2.5 Population Structuring
3.2.6 Chloroplast DNA（cpDNA）sequencing
3.2.7 Phylogeography& Divergence estimate
3.2.8 Past,present and future distribution of Streptocarpus ionanthus
3.3 Results
3.3.1 Genetic Diversity
3.3.2 Genetic Clustering
3.3.3 Demography statistics
3.3.4 Chloroplast DNA Diversity,Phylogeography& Divergence estimate
3.3.5 Past,present and future distribution of Streptocarpus ionanthus
3.4 Discussion
3.4.1 Genetic Diversity
3.4.2 Genetic structuring
3.4.3 Diversification of Streptocarpus ionanthus
3.4.4 Highlights on Streptocarpus ionanthus conservation
3.5 Conclusion
Chapter 4 Chloroplast phylogenomics reveal low polymorphism within Streptocarpus ionanthus（Gesneriaceae）:comparative analyses of five subspecies
4.1 Introduction
4.2 Material and Methods
4.2.1 Sampling,Laboratory experiments and Sequencing
4.2.2 Assembly and gene annotation
4.2.3 Genome comparisons
4.2.4 Identification of divergent hotspots and SSRs
4.2.5 Phylogenetic analysis
4.3 Results
4.3.1 Overall features of Streptocarpus ionanthus chloroplast genome
4.3.2 Genome comparison within Streptocarpus ionanthus
4.3.3 Divergent hotspots and SSRs in Streptocarpus ionanthus
4.3.4 Phylogenetic analysis
4.4 Discussion
4.4.1 Analysis of Genome features
4.4.2 Divergence hotspots in Streptocarpus ionanthus
4.4.3 Phylogenetic relationship within Streptocarpus ionanthus
4.5 Perspectives on Streptocarpus ionanthus research
4.6 Conclusion
Chapter 5 Integrating molecular phylogeny and morphological characters to discuss Streptocarpus ionanthus complex（Gesneriaceae）taxonomy
5.1 Introduction
5.2 Materials and Methods
5.2.1 Study plan& data source
5.2.2 Morphological analysis
5.2.3 Distribution& habitat
5.2.4 Molecular Phylogenetic Analyses of nuclear and chloroplast DNA Regions
5.3 Results
5.3.1 Review of morphological characters in Streptocarpus ionanthus
5.3.2 Molecular combinations
5.4 Discussion
5.5 Highlights on Streptocarpus ionanthus taxonomy
5.6 Conclusion
Chapter 6 Conclusion and Prospects
References
Appendices
Acknowledgement
Author profile and Publications
本文编号：2974071
【文章来源】：中国科学院大学(中国科学院武汉植物园)湖北省
【文章页数】：129 页
【学位级别】：博士
【文章目录】：
摘要
abstract
Chapter 1 Introduction
1.1 Background information
1.1.1 Taxonomy,distribution& ecology of section Saintpaulia
1.1.2 Conservation status of Streptocarpus section Saintpaulia
1.2 Literature review
1.2.1 Phylogenetic history of Str.sect.Saintpaulia
1.2.2 Evolutionary complexity of Streptocarpus ionanthus
1.2.3 Genetic diversity studies in Str.sect.Saintpaulia
1.3 Problem statement
1.4 Justification of the study
1.5 Research objectives
1.5.1 Main objective
1.5.2 Specific objectives
CHAPTER 2 Development of Molecular markers for Streptocarpus section Saintpaulia
2.1 Introduction
2.1.1 Molecular markers
2.1.2 Previous Molecular markers in Saintpaulia
2.2 Material and Methods
2.2.1 Sampling and DNA isolation
2.2.2 Development of Microsatellite markers for Streptocarpus teitensis
2.2.3 Development of Microsatellites for Str.ionanthus subsp.grandifolius
2.2.4 Chloroplast DNA（cpDNA）markers
2.3 Results and Conclusion
Chapter 3 Multiple Pleistocene refugia and recent diversification for Streptocarpus ionanthus（Gesneriaceae）complex:insights from multiple molecular sources
3.1 Introduction
3.2 Material& Methods
3.2.1 Study species& Sampling
3.2.2 Morphological representation
3.2.3 DNA Extraction
3.2.4 Microsatellite genotyping
3.2.5 Population Structuring
3.2.6 Chloroplast DNA（cpDNA）sequencing
3.2.7 Phylogeography& Divergence estimate
3.2.8 Past,present and future distribution of Streptocarpus ionanthus
3.3 Results
3.3.1 Genetic Diversity
3.3.2 Genetic Clustering
3.3.3 Demography statistics
3.3.4 Chloroplast DNA Diversity,Phylogeography& Divergence estimate
3.3.5 Past,present and future distribution of Streptocarpus ionanthus
3.4 Discussion
3.4.1 Genetic Diversity
3.4.2 Genetic structuring
3.4.3 Diversification of Streptocarpus ionanthus
3.4.4 Highlights on Streptocarpus ionanthus conservation
3.5 Conclusion
Chapter 4 Chloroplast phylogenomics reveal low polymorphism within Streptocarpus ionanthus（Gesneriaceae）:comparative analyses of five subspecies
4.1 Introduction
4.2 Material and Methods
4.2.1 Sampling,Laboratory experiments and Sequencing
4.2.2 Assembly and gene annotation
4.2.3 Genome comparisons
4.2.4 Identification of divergent hotspots and SSRs
4.2.5 Phylogenetic analysis
4.3 Results
4.3.1 Overall features of Streptocarpus ionanthus chloroplast genome
4.3.2 Genome comparison within Streptocarpus ionanthus
4.3.3 Divergent hotspots and SSRs in Streptocarpus ionanthus
4.3.4 Phylogenetic analysis
4.4 Discussion
4.4.1 Analysis of Genome features
4.4.2 Divergence hotspots in Streptocarpus ionanthus
4.4.3 Phylogenetic relationship within Streptocarpus ionanthus
4.5 Perspectives on Streptocarpus ionanthus research
4.6 Conclusion
Chapter 5 Integrating molecular phylogeny and morphological characters to discuss Streptocarpus ionanthus complex（Gesneriaceae）taxonomy
5.1 Introduction
5.2 Materials and Methods
5.2.1 Study plan& data source
5.2.2 Morphological analysis
5.2.3 Distribution& habitat
5.2.4 Molecular Phylogenetic Analyses of nuclear and chloroplast DNA Regions
5.3 Results
5.3.1 Review of morphological characters in Streptocarpus ionanthus
5.3.2 Molecular combinations
5.4 Discussion
5.5 Highlights on Streptocarpus ionanthus taxonomy
5.6 Conclusion
Chapter 6 Conclusion and Prospects
References
Appendices
Acknowledgement
Author profile and Publications
本文编号：2974071
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