象科动物线粒体蛋白编码基因的进化和物种鉴定研究

发布时间：2021-03-09 05:06

　　线粒体蛋白编码基因（MPCG）序列被广泛地用于分析物种的适应性进化、系统进化关系,也用于物种鉴定,其有效性在很多分类单元中都进行了评估。但是在象科动物的系统研究较少,如猛犸象的线粒体基因如何适应寒冷、干旱的环境;细胞色素b（Cyt-b）和COI基因的种间变异以及在鉴别象科动物的有效性;和如何就线粒体基因有效鉴别象科动物,同时还能有效排除其他物种及人源DNA的污染等方面少有报道。本研究针对三种现生象（即亚洲象、非洲草原象和非洲森林象）和已灭绝的猛犸象,通过13个完整的MPCG序列,检测猛犸象对干旱寒冷环境适应性选择的证据;对比评价Cyt-b和COI部分短序列区分4种象科动物的有效性;开发一种基于PCR的物种鉴定方法。首先,我们分析了 75头分布广泛的长毛象的13个线粒体蛋白质编码基因序列,继进行阳性选择的信号检测,生化和蛋白质结构分析以及生化和同源蛋白分析。结果显示:6个MPCGs基因（ND1、ND4、ND5、ND6、ATP6和Cyt-b）中的11个氨基酸位点显示出正向选择,一些突变能够影响线粒体复合体Ⅰ中蛋白-蛋白相互作用和氧化磷酸化过程,尤其是ATP6和Cyt-b残基的突变能够影响代... 

【文章来源】：东北林业大学黑龙江省 211工程院校 教育部直属院校

【文章页数】：136 页

【学位级别】：博士

【文章目录】：
摘要
Abstract
1 Literature Review:evolutionary analysis and genetic species identification ofelephantids: current knowledge and gaps
    1.1 Introduction to evolution and evolutionary relationship among elephantids
    1.2 Threats and present status of elephants
    1.3 The role of wildlife forensics in curtailing poaching and ivory trade
    1.4 Species concept and principles of species identification
    1.5 Current methods of identifying species
        1.5.1 Morphology
        1.5.2 DNA-based species identification
    1.6 Statistical methods for DNA species identification
        1.6.1 Similarity based method
        1.6.2 Genetic distance strategy
        1.6.3 Tree-based method
        1.6.4 Diagnostic nucleotide method
    1.7 Challenges in DNA based species identification
    1.8 Elephantids identification using Cyt-b and COI genes
    1.9 Intra-and interspecific divergence among elephantids based on mtDNA
    1.10 Purpose and main objectives of research
        1.10.1 Purpose and general objective
        1.10.2 Main objectives of the research
2 Positive selection in the mitochondrial protein-coding genes of woolly mammoths
    2.1 Introduction
    2.2 Methods
        2.2.1 Sequence collection
        2.2.2 Alignment and selection analyses
        2.2.3 Protein modelling and structural analyses
    2.3 Results
        2.3.1 Phylogenetic analyses
        2.3.2 Physicochemical property changes
        2.3.3 Amino acid substitutions in OXPHOS complex 1
        2.3.4 Amino acid substitutions in OXPHOS complexes Ⅲ,Ⅳ and Ⅴ
    2.4 Discussion
3 Assessing the effect of the reduced fragments sizes of cytochrome b and COI geneson species identification of elephantids
    3.1 Introduction
    3.2 Materials and methods
        3.2.1 Extraction, amplification and sequencing of DNA
        3.2.2 Sequence alignment and analyses
        3.2.3 Phylogenetic resolution analysis
        3.2.4 Similarity based species assignment
    3.3 Results
        3.3.1 Sequence conservation and variability
        3.3.2 Intra-and interspecific pairwise distances
        3.3.3 Phylogenetic resolution
        3.3.4 Success rate of similarity based identifications
    3.4 Discussion
4 Species identification of extant and extinct elephantid specimens using a shortfragment of cytochrome b gene
    4.1 Introduction
    4.2 Materials and methods
        4.2.1 Sample collection and DNA isolation
        4.2.2 Designing primers
        4.2.3 Primer Validation
    4.3 Results
        4.3.1 Reproducibility and specificity
        4.3.2 Resolution for species identification
        4.3.3 Sensitivity
    4.4 Discussion
Conclusion
References
Appendix
Academic papers published during the study
Acknowledgements



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