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题名	棕颈钩嘴鹛 (Pomatorhinus ruficollis) 的分子系统学和谱系地理学研究
作者	董锋
学位类别	博士
答辩日期	2013-11
授予单位	中国科学院研究生院
授予地点	北京
导师	杨君兴,杨晓君
关键词	棕颈钩嘴鹛 分子系统学 线粒体支系同域分布 并系性 线粒体袭夺
其他题名	Molecular phylogenetics and phylogeography of Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis)
学位专业	动物学
中文摘要	棕颈钩嘴鹛隶属于雀形目画眉科，是东洋区特有鸟类。具有复杂的分类历史，主要体现在其与灰头钩嘴鹛的分类关系及其台湾亚种的分类地位上。为探讨棕颈钩嘴鹛的分类地位，本研究共采集或收集了所有15个中的14个亚种的两个线粒体基因（总计2184bp），并对中国分布的10个亚种进行了5个核基因（总计2657bp）的测定。基于线粒体数据集的系统发育分析揭示棕颈钩嘴鹛是并系群，来自灰头钩嘴鹛的olivaceus支系聚合于其内部；传统棕颈钩嘴鹛共分化为4个地理支系, 即东部支系，台湾支系，中部支系和西部支系。结合棕颈钩嘴鹛与olivaceus支系在东南亚北部存在杂交的现象，建议将这一支系合并进入棕颈钩嘴鹛。基于多核基因的网络图和物种树分析皆显示台湾亚种独立于大陆所有亚种的支系，而后者内部无显著分化。这一结果支持近期基于形态分析将台湾亚种提升到种（台湾钩嘴鹛）的分类处理。研究中揭示了基于形态特征的传统分类学与分子系统学的显著不一致性，暗示多基因数据在分类学研究中的优势。 棕颈钩嘴鹛分子系统学研究同时暗示在某些区域存在线粒体支系同域现象。为更加明确的揭示这些现象，随后的研究加大了采样力度，包括133棕颈钩嘴鹛个体和4个完整的线粒体基因（共计3054bp）。基于线粒体数据集的系统发育分析共鉴别出4个线粒体支系同域地区，包括华中地区、滇西北地区、滇南地区和滇东南地区。这些现象可由两个截然不同的进化过程 - 谱系分化不完全或杂交导致。然而，目前尚未有效方法对二者进行区分。基于溯祖理论，本研究部分提出了一个新的分析思路：近缘种群间的杂交会显著增加线粒体基因的遗传多样性，而对核基因的影响轻微，因此，可使用核基因估算的种群参数进行预测性模拟分析，进而检验谱系分化不完全是否可足以揭示观察到的线粒体支系同域现象。研究中对71 – 78个棕颈钩嘴鹛个体补测了7个常染色体核基因（共计3708bp）以估计种群参数。模拟分析显示，所有四个地区的线粒体支系同域皆由杂交引起。对这些杂交区的进一步分析揭示了棕颈钩嘴鹛谱系地理研究的数个新格局：包括中国西南地区的次级相遇区，华中地区的完全混群以及华南地区的支系间断分布。 前述分子系统学研究同时揭示棕颈钩嘴鹛相对于台湾钩嘴鹛在线粒体基因树上的并系性，但当时的支持率并不高。为了进一步证明该格局的存在并阐明其背后的成因，随后的研究分别加大了两物种的基因采样力度。研究中使用三种溯祖模拟分析方法（MD, DC和ABC）三种模拟分析方法分析了棕颈钩嘴鹛（47个体）和台湾钩嘴鹛（18个体）的四个线粒体基因（共计3054bp）和9个核基因（4930bp）。基于线粒体的系统发育重建显示台湾钩嘴鹛高支持率与棕颈钩嘴鹛东部支系聚合，而基于核基因的物种树及网络图分析皆显示两物种的分化地位。溯祖模拟分析揭示由中国大陆向台湾的单向基因流导致了这种线粒体 - 核基因系统发育信号的不一致性。本研究提出的线粒体袭夺理论将为日后类似研究提供参考作用。
英文摘要	The streak-breasted scimitar babbler, Pomatorhinus ruficollis (Passerformes: Timallidae), is a babbler edemic to Oriental Region. This species has long been subject to taxonomic dabate, in terms of its relationship with P. schisticeps and the status of the Taiwanese subspecies. To infer the phylogeny of the P. ruficollis, the sequences of two complete mitochondrial genes (2184bp in total) from fourteen of the fifteen known subspecies, and an additional five nuclear genes (2657bp in total) from ten subspecies from China were examined. The mitochondrial phylogeny indicates four major clades (EAST, TAIWAN, CENTRAL and WEST) with large geographical identity in P. ruficollis and paraphyly of the P. ruficollis species complex, with the inclusion of the olivaceus group of congeneric P. schisticeps. Together with their interbreeding in northern Indochina, it was proposed to lump this group into P. ruficollis. Analysis of both multilocus networks and species-tree inference recovered poor phylogenetic structure among mainland subspecies and exclusive groupings of the Taiwanese subspecies, consistent with the recent taxonomic revision of its species status (P. musicus). The analyses also suggest strong incongruence between the morphological-based classification and molecular systematics, implying the strength of multilocus data for taxonomy. Molecular systematics on P. ruficollis suggested several cases of co-distribution of divergent mitochondrial lineage. An extensive sampling of four complete mitochondrial genes (3054bp in total) from 133 Streak-breasted Scimitar Babbler birds was used to identify regions with multiple mtDNA lineages. The mitochondrial phylogeny totally identifies four populations with multiple mtDNA lineages, including central China, northwest, south and southeast Yunnan. Yet no effective and widely applied approach exists. Hence, a new statistical framework based on coalescent simulations is proposed in this section. This approach is based on different predictions of the consequences of incomplete lineage sorting and introgression on molecular diversity for comparing mtDNA with nuDNA. Specifically, population parameters were estimated from nuclear loci, and then conducted predictive posterior simulations to test whether ILS was a sufficient explanation. For this aim, additional seven nuclear genes (totally 3708bp) from 71-78 birds are sequenced to estimate population parameters. The results of this analysis showed that all four identified populations with multiple mtDNA lineages are likely rendered by historical hybridization. Further analyses on these admixtures suggested several emergent patterns from phylogeography of this babbler, including additional contact zones in southwest China, complete admixture in central China and genealogical disjunction in south China. Molecular systematics on P. ruficollis also suggested plausible mitochondrial-gene-tree paraphyly of Pomatorhinus ruficollis with respect to P. musicus, but with low supports. To further verify this phylogenetic pattern and to clarify its potential causes, subsequential rearch was conducted with extensive gene sampling as four mtDNA (totally 3054bp) and nuDNA (totally 4930bp) and using three kinds of coalescent-based simulations. Phylogenetic reconstruction based mtDNA retrieved affinity of P. musicus and EAST clade of P. ruficollis with robust support. All simulation analyses suggest the cause of observed mitochondrial gene-tree paraphyly resulted from unidirectional gene flow from mainland to Taiwan. Mitochondrial capture theory proposed would provide a framework for future studies.
语种	中文
公开日期	2013-12-23
内容类型	学位论文
源URL	[http://159.226.149.42:8088/handle/152453/7744]
专题	昆明动物研究所_系统进化与生物地理学 昆明动物研究所_鸟类学
推荐引用方式 GB/T 7714	董锋. 棕颈钩嘴鹛 (Pomatorhinus ruficollis) 的分子系统学和谱系地理学研究[D]. 北京. 中国科学院研究生院. 2013.

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