基于叶绿体基因组构建辐射演化类群报春花属系统发育框架的研究

The estimation of phylogenetic relationships is an essential component of understanding evolution. Accurate phylogenetic estimation is difficult, especially for low taxonomic levels, recent divergence and rapid radiations. The main challenge of constructing the robust backbone relationships for rapid radiations is how to obtain enormous informative loci. Phylogenomics has proven useful for overcome low phylogenetic signal to noise ratios characteristic of rapid radiations. With current Next-generation sequencing (NGS) technologies, phylogenetic matrices based on hundreds of genes and involving thousands of species are readily feasible. Using NGS, rapid and complete chloroplast genome sequencing is now routine, which make us possible to obtain huge number of chloroplast genomes for any species in a short time at low cost. Chloroplast phylogenomics has clarified basal angiosperm relationships, and resolved rapid radiations that were intractable with smaller datasets. Therefore, the analyses is useful for tackle difficult phylogeny. The genus Primula is considered as a rapid radiation plant group, which contains 24 sections ca. 300 species in China, and most of them narrowly distributed in Himalaya-Hengduan Mountains. Constructing a robust phylogeny for the groups based on limited gene sequences (including intron and IGS) is particularly difficult. In this project, we plan to collect about 70-80 Primula species, which represent all major lineages of the genus. We then attempt to estimate the backbone relationships of the genus with chloroplast phylogenomic analyses, and to evaluate the potential of whole chloroplast genomes to resolve the phylogeny of intractable plants at lower taxonomic levels. This project will not only bring the benefits of improving the Primula phylogeny, but also make us easier to further address several fundamentally evolutionary questions in the genus, such as adaptive evolution, speciation, etc. We also hope the study will be a novel reference to resolve other recent radiations.

重建可靠的系统发育关系是进化生物学研究的基础，也是辐射进化类群研究的难点。对于年轻辐射演化类群而言，采用常规序列片段很难获得可靠的系统发育框架，采用海量序列信息是重建年轻辐射演化类群系统发育框架的唯一途径。叶绿体基因组单亲遗传，结构简单，大小合适，采用高通量测序平台的技术成熟，价格合理，是目前进行系统发育重建最有效的数据来源，为重建年轻辐射演化类群可靠的系统发育框架提供了契机。报春花属是典型的年轻辐射演化类群，至今还缺乏可靠的属下系统发育框架。本研究拟以报春花属为研究对象，选择来自属下不同位置的70-80个代表种，基于叶绿体基因组重建属下可靠的系统发育框架，并分析叶绿体基因组在报春花属内的变异规律。本项目将为进一步获取精细的报春花属系统发育关系以及更深入的进化生物学研究奠定基础，为其他近期辐射演化植物类群的系统发育研究提供典型案例。

本研究利用报春花属和广义报春花科的叶绿体基因组信息分别构建两种层面的系统发育关系，获得了这两个类群系统发育关系方面的一些全新的认识。同时也进行了一些关键类群的叶绿体基因组描述，为准确理解报春花科的叶绿体基因组结构和进化提供了大量数据。得到了以下主要结论：（1）本研究发现报春花属可分成四个主要分支（分支A，分支B，分支C和分支D的支持率都为100）。分支C（北美洲的两个分类群）与AB分支互为姐妹群。该系统关系在报春花属内第一次发现，为我们进一步理解报春花属的演化方式提供了新视角。在报春花属的组间关系方面，灯台报春组（sect. Proliferae）、雪山报春组（sect. Crystallophlomis）、球花报春组（sect. Denticulata）、粉报春组（sect. Aleuritia）、鄂报春组（sect. Obconicolisteri）、指叶报春组（sect. Cortusoides）、报春花组（sect. Monocarpicae），高峰报春组（sect. Minutissimae）、紫晶报春组（sect. Amethystina）都不是单系类群，这说明报春花属下的分类系统需要进一步改进。（2）整个广义报春花科构成单系群；杜茎山亚科（Measoideae）位于整个科的基部，与其他三个亚科组成的分支构成姐妹群，和以往的研究结果相一致；分布于中南美洲的假轮叶亚科（Theophrasteae）包含的属构成一支单系群（支持率为100），与报春花亚科和紫金牛亚科共同形成的分支互为姐妹群。其中东亚特有的假婆婆纳属（Stimpsonia）处于报春花亚科的基部；仙客来属的系统位置仍然不确定。总体而言，本研究得到的绝大多数分支都有很高的支持率，得到了更为精细系统发育关系。这证明利用叶绿体基因组数据可以获得较好系统发育关系，可为其他辐射类群的相关研究提供了典型案例。