基因流频繁发生下中菊头蝠类群间遗传分化与物种形成的基因组学研究

Speciation is the foundation of biodiversity. Ever since Darwin, it has been always the focus of evolutionary biology. With the introduction of next generation sequencing, it is possible to study genetic mechanism of speciation (i.e. evolution of reproductive isolation) from a genome-wide scale. At present, such studies are still very few. Hybrid zone formed between divergent lineages has been regarded as 'natural laboratory' in speciation. Our former phylogeographic studies on the intermediate horseshoe bat (Rhinolophus affinis) revealed the occurrence of introgressive hybridization and the formation of hybrid zone between two mainland subspecies of this species although they exhibited extremely divergent call frequencies that have been shown to be involved in prezygostic isolation. These results have been further confirmed by our preliminary experiment. In this project, we will apply a genome resequencing strategy to investigate levels of genetic differentiation and gene flow across the hybrid zone of the two subspecies from a genome-wide scale. Our first aim is to test whether genetic differentiations between the two subspecies mainly concentrate on a small number of genomic islands. By performing function enrichment and pathway analysis on candidate speciation genes which reside in those genomic islands, our second aim is to test whether these genes are related to either echolocation or hearing in bats. Our project will provide us an opportunity to put forward new mechanisms of speciation by studying the relationship of divergence and gene flow with two levels of gene and phenotype from a genomics view.

物种形成是生物多样性的基础，自达尔文以来，一直都是进化生物学领域的热点。下一代测序技术的引入，使从整个基因组层面研究物种形成（即生殖隔离演化）的遗传机制成为可能。目前，此类研究甚少。不同遗传类群间形成的杂交带是研究物种形成的‘天然实验室’。本课题申请者之前对中菊头蝠类群的系统地理学研究表明，该类群在大陆分布的两个亚种，虽然呈现极大差异的叫声频率（参与生殖前隔离），但彼此间仍能进行渐渗杂交，并形成杂交带。这一结论在我们的预实验中被进一步证实。本课题将应用基因组重测序技术，从整个基因组层面研究形成杂交带的两个亚种间遗传分化和基因流，证实它们间的遗传差异主要集中在少数几个基因组岛上，通过对基因组岛内蕴含的候选物种形成基因进行功能和通路的富集分析，验证这些基因是否与蝙蝠回声定位或听力相关。本课题立足于基因组学，结合基因和表型两个层次，来研究物种分化和基因流的关系，将有望揭示新的物种形成机制。

物种形成研究，即研究新物种是如何形成的，一直都是进化生物学领域的热点。随着测序技术的不断发展，物种形成研究已经过渡到从整个基因组层面研究物种间生殖隔离的产生机制。本项目主要研究中菊头蝠在中国的三个亚种，其中两个亚种在大陆东部地区形成杂交带，虽然它们间仍频繁发生杂交，但它们各自的回声定位叫声（听力）频率保持显著差异（相差近20 kHz）。本项目力求从整个基因组层面研究形成杂交带的两个亚种间遗传分化和基因流历史，检验它们间遗传差异是否集中在少数几个基因组岛上，并鉴定候选物种形成基因，检验它们是否与回声定位听力频率的变异相关。已有的重要结果：1）通过对2000多个核基因的重测序数据进行分析，发现形成杂交带的两个亚种间极少发生核基因的交流，虽然它们间可以发生整个线粒体基因组的完全置换；2）通过对三个亚种耳蜗转录组数据的分析，发现2个听力基因在不同听力频率亚种间存在显著的差异表达，其中一个基因已经通过荧光定量PCR得到验证；3）通过三代Nano pore和Hi-C测序技术，已完成中菊头蝠染色体级别的基因组组装，并对其进行了基因注释；4）已获得22个个体的基因组重测序数据，初步的基因组遗传差异分析显示，除X染色体外，存在极显著差异的基因组区域并没有集中在少数几个基因组岛上，而是在基因组中呈分散分布，下一步工作将扩大重测序个体的样本量来进一步检验基因组岛理论，并确定候选物种形成（或生殖隔离）基因。本项目和随后的进一步工作（以中菊头蝠为系统研究回声定位听力频率变异的遗传学基础）力求理解表型变异（回声定位听力频率的变异）和生殖隔离的产生（或物种形成）之间的关系，从而探讨生态物种形成（Ecological Speciation）的新机制。