基于系统发育基因组学方法构建果蝇科主干类群进化关系

The family Drosophilidae is large, diverse and widely distributed. Numbers of species (eg. Drosophila melanogaster) in this family have served as classical model species and received extensive attention from geneticists and evolutionary biologists. However, most of the previous molecular phylogenetic works concerning the basal phylogeny in this family suffered from either restricted numbers of characters or insufficient or biased taxon-sampling. The resulting phylogenies in these studies proved to be more or less imperfect in light of reliability and completeness, hindering their usage in evolutionary inference and in drosophilid taxonomy. Phylogenomics shed a new light on this field. In the present proposal, we intend to reconstruct the phylogenetic relationship of the Drosophilidae using phylogenomics methods. About 70-80 representative species covering main evolution branches of the Drosophilidae will be picked through a reasonable taxon-sampling approach, especially the species distribution in Yunnan. Total RNA of samples will be extracted, following deep RNA-seq and assembly. Combined published genomes and transcriptomes of the Drosophilidae, the molecular markers will be filtered by orthologous and bioinformatics analysis. Then, and we will construct a full and reliable phylogenomic framework of the Drosophilidae. Upon it, divergence time of different branches and evolutionary rate of genes can be calculated. It will offer a dependable reference for taxonomy and evolutionary studies of the Drosophilidae. Furthermore, combined geographical and phenotypical data, we will defined the genes and sites under the select pressure on different species through PAML, and decipher the genetic basis of geographical distribution patterns and adaptive evolution of the Drosophilidae.

果蝇科是一个高度多样化的类群，其分布遍及世界。科内的黑腹果蝇等是经典的模式物种，受到遗传和进化生物学家的广泛关注。以往的果蝇科系统发育关系构建主要基于少量基因的序列，在类元取样上也无法覆盖科内大多数主要分枝，其结果不够完整和可靠，无法支撑基于其上的进化分析，也不利于该科分类学的完善和发展。本项目拟使用系统基因组学的方法，通过科学的类元取样设计，选取70-80种果蝇科内大部分主干类群的代表物种（尤其是一些云南有分布的物种）进行深度转录组测序并组装，结合已公布的果蝇科物种基因组数据，筛选出直系同源单拷贝基因，以此获得氨基酸/核酸序列矩阵构建一个较为可靠、全面的果蝇主干系统发育框架。并基于此估计谱系间分歧时间，计算基因的进化速率，为修订果蝇科分类关系提供新的依据。在此基础上根据序列差异界定不同进化枝上受选择的基因和位点，并结合地理分布、表型数据等探讨果蝇科现有地理分布模式及适应性进化的遗传基础。

果蝇科的遗传和进化备受关注。以往的果蝇科系统发育关系构建主要基于少量基因的 序列，在类元取样上也无法覆盖科内大多数主要分枝，其结果不够完整和可靠，无法支撑基于其上的进化分析，也不利于该科分类学的完善和发展。本项目通过科学的类元取样设计，选取66种果蝇物种及4种外群物种，涵盖科内大部分主干类群的代表物种。其中16个物种的编码基因的氨基酸序列和核酸序列下载自数据库NCBI和OrthDB，另54个物种经过表型和DNA条形码鉴定出物种后，提取RNA进行深度转录组测序并组装出编码基因的氨基酸序列和核酸序列。基于OrthDB数据库中双翅目同源基因数据库，以Blast的方法筛选出以上所有70个物种的直系同源单拷贝基因。经过序列比对和筛选后，通过多种不同方法构建最大似然树，包括联合基因构树、联合记基因分区构树、部分物种联合基因构树等不同方法，最终综合得出果蝇科主干类群的系统发育关系。分析果蝇科各分枝所含属和物种，对各属和各物种所处系统发育关系位置进行探讨。基于此重建的果蝇科主干类群系统发育关系，计算基因的进化速率，估计谱系间分歧时间，为修订果蝇科分类关系提供新的依据。