Inferring speciation history of Drosophila by massive parallel sequencing

如何能使一個新物種形成，對演化生物學家來說仍然是有趣且重要的待解決問題。雖然已經有很多理論被提出，對於種化的進程的瞭解和能夠支持的適當例子仍相當有限。最近隨著大量平行定序技術的發展，比起以往我們能夠更容易的得到大量序列資料。這些充足的序列資料提供了一個絕佳的機會來研究過去缺乏序列資料時所難以回答的種化問題。此篇論文中，有兩個系統藉著大量平行序列資料來研究種化的問題。其一，為了演示種化的基因觀點，擬黃果蠅類群被作為研究的對象。藉由 4348 個基因序列資料，種化模型檢定揭露了這些基因間分歧時間有顯著的不同。此外，也發現了不同演化樹型的支持度鑲嵌在基因體中的現象。這些結果演示了基因體層次上的演化樹型不一致，且提出了在這個類群的種化過程中，扮演重要角色的候選基因。其二，為了分析造成種化的機制，黃果蠅的初期種化模型成為研究的對象。這個模型由具有行為隔離的全球型與辛巴威型組成。藉由族群基因體序列，分析出在各行為種中可能在演化歷史上經歷過適應的位點。另外藉由全轉錄體定序，分析得到在兩不同行為種間表現量有顯著歧異的基因。有趣的是，在辛巴威型果蠅中有顯著較高表現量的基因中，被發現和視覺有關功能的基因占有顯著的比例，而在全球型果蠅中有顯著較高表現量的基因，則是和代謝有關的基因。這些結果不僅提供研究行為隔離的遺傳基礎，也建議了種族分化的可能機制。To evolutionary biologist, how a new species arise remains an interesting and important question to solve. Though many hypothetical scenarios were proposed, it is still limited to understand how speciation progresses and discover proper cases to support. Currently, it is easier to sample the considerable sequences with the development of massive parallel sequencing (MPS). These abundant sequences provide a superior opportunity to approach speciation questions which were hard to assay before. Here, two systems with speciation questions were studied via the help of MPS. First, to demonstrate the genic view of speciation, Drosophila simulans clade were used as a model to analyze. With the sequences of 4348 genes, significantly heterogeneous divergence was revealed by the speciation model test. In addition, the genome-wide mosaic nature of phylogeny inference was also discovered. These results demonstrate the discordance of topologies among loci at the genomic level and proposed the candidates which can be crucial during speciation. Second, to assay the mechanisms which play an important roles in speciation, the incipient speciation model of Drosophila melanogaster were analyzed. This model comprises two behavioral isolated races, M (for cosmopolitan) and Z (for Zimbabwe). In each race, the adaptive loci were suggested by using population genome sequence. Moreover, the differentially expressed genes were found by using RNA-seq. Interestingly, the genes upregulated in the Z race are enriched for vision whereas genes upregulated in the M race are enriched in metabolic processes. These results not only provide the genetic basis of behavior isolation but also suggest the driving force underlying racial differentiation