Final Report Summary - RHINOSPEC (Dissecting speciation using a genomics approach) It is well known that hybridization play a very important role in the evolutionary process, however, its role in speciation has been intensely debated. And without genome-wide datasets it would be very difficult to distinguish between hybrid speciation, incomplete lineage sorting and introgression. Our project focused on the test of hybrid speciation in the R. sinicus-complex.The main aim in the returning phase of the Marie Curie grant is to start new projects using the knowledge and techniques learned during the two years in UK. For this aim, one the one hand, Dr. Mao continued his work in UK, and on the other hand, he started his new project on the speciation in the R. sinicus complex, including three recent diverged taxa (R. s. septentrionalis, Central R. s. sinicus and East R. s. sinicus). In this new project, he aim to test the hypothesis of hybrid speciation for the origin of Central R. s. sinicus. For this, he test two main predictions of this hypothesis:(1) a historical hybridization will be detected in the parental taxa, R. s. septentrionalis and East R. s. sinicus;(2) the number of loci clustering Central R. s. sinicus and either R. s. septentrionalis or East R. s. sinicus could be similar.Firstly, we generated RNA-seq datasets from three focal taxa (R. s. septentrionalis, Central R. s. sinicus and East R. s. sinicus) and three other horseshoe bats (R. pearsoni chinensis, R. rex and R. ferrumequinum). This work has been done.Secondly, for samples from the R. sinicus-complex, we also used targeted resequencing strategy which has been used in R. pearsoni complex when Dr. Mao worked in UK. This method can generate sequences from 1935 genes in 36 samples including three focal taxa (R. s. septentrionalis, Central R. s. sinicus and East R. s. sinicus). We have finished the data collection.We have finished the analysis of the RNA-seq data for the R. sinicus-complex. The evidence of hybridization among the three focal taxa was supported by three different methods. First, in BUCKy analysis, we found two alternative bipartitions (not in the concordance tree) with CFs higher than 0.1 and their credibility intervals are non-overlapping, suggesting evidence for hybridization. Second, an asymmetry in support for one of the two non-species tree topologies suggested the occurrence of hybridization between Central R. s. sinicus and R. s. septentrionalis. Third, D-statistic in the ABBA-BABA test for the comparison of (((East R. s. sinicus, Central R. s. sinicus), R. s. septentrionalis), R. rex) was positive and significantly different from zero (D = 0.1327 P = 1.6 x 10-5), suggesting introgression between Central R. s. sinicus and R. s. septentrionalis. Thus, this study provides evidences for supporting the hybrid speciation hypothesis in this group of taxa.We are still in the process of analysing the targeted resequencing data. Currently, we have obtained sequences of 13 mitochondrial protein-coding genes from all samples. Phylogenetic analysis revealed similar tree topology with the one in our previous study.In the coming months, we will continue to analysis the rest of data and test for the hybrid speciation hypothesis using genome-wide data from populations. We anticipate that our method (the combination of RNA-seq and targeted resequencing data) and findings will be greatly helpful to understand the role of hybridization in speciation.
