Dietary Diversification In Birds And Species Divergence In Spiny Mice Revealed By Whole Genome Data

With the rapid development of genomics and next generation sequencing,comparative genomics plays an important role in zoology,genetics and evolutionary biology.Based on genomic data,this dissertation uncovered the potential genetic bases of dietary diversification in birds and species divergence in spine mice using comparative genomics and relevant bioinformatics.Firstly,we studied bitter taste receptor genes in birds with diverse feeding habits through comparing 48 published avian genomes.As they belong to themost species-rich classof tetrapod vertebrates,birds have long been believed to possess an inferior taste system.However,the bitter taste is fundamental in birds to recognize dietary toxins(which are typically bitter)in potential food sources.To characterize the evolution of avian bitter taste receptor genes(Tas2rs)and to testwhether dietary toxins have shaped the repertoire size of avian Tas2rs,we examined 48 genomes representing all but 3 avian orders.The total number of Tas2r genes was found to range from 1 in the domestic pigeon to 12 in the bar-tailed trogon,with an average of 4,which suggested that amuch smaller Tas2r gene repertoire exists in birds than in other vertebrates.Furthermore,we uncovered a positive correlation between the number of putatively functional Tas2rs and the abundance of potential toxins in avian diets.Because plant products contain more toxins than animal tissues and insects release poisonous defensive secretions,we hypothesized that herbivorous and insectivorous birds may demandmore functional Tas2rs than carnivorous birds feeding on noninsect animals.Our analyses appear to support this hypothesis and highlight the critical role of taste perception in birds.Secondly,the whole genome of the spiny mouse Acomys cahirinus was sequenced and de novo assembled.This study is the first report of the draft genome for spiny mice.Further analysis indicated that the genome quality of Acomys cahirinus is comparabale to other rodents with public genome sequence,representing a valuable genomic resource for studying the evolution of specialized morphological traits and ecological adaptation of spiny mice.Moreover,we analyzed the phylogenetic relationship between spiny mice and other glires based on phylogenomics.The results are consistent with previously phylogenetic studies about glires on the basis of nuclear or mitochondrial data,which showed that Lagomorpha and Rodentia are the sister group;rodents are divided into 3 distinct clades(Ctenohystrica?Mouse-related clade and Squirrel-related clade);spiny mice is a member of Muridae.This study confirmed the phylogenetic relationship within examined taxa from glires in this study.Thirdly,taking advantage of whole-genome resequencing approach,we revealed the potential genetic basis for species divergence in spiny mice from the Evolution Canyon(EC-I),Mount Carmel Israel.Speciation with ongoing homogenizing gene flow is a fascinating and debated topic since it was proposed by Darwin,which was taken as sympatric speciation later.Here we show a case of incipient sympatric speciation with gene flow revealed by whole genome sequencing from the Evolution Canyon(EC-I),Mount Carmel Israel The two slope populations from EC-I displayed two sharp genomic clusters by both neighbor-joining tree and principal component analysis,which was consistent with their ecological origins.Population structure analysis shows that animals from the African slope(AS)were perfectly clustered into one group,while those from the European slope(ES)showed two substructures,possibly due to the multiple migration from AS.The genetic diversity of the AS population is significantly higher than that of the ES population,which was due to the balancing selection on this population The recombination rate of the AS population is significantly higher than that of ES population,which possibly increases the diversity of the population.The two populations diverged about 0.0397 Mya,and the gene flow from the AS population to the ES population was 6.989 individuals per generation and 2×10-4 individuals from the ES to AS per generation Functional analyses revealed that the AS population was selected for reproduction,metabolism,regulation,and protein degradation,and the ES population was highlighted for energetics,neurogenetics,metabolism,reproduction and regulation.Analyses about transposable elements(TE)demonstrate that TE plays important roles in adaptation and new species invasion to new environments.