| Chiroptera,commonly known as bats,belonging to the Laurasiatheria,are the only mammals capable of true powered flight.In addition to a suite of specific traits such as strong immunity,longevity,sleeping upside-down,and nocturnality,bats possess complex and diverse sensory systems,including echolocation,vision,taste,smell and auditory systems.Moreover,bats possess a variety of diet habits,including herbivorous,insectivorous,nectarivorous,carnivorous,piscivorous,omnivorous and sanguivorous.These characteristics make bats a vital study system.This study attempts to explore molecular evolution of bats from the perspectives of phylogenomics,lineage-specific traits,dietary transition and visual function.The first part of this dissertation is to explore the phylogenetic relationship of Chiroptera.As a member of the Laurasiatheria,the phylogenetic position of the bats has been under debate.In this study,transcriptome sequencing of mixed tissues for seven bat species that are phylogenetically divergent was performed to obtain their transcriptome data.In combination with the genome data of the 12 bats and 15 mammals that are publicly available,we constructed the phylogenetic relationships among Laurasiatheria.Our results supported the "Yinpterochiroptera-Yangochiroptera"classification of bats,and we found that the order Perissodactyla is the sister group to the order Chiroptera.In addition,we call for attention to gene heterogeneity that is needed to be considered in phylogenetic construction.The second part of this dissertation is to explore the origin of the lineage-specific traits in bats.Comparative transcriptomic analysis was conducted by employing the transcriptome data for mixed tissue of seven bat species and combining them with the released genomes of 12 bats and other 15 representative mammals.The results showed that among the identified 6645 orthologous genes,206 genes(3.1%)were subjected to natural selection pressure in the bat ancestor.These genes were closely associated with categories of immunity,cardiovascular,and reactive oxygen species scavenger,reproduction,autidory,longevity and skeletal development.Functional cluster analysis of these genes under selection indicated that these categories were significantly enriched.Moreover,bat lineage-specific amino acid analysis also suggested that genes possess lineage-specific amino acid sites were associated with these categories.Our study preliminarily explores the pattern as to how natural selection shapes the bat ancestor,which may be helpful to understand the origin and evolution of bats.The third part of this dissertation is to study the dietary transition in bats.Two studies were conducted:1)comparative transcriptome analysis aiming to reveal the mechanisms of diet switch in the Old World fruit bats;2)expression profiles analysis of liver tissues for bats with different dietary habits.In order to study the molecular mechanism of the dietary switch in the common ancestor of Old World fruit bats,we used transcriptome data for mixed tissue of seven bats,and combined them with the released genomes of 12 bats to conduct comparative transcriptome analysis.Results showed that among the 7389 orthologous genes,78 genes(1%)were found to be under natural selection pressures along the ancestral lineage of Old World fruit bats.These genes were closely associated with carbohydrate,protein metabolism and visual perception,which is also supported by lineage-specific amino acid site and functional clustering analysis.In addition,we conducted the analysis of expression profiles of the liver transcriptomes of two frugivorous bats and three insectivorous bats.Results showed that genes associated with immunity and detoxification were highly expressed in liver tissues of all bats,suggesting that these genes are needed to maintain basic functions of the liver in bats;compared with the insectivorous bat,the expression levels of genes associated with insulin,carbohydrate and cholesterol metabolism are significantly up-regulated in the liver tissues of the frugivorous bats,indicating that these genes are important for the normal functions of liver in frugivorous bats,which may further suggest that expression divergence of genes related to metabolic needs in liver may be associated with dietary diversification in bats.Together,these studies may contribute to in-depth understanding of the evolution of diets in bats.Finally,we explored molecular evolution of visiual function in bats.Previous studies have shown that Old World bats with constant frequency echolocation(Hipposideridae + Rhinolophidae bats)have lost the dichromatic colour vision,and thus proposed a sensory tradeoff hypothesis:the generation of constant frequency echolocation and the loss of colour vision.In order to test the sensory tradeoff hypothesis,we turned to the New World bats.The SWS1 gene sequence of 16 New World bats(29 individuals)was obtained through sequencing.We found that there is a new polymorphism in the short-wave opsin gene SWS1 in the Pteronotus mesoamericanus with constant frequency echolocation:one allele is intact and the other allele is a pseudogene.To our knowledge,this polymorphism has not been reported in bats and other animals previously.The pseudogeneized SWS1 means the loss of dichromatic colour vision,while both the Old World bats(Hipposideridae +Rhinolophidae bats)and the New World bat(Pteronotus mesoamericanus)that independently evolved constant-frequency echolocation have lost the dichromatic colour vision.Thus,the same evolutionary events can be repeated in the two divergent lineages of HDC echolocators,supporting the sensory tradeoff hypothesis.This study also found that all three vampire bat species in the world have lost the dichromatic colour vision,and thus proposed a new mechanism of evolution of sensory systems:the generation of infrared sense ability may compensate the loss of colour vision in animals.This finding helps to advance the understanding of evolutionary shifts in animal sensory systems. |
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