Study On Population Differentiation And Ecological Adaptation Of Tree Shrews,Tupaia Belangeri

The tree shrew,Tupaia belangeri(Mammalia: Scandentia: Tupaiidae),is the endemic taxa of Oriental realm,which is widely distributed throughout Yunnan,Guizhou,Sichuan,Guangxi and Hainan island of China,and it’s the only representative of Scandentia in China.The distributive-environment of tree shrews is significantly different,including mountains,plateaus and tropical islands,etc.It is an ideal group to study the origin and evolution of biodiversity.At the same time,the tree shrew and extant primate animals have close genetic relationship,which is an important model animal in biomedical research.In this paper,the distribution of tree shrews in China were systematically researched from different disciplines and organizations by using genomics,metabolomics and morphology methods.Aims to clarify the differentiation degree of tree shrews from different populations and its relationship with the ecological environment,which provide theoretical basis for selecting the initial population of experimental animal strains.Moreover,these data provide some scientific basis for small mammals of sympatric distribution adapting to different environment and cultivation and protection the resources of tree shrews.This thesis mainly consists of five parts:(1)The genomics research of tree shrews from different populationsThe enzyme digestion efficiency of RsaI was 92.04% in the experiment,and a total of obtained 290.52 Mreads.240770 SLAF tags were obtained,of which polymorphism SLAF tags were 200698.A total of obtained 4099128 population SNPs,of which the high consistency group SNPs were 208184.Based on SNPs,phylogenetic trees and principal component analysis showed that 12 populations of tree shrews were clustered into 4 branches: Hainan population,Daxin population,Pianma and Tengchong populations,Leye,Xingyi,Hekou,Kunming,Xichang,Mengla,Dali and Luquan populations.Population genetic structure analysis also showed that the clustering number K = 4 was reasonable,that all the samples may come from 4 primitive ancestors.Compared with other populations,the nucleotidepolymorphism(π)and pool heterozygous(hp)values in Hainan and Hekou populations were smaller,the genetic diversity and population differentiation were low.Linkage disequilibrium(LD)analysis results showed that the LD of Luquan population(laboratory domesticated population,its parents from luquan)was higher than other populations,domesticated populations due to the role of positive selection,exhibited higher values of LD.By selecting elimination analysis,1225,1195,179 and1199 genes were detected strongly in Hainan,Daxin,Kunming and Pianma populations,respectively.These genes were mainly involved in energy metabolism process.Pst and Fst comparative analysis results showed that the Fst between the larger geographic distance populations were significantly greater than the Pst of phenotypic traits,group in stable equilibrium selection;the Fst between the small geographic distance populations were significantly less than the Pst of some phenotypic traits,groups have been-under obvious selection pressure.Genome-wide association analysis found that many phenotypic traits,such as the body mass,body length,tail length,chest width,fore limb length,hind limb length,ear length,ear width,relative fatness,pelage color,skull and molar shape etc all are correlation with SNPs loci.Functional annotation analysis of the genes of associated regions found that the associated genes were all annotated function in nr,SwissProt,GO,COG,Pfam and KEGG Pathway.These genes may be important genes which affect the phenotypic traits of tree shrews.(2)The metabonomics research of serum and liver of tree shrews from different populationsA total of 96 metabolites were annotated in the serum,and a total of 90 metabolites were annotated in the liver.These metabolites are mainly concentrated in primary metabolites: including amino acids,organic acids,fatty acids,nucleotides,phosphoric acids,polyols,sugar,amine and others.Principal component analysis and partial least squares discriminant analysis showed that Pianma population get together,Xichang population get together,Leye,Xingyi and Kunming populations get together,Dali and Tengchong populations get together,Hainan,Daxin,Hekou,Mengla and laboratory populations get together in serum metabolites,but each group had a few samplesoverlap.The samples of each group overlap to some degree in the liver metabolites.Serum metabolomics revealed that concentrations of five tricarboxylic acid cycle intermediates(citric acid,fumaric acid,α-ketoglutarate acid,succinic acid and malic acid)were higher in high altitude populations than low altitude populations.Liver metabolomics revealed that there were higher concentrations of lipids,amino acids and urea,but lower concentrations of glucose and glycolytic intermediates in high altitude populations than low altitude populations.The difference of metabolite levels of each metabolic pathways of tree shrews in different populations may be the mechanism of animals adapt to different living environment.(3)The geometrical morphology research of skull and molar of tree shrews from different populationsThe morphological characteristics of the dorsal cranium,lateral cranium,ventral cranium,lateral mandible and molars(upper molars and lower molars)of tree shrews of 12 different populations were measured by geometric morphometric techniques.The results showed that the variation of lateral cranium,lateral mandible and lower molars was larger,more appropriate and reference valuable to be considered as morphological index in the study on morphologye difference of skull and molar of different populations.Thin plate spline analysis showed that the deformation was more concentrated in perception part(nasal bone and eye socket)and feeding habits related sites(molar alveolar and occlusal surface),which may reflect its adaptation to geographical differences in climate and environment.Multidimensional scaling analysis showed that the skull and molar shape of tree shrews in Hainan,Daxin,Pianma and Tengchong populations had significant regional differences.These differences may be related to longitude and latitude of their habitations.These results indicated that the skull and molar shape of tree shrews from different populations all had differences,among them,the variation in Hainan,Daxin,Pianma and Tengchong populations were larger,which may reflected the adaptive variation to different environment of tree shrews.The experimental results can provide a basis for research on morphological adaptation and system evolution of tree shrews.(4)The comparative study of pelage color and body index of tree shrews from different populationsThe pelage color,shape and the skull data of tree shrews from different populations were all significant differences.The shape and skull data all shown as Hainan and Daxin populations were larger,while Leye,Xingyi,Kunming and Xichang populations were small.The pelage color of Leye,Xingyi,Kunming and Xichang populations were similar,and the Hekou,Dali,Mengla and Tengchong populations were also similar;but Hainan,Daxin,Pianma and laboratory populations were larger differences.The variation may be related to survival environment of tree shrews.In addition,the pelage color and the vegetation of their living environment(background color)were similar,may be a strategy of evading predator and self protection of tree shrews.(5)The comparative study of relative fatness and body composition of tree shrews from different populationsThe body mass and relative fatness of tree shrews from different populations showed significant difference,were characterized by Hainan and Daxin populations were larger,Kunming population was the minimum;the internal organs and digestive tract morphology of tree shrews from different populations were also significant difference.These differences and living environment of tree shrews(food,temperature,photoperiod and altitude,etc.)are closely related.The results may provide some theoretical basis for the physiological ecological strategies of small mammals to deal with the different habitats.In conclusion,due to the distribution area environment of tree shrews was significantly different,complex and changeable natural environment provided the broad ecological niche for population differentiation and proliferation of tree shrews,it had high genetic diversity and phenotypic polymorphism.12 populations of tree shrews can be divided into 4 subgroups: Hainan subgroup,Daxin subgroup,Pianma and Tengchong subgroup,Leye,Xingyi,Hekou,Kunming,Xichang,Mengla,Dali and Luquan subgroup;the Chinese tree shrew might originate from 4 primitive ancestors.There are obvious genetic background differences of tree shrews in the mountains,plateau and island populations,genetic structure difference caused by geographical isolation or even more than the difference between wild and domesticated.Compared with other populations,Hainan and Hekou populations were suitable for the initial population of experimental animal strains to establish closedgroup,and can be used as a base group for cultivation and protection of genetic resources of tree shrews.The genes of sufferring strong selection in Hainan,Daxin Kunming and Pianma populations were detected by the selective elimination analysis,and these genes mainly involved in energy metabolism,played an important role in the process of adaptation to high altitude and low temperature environment of tree shrews.There were regions and genes of affecting phenotypic traits(body mass,pelage color,skull and molar shape,etc.)in the genome.The differences of metabolites(especially the metabolites associated with tricarboxylic acid cycle,lipid metabolism,amino acid metabolism,glycolysis and glucose)concentration of tree shrews from different populations and their living environment(altitude,temperature and food,etc.)were closely related.The tree shrew have strong plasticity to adapt to different environment.Comprehensive genome,metabolomics and morphological data indicated that tree shrews from different populations were not only influenced by genetic drift and gene flow,but also by the strong effect of natural selection in the evolutionary process,and there were both latitude effect and altitude effect.