Molecular Basis Of Local Adaptation And Speciation Of Quasipaa Spinosa

Quasipaa spinosa belongs to the genus Quasipaa in the Dicroglossidae family of amphibians.It is mostly distributed in the south of China and a little in the north of Vietnam.It has high economic and edible value.Early molecular data showed that there were three branches of Q.spinosa distributed in China,and there was significant genetic differentiation among them.In this study,the whole genome sequencing technology,combined with phenotypic differentiation and key environmental factors,was used to provide genetic information basis for revealing the adaptive evolution and species formation mechanism of Q.spinosa.The research conclusions include the following aspects:(1)Phenotypic analysis: 16 morphological features indexes of 12 different geographic populations of Q.spinosa were analyzed by principal component analysis,cluster analysis and discriminant analysis.The results of PCA displayed that the cumulative contribution rate of the first three principal components was 64.854%.PCA scatter map was drawn based on the scores of the PC1 and PC2.The search results displayed the samples of Hezhou City,Guangxi Province,are obviously different from other populations.The results of discriminant analysis displayed that the specimens of Q.spinosa from different geographical populations were divided into three groups,of which the highest discriminant accuracy was 87.5% in Chizhou,Anhui Province,followed by 76.9% in Hezhou,Guangxi Province.The result of Mahalanobis distance shows that 60.9% of the individuals in the total sample are correctly allocated to their own population,and the correct rate of discrimination is high.The research findings of cluster analysis displayed that the geographical populations of Longyan in Fujian,Hezhou in Guangxi and Shaoguan in Guangdongwere close to each other.There are some differentiation between the three populations and the rest of populations,especially morphological features.(2)Analysis of key climate factors: the correlation analysis of 12 environmental variables displayed that there was a significant positive correlation between the five temperature factors(P<0.01),a significant positive correlation between latitude factors and precipitation factors,humidity factors(P<0.01),and a negative correlation with five temperature factors(P<0.01).Two principal components were extracted by principal component analysis.The first component contains four environmental factors,namely,temperature factor(0.955-0.978),precipitation factor(-0.941,-0.975),humidity factor(-0.823),latitude factor(-0.946).The second component contains two environmental factors,namely,altitude factor(0.907)and air pressure factor(-0.881).Six major component factors can be solved 89.063% of the variation of 12 environmental factors.The results showed that the ratio of hand length to body length was positively correlated with temperature(P<0.05),negatively correlated with yearly precipitation,air pressure and latitude(P<0.05),and the ratio of eye diameter to body length was positively correlated with temperature(P<0.05),positively correlated with yearly precipitation and latitude(P<0.05).There was a significant negative correlation(P<0.05),and the ratio of length of tarsal fold to body length was remarkably negative correlation with longitude factor(P<0.01).The consequences displayed that there was a significant positive correlation between the highest temperature and the ratio of hand length to body length(P<0.05),and a remarkable positive correlation between the average temperature and the ratio of tarsal fold length to body length(P<0.05).The consequences of principal component analysis of morphological features of Q.spinosa extracted three principal components,of which the PC1 accounted for 49.781% of the total variation was mainly related to the longitudinal measurement level of the hand length of Q.spinosa,and the PC2 accounted for 8.271% of the all variation was mainly interrelaed to the transverse measurement of the head shape reflecting the size of Q.spinosa.It can be seen that the most important environmental factor affecting the phenotypicaldifferentiation of Q.spinosa is the temperature index,and the principal one is the maximum and the extreme high temperature.The higher the temperature is,the larger the phenotypical index related to the longitudinal measurement of the hand length of Q.spinosa is,and then the size of the head morphological index.(3)Population genome sequencing: Based on MGISEQ-2000,36 population samples of Q.spinosa were resequenced,and the effective sequencing data was1314.97 Gb,compared with the reference genome of Q.spinosa,the effective genome size was 2.84 Gb.Through quality control and data filtering,12.68 M high-quality SNP calling data set was obtained.Based on the selected SNP,the population principal component,population genetic structure and phylogenetic tree analysis were carried out.The results showed that the hybrid species of Q.spinosa could be divided into three branches,and the western branch had obvious differentiation,which was consistent with the consequences of phenotypical differentiation and environmental factor analysis in the previous two chapters.According to the results of population structure division,the selection population analysis displayed that the Eastern branch experienced positive selection.The genetic diversity differences between the East and West branches were compared by using Fst and ?? analysis,the results showed that there was obvious genetic differentiation between the East and West branches,and the candidate selection areas were determined by selection elimination analysis.Go function enrichment analysis was carried out for candidate region genes,the consequences displayed that the candidate genes were mainly related to biological regulation,metabolism,cell process and signal transduction process;the molecular functions were mainly related to binding,catalysis and molecular transport.Based on pathway analysis,the foremost biochemical metabolic and signal transduction channel involved in candidate genes are mainly related to environmental signaling process,RNA transport and hormone signal transduction.On the basis of the ancestral theory and the analysis of the historical dynamics of PSMC population,the research findings displayed that the three branch populations of Q.spinosa complex had experienced a large range of population contraction in the early stage,while theEastern branch population had experienced population expansion in the near future.The reasons for the historical dynamics of this population need to be inferred in integration with the global climate fluctuation and the change of local geographical environment.Treemix was used to analyze the population migration.The results showed that there was gene flow among the branches of Q.spinosa,and there was a mixture among the branches with similar genetic information.