Research On Local Adaptation Of Hipposideros Larvatus Based On Genotyping By Sequencing

The process of species formation and differentiation has always been one of the core problems in evolutionary biology.With the intensification of climate change,the phenomenon of adaptive differentiation of species to local environmental conditions(local adaptation)has attracted more attentions.Islands have special geographical and environmental conditions.The comparison of genetic patterns between island and inland populations can provide important insights into the processes and mechanisms of local adaptation.Leaf-nosed bats(Hipposideros larvatus,Hipposideridae)are widely distributed in southern China and southeast Asia.Phenotypic and genetic differences were detected between inland and Hainan Island populations.In this study,we integrated genotyping-by-sequencing technique and environmental niche models,conducted a study of population genomics and landscape genetics,revealed the genetic mechanisms of local adaptation of H.larvatus populations in China,and further predicted the population changes under the future climate.A total of 111 individuals from 15 populations(9 inland populations and 6 Hainan populations)were sequenced by genotyping-by-sequencing,and 60911 unlinked high-quality SNPs were obtained.Population genetic structure and phylogenetic analyses showed that inland and Hainan populations separated into two lineages,and the latter formed earlier than the former.The results of gene flow analysis and dynamic history construction based on neutral SNPs supported the secondary contact model which showed the initial differentiation time of two lineages was about 1.03 Ma(95% CI: 1.17–0.90 Ma)corresponding to Poyang Glacial Period(1.10–0.80 Ma),and the secondary contact occurred about 0.008 Ma(95% CI:0.009–0.007 Ma)after Dali Glacial Age(0.10–0.01 Ma).The results of Treemix and Fastsimcoal showed the gene flow from Hainan Island lineages to inland lineages was higher than the reverse.Principal component analysis based on 19 climate factors showed significant differences between inland China and Hainan Island.With non-highly correlated climate factors,948environment-related SNPs were obtained by PCAdapt,Baye Scan,LFMM and RDA,and 395 genes were obtained after annotation.These genes were significantly enriched in the terms of growth and development(including nerve,bone,and muscle)and energy metabolism.Some genes,such as TNR,SEMA4 B,PTPRT and ABCA1,showed significant allelic frequency differences between the two lineages,which may be the key genes contributing to the local adaptation.According to the gradient forest analysis and mantel test,the lowest temperature in the coldest month and the annual temperature difference were the important environmental factors which could have affected the local adaptation of Chinese H.larvatus.In order to predict the change of population distribution and its genomic plasticity under future climate conditions,the current and future suitable habitats(2050 and 2070)were constructed based on Maxent,and the genomic offset under future climate was calculated using the gradient forest analysis.The results showed that the suitable habitat of Chinese H.larvatus is mainly in the low latitude,and the habitats in high latitude will be largely lost in future.The results of genomic offset showed the Hainan Island populations have a higher survival potential than the inland populations when temperature increases in future,but there was still a higher extinction risk under extreme environmental changes.When they were unable to adapt to local environment,populations with high dispersal capacity would migrate to suitable habitats.Mountainous areas in Guizhou province may be the refuge for Chinese H.larvatus and should be priorly protected.In conclusion,this study revealed the differentiation process and local adaptation mechanism of leaf-nosed bat populations in China,and predicts the changes of distribution and genetic composition in the future climate.The results of this study emphasized the importance of integrating genome and environmental data to elucidate the local adaptation process and adaptive capacity.This study provided new insights into the adaptive differentiation process,proposed theoretical basis for the conservation and management strategies of Chinese H.larvatus,and contributed to understanding and quantifying the evolutionary potential of species in adapting to future environmental changes.