Conservation Genomics Of The Snub-nosed Monkeys And Tibetan Antelope

Due to the change of climate and the increasing interference of human activities,many species have been declining or isolated into small populations,leading to different degrees of their survival crisis.Therefore,exploring the relationships between environmental factors/human activities and population fluctuation of endangered species,as well as the impact of population decline on the genetic consequences and the survival potential,is critical for conservation and management plans for the endangered species.Snub-nosed monkeys(Rhinopithecus)and Tibetan antelope(Pantholops hodgsoni)are listed in the Class I protected species in China and CITES.In this paper,we performed the conservation genomic studies of the snub-nosed monkeys and Tibetan antelope.By analyzing their genetic diversity,population structure,and demographic histories,we investigated their endangered mechanism and assessed their survival potential,providing theoretical support for their conservation and management.In the first part,we analyzed population genomic data of all five snub-nosed monkey species(golden snub-nosed monkey,black snub-nosed monkey,gray snub-nosed monkey,Nujiang snub-nosed monkey,and Tonkin snub-nosed monkey)to assess their genetic diversity,inbreeding level and genetic load.The results showed that the species and the population with small population size,including gray snub-nosed monkey species,Tonkin snub-nosed monkey species and Shennongjia population of golden snub-nosed monkey species,possess a high level of genetic diversity,low level of genomic inbreeding and recent inbreeding,indicating that although their population sizes are small,they did not lose too much genetic variation and might maintain a high evolutionary potential.In contrary,golden snub-nosed monkey species with large population size possesses high genetic diversity and low level of genomic inbreeding,but they show a high level of recent inbreeding and moreover,do not accumulate substantial deleterious mutations.Therefore,for the conservation of golden snub-nosed monkey,the habitat connectivity and gene flow among populations should be strengthened to avoid inbreeding depression.In addition,further analysis of the deleterious mutation genes found that many genes are related to immune response,especially in the small population of species.These results suggest that the long-term consequences of inbreeding may lead to the decline of immune capacity of the snub-nosed monkeys,which may threaten their long-term survival prospects and adaptation potential.This study provides new insights into the genomic imprinting of population decline of the snub-nosed monkeys.More importantly,we reveal different patterns of genetic diversity in small and large populations,which are crucial for the conservation and management of these endangered species.In the second part,we studied the long-standing controversial population structure and demographic history of golden snub-nosed monkey(Rhinopithecus roxellana).We integrated multiple genomic markers,including autosomes,mitochondrial genomes and Y chromosomes of 54 golden snub-nosed monkey individuals from all three geographic populations(Sichuan/Gansu population,Qinling population,and Shennongjia population)to study their population structure and demographic history.We found that different population structure and relationship were obtained by three genetic markers.The nuclear genome showed that there was bidirectional gene flow among populations,while the mitochondrial genome and Y chromosome showed asymmetric gene flow.We hypothesis that the different population structure and gene flow among genetic markers were related to the complex social structure and sex-biased dispersal patterns of golden snub-nosed monkey.In addition,the demographic history simulation analysis supports that the ancestral populations of golden snub-nosed monkeys were once widely distributed in the mountainous areas of central and southwest China,and then isolated due to the impact of paleoclimate change.About 24,500 years ago,Shennongjia population first diverged from other populations,and then gradually contracted to Shennongjia and other mountains in Hubei Province;then Qinling population migrated from Sichuan/Gansu population around 13,500 years ago.The migration process was accompanied by frequent gene flow.This study provides a more complete origin and demographic history framework of golden snub-nosed monkey,which is of great significance to the biogeographic study of other species with the overlapping distribution areas and experiencing similar climate and geographical changes.In the third part,we obtained a high-quality Tibetan antelope de novo genome and analyzed genome data from 85 Tibetan antelopes representing three geographical populations(Tibetan population,Qinghai population,and Xinjiang population)in order to investigate their genetic diversity,population structure and demographic history.Based on the analysis of nuclear genome,mitochondrial genome,and Y chromosome,we found that Tibetan antelope population maintained a high level of genetic diversity.The results of population structure analysis showed that the three geographical populations are mixed together,and do not have significant genetic differentiation.In addition,by comparing the population differentiation level of mitochondrial genome and Y chromosome,we found that not only females migration plays an important role in the genomic homogenization of Tibetan antelope population,but also males migration contributes to the genomic homogenization.Therefore,although the Tibetan antelope has suffered population decline,frequent migration between different populations may buffer the loss of genetic diversity.The demographic history analysis shows that the population size fluctuation of Tibetan antelope is closely related to the paleoclimate change on the Qinghai-Tibetan Plateau and the change of lifestyle and production activities of prehistoric Tibetan human.However,we do not observe that human hunting has caused recent bottleneck since 1950 s,in contrary,the population goes through the process of continuous expansion.In conclusion,our research shows that the Tibetan antelope still maintains high evolutionary potential and survival potential,indicating the prospects for their population recovery and growth.Take it all together,we investigated the population genetic pattern,reconstruction of population history and the causes of their formation of the snub-nosed monkeys and Tibetan antelope,which provided theoretical support for the formulation of scientific and forward-looking conservation and management strategies for these endangered species.