| The Ursidae species is the largest living land carnivore,which is widely distributed,including eight species,giant panda（Ailuropoda melanoleuca）,spectacled bear（Tremarctos ornatus）,Asiatic black bear（Ursus thibetanus）,sun bear（Helarctos malayanus）,sloth bear（Melursus ursinus）,American black bear（Ursus americanus）,brown bear（Ursus arctos）and polar bear（Ursus maritimus）.The Ursidae have undergone rapid evolutionary radiation and diversified into different species in short period of time.The interspecific relationships are extremely complex.Therefore,the research on the speciation and phenotypic diversity of Ursidae has always been a hot and difficult topic in mammal research.In particular,Ursinae,which contains the other six species except panda and spectacled bear,diverged within about five million years and showed extensive interspecific hybridization signals,which made the complex interspecific relationship even more complicated.In addition to diversity of species,phenotypic diversity also exists,for example,body size,coat color,eating habits and so on.Therefore,to research the speciation and phenotypic diversity of Ursidae,we have carried out the following two research works.First,based on the largest population-level genomic data set to date involving all Ursinae species,included high depth resequencing data for 60 individuals from 6 species of Ursidae and 1 outgroup species（spectacled bear）,and recently-developed methods for detecting hybrid speciation,we first provide evidence for the hybrid origin of Asiatic black bear.Based on phylogenetic analysis,Hy De,PCA,FST and mutation sharing analysis,we provide evidence for the hybrid origin of Asiatic black bear which might arise through sex-biased hybridization between the ancestor of polar bear-brown bear-American black bear,and the ancestor of sun bear-sloth bear.It was inferred to have occurred soon after the divergence（～5.66 Mya）of the two parental lineages in Eurasia based on the simulation analysis of hybrid speciation.In addition,we used the new selection analysis scheme to find that the intermediate body size of this hybrid species arose from its hybrid combination of related genes（AKT2,PID1,MKRN1 and PRKAB1）derived from two parental lineages of contrasting sizes.Furthermore,we found 16 highly differentiated loci in Asiatic black bear genome that were fixed alternately between two parents,suggesting that the appearance of intermediate size and highly differentiated loci might lead to the establishment of reproductive isolation between Asiatic black bear and its parents.We also found that some loci associated with reproductive traits underwent positive selection after the hybrid origin of genome,which further enhanced reproductive isolation between Asiatic black bear and its parent lineages.This study sheds further light on the evolutionary history of bears and documents the importance of hybridization in new species formation and phenotypic evolution in mammals.Secondly,we chose the glacier bear belong to American black bear with special coat color as the research object.There is little research background about the glacier bear,and the molecular genetic basis of the rare silvery gray coat color has little research.We performed genome assembly on glacier bear and obtained a high quality assembled genome.Subsequently,four other glacier bear individuals were resequenced in high depth,and the data of eight American black bears were obtained through sequencing and NCBI.To obtain more information about American black bear populations,Restriction-site Associated DNA（RAD）data of 94 individuals were also downloaded.First,phylogenetic analysis,mitochondrial Cytb haplotype analysis and genomic genetic distance analysis were firstly used to find that glacier bear is a geographic population rather than an independent subspecies of American black bear.Secondly,population structure analysis,principal component analysis,gene flow analysis and so on,found that glacier bear was part of the Alaska population,and there were signals of gene flow between the glacier bear population and other American black bear population with closely geographic distribution（Ursus americanus perniger,Ursus americanus cinnamomum and Ursus americanus pugnax）.In addition,we use the analysis of genetic diversity,heterozygosity and inbreeding coefficient found that glacier bear with isolated habitat have high inbreeding coefficient as well as with a high level of genetic diversity and heterozygosity,which may be caused by the introduction of genetic components of other American black bear and the recent high inbreeding within glacier bear.Based on the published research,we conducted the unique mutation across genome of rare coat color individuals of glacier bear,and combined with the coat color gene database,we found a gene SOX10 related to coat color.By ENCODE database and multi-species sequence comparison,it was found that the unique heterozygous mutation of this gene occurred in the enhancer region and was extremely conserved in other species.Three independent repetitions of the dual-luciferase reporter assay in both groups of cell lines showed that the specific mutation of this gene in glacier bear with silvery gray resulted in a significant decrease in gene transcriptional activity,which may lead to the decrease in gene expression.Combined with the fact that the deletion of the enhancer fragment of this gene can cause the hair color to turn white,it is speculated that the unique mutation of SOX10 gene promoter region may lead to the silver gray coat color of glacier bear.This study redefined the taxonomic status of glacier bear,enriched the genetic information of glacier bear,and the molecular basis research of the silvery gray coat color,which provided molecular evidence for the protection of the rare coat color population of glacier bear.In conclusion,by genomics research for Ursinae sepcies,we explored the importance of hybridization in the speciation and phenotypic diversity of the Ursinae,and revealed the unknown genetic background of glacier bear and the molecular genetic basis of the diversity of intraspecific coat color.It provided new insights into the complex evolutionary history and phenotypic molecular mechanisms of mammals. |
