Genetic Structure And Diversity Of Garrulax Courtoisi Based On Resequencing Technology

Population genetic analysis of rare and endangered species is helpful to further explore the endogenous mechanism of endangered species.Garrulax courtoisi is listed as the national classⅠprotected animal and the population is rare and isolated.In this study,the whole genome of 40 Blue-crowned Laughingthrush(wild individuals such as Wuyuan and Simao,as well as those raised in Jurong Bird Park,Singapore)was re sequenced.Based on SNPs technology,the genetic differentiation degree of Blue-crowned Laughingthrush from different sources was analyzed to clarify the effectiveness of Simao population as a subspecies,and the trade source of Singapore samples was traced.The main research results are as follows:(1)There are 5,866,346 high quality SNPs markers were obtained by comparison with the reference genome.PCA principal component analysis was conducted based on these markers,and Admixture analysis was used to verify the population structure.It was found that when K=2,when Wuyuan population and Singapore samples were divided into two subgroups,there was partial genetic mixing between Wuyuan,Singapore and Simao samples,which was consistent with PCA image showing that Wuyuan population and Singapore Zoo samples were clustered,but Simao samples were dispersed.These results suggest that the Singapore samples are highly likely to be descendants of the historical trade of Wuyuan population into European and North American zoos.There were no obvious differences in genetic structure among different breeding subpopulations in Wuyuan,which proved that there were individual and gene exchanges among different breeding subpopulations.(2)Fst results showed that:Wuyuan and Singapore samples were from the same population(Fst=0.033651<0.05),while Simao and Wuyuan samples were highly differentiated(Fst=0.22675>0.15).Genome resequencing results supported that Simaoensis was an effective subspecies of Blue-crowned Laughingthrush.(3)The results of genetic diversity showed that the average observed heterozygosity of Wuyuan population was H_o=0.2822(0.2764～0.3625),simao population was H_o=0.079(0.0372～0.1203),and Singapore sample was H_o=0.2577(0.2511～0.2642).Compared with other endangered species,the average heterozygote of Laughingthrush was much lower.It can be seen that the genetic diversity of Blue-crowned Laughingthrush is still low.The inbreeding number Fis of each population showed that the inbreeding degree of Laughingthrush in Singapore(0.0285)was higher than wuyuan wild population(-0.054).The inbreeding degree of Simao sample is the highest(0.7048),which may be the endogenous factor leading to the extinction of its population.(4)The results of kinship and phylogenetic tree support the existence of first-order relationship(parent or sibling relationship)between the two nestlings of WYHK and the two sisters of Singapore,which proves the effectiveness of King software and phylogenetic tree to analyze the relationship between individuals in the population.King results also showed that there was a first-order genetic relationship between the young WYHK-01 and another brood(WYHK-02,04,05,11)which is in the same period,This suggested that there might be extra pair paternity among Blue-crowned Laughingthrush in wuyuan.Between different breeding plcaes in Wu Yuan,there was found that 1 1st relatives,41 2nd relatives and 64 3rd relatives exist.This is consistent with the results of PCA,which proves that there is gene exchange between different populations.This is also one of the reasons why the inbreeding levels of Blue-crowned Laughingthrush still remains low despite with a small population.(5)The effective population size and historical dynamics of Blue-crowned Laughingthrushes among 6 samples in Wuyuan and Singapore showed that:the population of Laughingthrush had experienced expansion and contraction in history,which was related to the last glacial period.Their population number declined rapidly in the last interglacial period,and different populations retreated to the shelter in the glacial Period respectively.Long-term geographical isolation may have led to the differentiation of Simao subspecies and named subspecies.The effective population size of Laughingthrush was about 100,000-500,000 before 10,000 years ago,and the population number of laughingthrush at present is far lower than the historical level.