Genetic Structure And Demographic History Of Han People In Liaoning Province Inferred From Genome-wide Array Data

ObjectiveIn order to investigate genetic affinity between Northern Han people in Liaoning province and other East Asian populations and explore the origin,development and admixture history of Northern Han people in Liaoning province,this study analysed genetic structure of Han people in Liaoning province by using Illumina We Gene Array.MethodsIn this study,we collected saliva samples from 80 Han individuals from four cities in Liaoning province,China.Every participant had signed the written informed consent before the study begins.All participants were required to be the indigenous residents whose ancestors have lived in the sampling sites for at least three generations,and the ethnic groups of all participates were used as their self-declaration based on their family migration history and corresponding family records.The DNA extraction was performed by Genomic DNA Extraction Kit following the manufacturer requirements,and DNA sequencing and genotyping were carried out by using the Illumina We Gene Arrays.After data merging,we obtained “Merged-HO” dataset containing41,585 SNPs and “Merged-1240K” dataset containing 113,144 SNPs to perform population genetic analysis.we used typical and advanced population genetic analysis methods(principal component analysis(PCA),ADMIXTURE,FST,f3‐statistics,f4‐statistics,qp Adm/qp Wave,qp Graph,ALDER and Tree Mix)to explored genetic structure and reconstructed demographic history basing on newly generated genome-wide data of 80 Han individuals from four different cities in Liaoning province.Results1.PCA,ADMIXTURE,FST,Tree Mix:we could find modern Liaoning Manchu people and ancient YRB population overlapped with Liaoning Han people,it revealed that there were close genetic relationships among them.Liaoning Mongolians,Japanese and Korean exhibited close genetic relationship.There were not significant genetic differences among Liaoning Han populations in Dandong,Dalian,Shenyang and Panjin.There were lowest genetic distances between Liaoning Han people and other northern Han people such as Shandong Han and Henan Han and Liaoning Manchu people.And Fuxin Mongolian,Korean,Japanese,Xibo and other northern populations also exhibited more close genetic relationship with Liaoning Han people.Dandong Hans,Panjin Hans and Shenyang Hans clustered with Henan Hans,Shanxi Hans and Liaoning Manchus,Dalian Hans clustered with Shandong Hans and also had close relationship with Japanese and Korean.2.Outgroup-f3、admixture-f3、f4,qp Wave and qp Adm,qp Graph:Liaoning Han people have genetic similarity with northern and southern Han people,Liaoning Manchu people,Japanese and Korean relative to other East Asian populations.Some Tibeto-Burman speakers such as Naxi,Tujia and Yi and southern East Asian populations also have close genetic relationship with Liaoning Han people.And we also found the obvious genetic differences between Liaoning Han and western Eurasian populations and Turkic-speaking populations.Liaoning Han people have genetic homogeneity,but we found Dalian Hans showed more close genetic affinity with Shandong Hans relative to Shenyang Hans.Liaoning Han people have 57%-98% Neolithic millet farmers related ancestry,40%-43% northern East Asian related ancestry and2% western Eurasian related ancestry.We next used ALDER method based on weighted linkage disequilibrium statistics to estimate admixture time.We found the western Eurasian related ancestry flowed to the gene pool of Liaoning Hans during 4,500 to 1,200 years before present,the northern East Asian and southern Siberia related ancestry flowed to the gene pool of Liaoning Hans during 4,500 to 1,300 years before present,and southern East Asian related ancestry flowed in the gene pool of Liaoning Hans around 2,000-1,100 years before present.Conclusions1.We found Liaoning Han people have genetic similarity with other northern Han people(Shandong,Henan and Shanxi)and Liaoning Manchu people,and millet farmers in Yellow River Basin and West Liao River Basin(57%-98%)and hunter-gatherers in Mongolian Plateau and Amur River Basin(40%-43%)were main genetic contributors.2.In general,our study further supported “Northern origin Hypothesis”,the YRB related ancestry was 83%-98% in genetic makeup of Liaoning Hans.And there are obvious genetic influences from northern East Asian populations,Mohe people shared more alleles with Liaoning Han people,and large-scale population admixture had happened between Tungusic Manchu people and Han people.3.Interestingly,there were genetic differences among Liaoning Han people,we found these differences were associated with different migration route of Han people during “Chuang Guandong” period in the historical records.