A comparison of biallelic markers and microsatellites for the estimation of population and conservation genetic parameters in Atlantic salmon (Salmo salar)

Biallelic markers such as single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms have become increasingly popular markers for various population genetics applications. However, the effort required to develop biallelic markers in nonmodel organisms is still substantial. In this study, we compared the estimation of various population genetic parameters (genetic divergence and structuring, isolation-by-distance, genetic diversity) using a limited number of biallelic markers (in total 7 loci) to those estimated with 14 microsatellite loci in 21 Atlantic salmon (Salmo salar) populations from northern Europe. Pairwise FST values were significantly correlated between biallelic loci and microsatellite datasets, as was overall heterozygosity when both anadromous and nonanadromous populations were analyzed together. However, when the anadromous and nonanadromous samples were analyzed separately, only genetic divergence correlations remained significant. Biallelic markers alone were not sufficient for reliable neighbor-joining clustering of populations but gave highly similar isolation-by-distance signals when compared with microsatellites. Finally, although several population prioritization measures for conservation exhibited significant correlation between different marker types, the specific populations highlighted as being most valuable for conservation purposes varied depending on the marker type and conservation criteria applied. This study demonstrates that a relatively small set of biallelic markers can be sufficient for obtaining concordant results in most of the analyses compared with microsatellites, although estimates of genetic distance are generally more concordant than estimates of genetic diversity. This suggests that a relatively small number of biallelic markers can provide useful information for various population genetic applications. However, we emphasize that the use of much higher number of loci is preferable, especially when the genetic differences between populations are subtle or individual multilocus genotype-based analyses are to be performed.     

Fine‐scale genetic structure of Tujia and central Han Chinese revealing massive genetic admixture under language borrowing

Archaeological, genetic, and linguistic evidence has supported the idea that northern China is the original center of modern Sino‐Tibetan‐speaking populations. However, the demographic history of subsequent southward migration and genetic admixture of Han Chinese with surrounding indigenous populations remain uncharacterized, and the language shifts and assimilations accompanied by movement of people, or just an adaptation of cultural ideas among populations in central China is still unclear, especially for Tibeto‐Burman‐speaking Tujia and central Han Chinese populations. To resolve this, we genotyped over 60K genome‐wide markers in 505 unrelated individuals from 63 indigenous populations. Our results showed both studied Han and Tujia were at the intermediate position in the modern East Asian North–South genetic cline and there was a correlation between the genetic composition and the latitude. We observed the strong genetic assimilation between Tujia people and central Han Chinese, which suggested massive population movements and genetic admixture under language borrowing. Tujia and central Han Chinese could be modeled as a two‐way admixture deriving primary ancestry from a northern ancestral population closely related to the ancient DevilsCave and present‐day Tibetans and a southern ancestral population closely related to the present‐day Tai‐Kadai and Austronesian‐speaking groups. The ancestral northern population we suspect to be related to the Neolithic millet farming groups in the Yellow River Basin or central China. We showed that the newly genotyped populations in Hubei Province had a higher proportion of DevilsCave or modern Tungusic/Mongolic‐related northern ancestries, while the Hunan populations harbored a higher proportion of Austronesian/Tai‐Kadai‐related southern ancestries.     

辽宁满族11个Y-STR基因座多态性及遗传关系的分析

调查了辽宁满族群体11个Y-STR基因座的多态性分布, 探讨其群体遗传学及法医学应用价值。应用Powerplex Y System荧光标记复合扩增系统检测203名满族无关男性个体的11个Y-STR基因座, 用ABI310遗传分析仪进行基因分型, 计算等位基因和单倍型频率, 并结合已公开发表的国内其他16个群体相应基因座的遗传学资料, 分析其遗传距离和聚类关系。满族个体中共检出189种单倍型, 单倍型频率多样性0.9991, 基因多样性GD值在0.4594(DYS391)～0.9258(DYS385a/b); 从遗传距离分析发现, 满族和东北汉族的遗传距离最小(0.0015), 与维吾尔族的遗传距离最大(0.1485)。结果表明, 11个Y-STR基因座在满族群体中具有较好的遗传多态性, 适用于当地区的法医学应用。与其他民族群体遗传多样性的研究, 对了解满族的起源、迁移以及相互关系有重要意义。     

Ancient DNA Reveals That the Genetic Structure of the Northern Han Chinese Was Shaped Prior to 3,000 Years Ago

The Han Chinese are the largest ethnic group in the world, and their origins, development, and expansion are complex. Many genetic studies have shown that Han Chinese can be divided into two distinct groups: northern Han Chinese and southern Han Chinese. The genetic history of the southern Han Chinese has been well studied. However, the genetic history of the northern Han Chinese is still obscure. In order to gain insight into the genetic history of the northern Han Chinese, 89 human remains were sampled from the Hengbei site which is located in the Central Plain and dates back to a key transitional period during the rise of the Han Chinese (approximately 3,000 years ago). We used 64 authentic mtDNA data obtained in this study, 27 Y chromosome SNP data profiles from previously studied Hengbei samples, and genetic datasets of the current Chinese populations and two ancient northern Chinese populations to analyze the relationship between the ancient people of Hengbei and present-day northern Han Chinese. We used a wide range of population genetic analyses, including principal component analyses, shared mtDNA haplotype analyses, and geographic mapping of maternal genetic distances. The results show that the ancient people of Hengbei bore a strong genetic resemblance to present-day northern Han Chinese and were genetically distinct from other present-day Chinese populations and two ancient populations. These findings suggest that the genetic structure of northern Han Chinese was already shaped 3,000 years ago in the Central Plain area.     

STR Polymorphisms of the Henan Population and Investigation of the Central Plains Han Origin of Chaoshanese

Allele frequencies for 15 short tandem repeat (STR) loci were obtained from a Chinese Han population in Henan province of middle China. No deviation from Hardy–Weinberg equilibrium was observed for the STR loci except for D3S1358. The 15 STR loci are potentially useful for paternity testing and forensic casework in the Henan population. A phylogenetic tree based on CODIS STR allele frequencies of 25 Han populations revealed noticeable but far less clear distinctions between southern and northern Chinese populations; the Henan Han population was located at an intermediate position between south and north Chinese Han populations, relatively closer to Chaoshan and Minnan Han. Moreover, admixture analysis showed a large proportion of Central Plains Han origin in Chaoshanese and Minnanese. Admixture and phylogenetic analysis also reflected the genetic similarity shared by these two groups.     

中国南北方汉族人群DNA甲基化表观遗传差异研究

目的 族群地域、体貌特征等表型是基因型与环境共同作用的结果。大量基因组学研究表明,汉族人群具有混合特征,内部存在明显的南北遗传差异。本研究旨在探索研究表观基因组在中国南北方汉族人群之间是否存在差异,并筛选差异遗传位点。方法 使用GLINT软件对483份汉族样本的全基因组甲基化芯片数据进行EWAS分析,使用Lasso回归方法筛选位点。使用多元逻辑回归算法构建南北方汉族人群预测模型,通过十折交叉验证的方法评估。结果 筛选出一组南北方汉族之间差异显著的CpG位点,准确性为99.03%,Kappa系数为0.979 6。结论 本研究表明南北方汉族人群之间存在表观遗传差异,本研究为进一步开展不同地域汉族人群之间的表观遗传差异研究奠定了基础。     

陕西渭南地区汉族人群17个Y-STR基因座多态性及遗传关系分析

调查陕西渭南地区汉族群体17个Y-STR基因座的多态性,探讨其群体遗传学及法医学应用价值。应用Y-fi ler荧光标记复合扩增系统,对413名陕西渭南地区汉族无关男性个体17个Y-STR基因座进行复合扩增,用ABI3130遗传分析仪进行基因分型,计算各基因座的群体遗传学参数,并结合已经发表的其他10个群体相应基因座的单倍型资料,分析各群体间的遗传距离。413名陕西渭南汉族个体共检出405种单倍型,其中397种单倍型仅出现1次,单倍型多样性达0.9999,基因多样性(GD)为0.4130(DYS391)~0.9734(DYS385a/b),累计GD值为0.9999。遗传距离分析提示,陕西渭南汉族与辽宁满族的遗传距离最小(0.00110),与青海藏族的遗传距离最大(0.22333)。结果表明,17个Y-STR基因座在陕西渭南汉族群体中具有丰富的遗传多态性和较高的非父排除能力,在法医学和人类群体遗传学研究中具有重要价值。     

Fine-scale north-to-south genetic admixture profile in Shaanxi Han Chinese revealed by genome-wide demographic history reconstruction

The Han Chinese are the world's largest ethnic group residing across China. Shaanxi province in northern China was a pastoral–agricultural interlacing region sensitive to climate change since Neolithic times, which makes it a vital place for studying population dynamics. However, genetic studies of Shaanxi Han are underrepresented due to the lack of high-density sampling and genome-wide data. Here, we genotyped 700 000 single nucleotide polymorphisms (SNPs) in 200 Han individuals from nine populations in Shaanxi and compared with available modern and ancient Eurasian individuals. We revealed a north–south genetic cline in Han Chinese with Shaanxi Han locating at the northern side of the cline. We detected the western Eurasian-related admixture in Shaanxi populations, especially in Guanzhong and Shanbei Han Chinese in proportions of 2%–4.6%. Shaanxi Han were suggested to derive a large part of ancestry (39%–69%) from a lineage that also contributed largely to ancient and present-day Tibetans (85%) as well as southern Han, supporting the common northern China origin of modern Sino-Tibetan-speaking populations and southwestward expansion of millet farmers from the middle-upper Yellow River Basin to the Tibetan Plateau and to southern China. The rest of the ancestry of Shaanxi Han was from a lineage closely related to ancient and present-day Austronesian and Tai-Kadai speaking populations in southern China and Southeast Asia. We also observed a genetic substructure in Shaanxi Han in terms of north–south-related ancestry corresponding well to the latitudes. Maternal mitochondrial DNA and paternal Y-chromosome lineages further demonstrated the aforementioned admixture pattern of Han Chinese in Shaanxi province.     

Y-chromosome haplotype distribution in Han Chinese populations and modern human origin in East Asians

We investigated the distribution of Y-chromosome haplotype using 19 Y-SNPs in Han Chinese populations from 22 provinces of China. Our data indicate distinctive patterns of Y chromosome between southern and northern Han Chinese populations. The southern populations are much more polymorphic than northern populations. The latter has only a subset of the southern haplotypes. This result confirms the genetic difference observed between southern and northern ethnic populations in East Asia. It supports the hypothesis that the first settlement of modern humans of African origin occurred in the southern part of East Asia during the last Ice Age, and a northward migration led to the peopling of northern China.     

Y-chromosome haplotype distribution in Han Chinese populations and modern human origin in East Asians

We investigated the distribution of Y-chromosome haplotype using 19 Y-SNPs in Han Chinese populations from 22 provinces of China. Our data indicate distinctive patterns of Y chromosome between southern and northern Han Chinese populations. The southern populations are much more polymorphic than northern populations. The latter has only a subset of the southern haplotypes. This result confirms the genetic difference observed between southern and northern ethnic populations in East Asia. It supports the hypothesis that the first settlement of modern humans of African origin occurred in the southern part of East Asia during the last Ice Age, and a northward migration led to the peopling of northern China.     

Y-chromosome Genotyping and Genetic Structure of Zhuang Populations

Zhuang, the largest ethnic minority population in China, is one of the descendant groups of the ancient Bai-Yue. Linguistically, Zhuang languages are grouped into northern and southern dialects. To characterize its genetic structure, 13 East Asian-specific Y-chromosome biallelic markers and 7 Y-chromosome short tandem repeat (STR) markers were used to infer the haplogroups of Zhuang populations. Our results showed that O*, O2a, and O1 are the predominant haplogroups in Zhuang. Frequency distribution and principal component analysis showed that Zhuang was closely related to groups of Bai-Yue origin and therefore was likely to be the descendant of Bai-Yue. The results of principal component analysis and hierarchical clustering analysis contradicted the linguistically derived north-south division. Interestingly, a west-east clinal trend of haplotype frequency changes was observed, which was supported by AMOVA analysis that showed that between-population variance of east-west division was larger than that of north-south division. O* network suggested that the Hongshuihe branch was the center of Zhuang. Our study suggests that there are three major components in Zhuang. The O* and O2a constituted the original component; later, O1 was brought into Zhuang, especially eastern Zhuang; and finally, northern Han population brought O3 into the Zhuang populations.     

壮族Y染色体分型及其内部遗传结构

壮族是中国最大的少数民族,与东南亚的泰老族群关系密切,在东亚人群的遗传结构研究中地位非常特殊。本研究调查了壮族各个支系的Y染色体多样性,通过主成分分析、聚类分析和分子方差分析,揭示壮族的内部父系遗传结构。结果发现,壮族的主要Y染色体单倍群为O%＊,O2a,O1。传统的对壮族按方言分为南北二组的分类方法在遗传上并没有依据,壮族支系体现出从东往西的梯度变化过程。这说明壮族的结构中有几个层次,最早的成分普遍出现在各个支系中,第二层是由东部来的百越核心成分,第三层是北方来的汉族成分。壮族内部遗传结构的分析将有助于对东亚人群的南来起源的研究。     

Randomly Amplified Polymorphic DNA Variation in Populations of Eastern Australian Koalas, Phascolarctos cinereus

Randomly amplified polymorphic DNA (RAPD) variation in populations of the koala, Phascolarctos cinereus, was investigated, revealing significant differences in the level of diversity between southern and northern regions of eastern Australia. Of the 20 polymorphic RAPD markers identified in koalas, 4-7 were polymorphic in southern populations, while 12-17 were polymorphic in northern populations. Analysis of molecular variance revealed a significant difference in the estimated variance between koalas from northern and those from southern regions (P < 0.001), where populations from the north were greater than twice as variable as their southern cousins. The total genetic diversity observed was attributed to regional differences (30.91%), population differences within a region (11.77%), and differences among individuals within a population (57.32%). For the within-region analyses, a large proportion of the genetic diversity was attributable to individual differences within a population, 80.34% for the north and 91.23% for the south. These results demonstrate that RAPD markers are useful for determining population structure among koalas.     

Northern gene flow into southeastern East Asians inferred from genome-wide array genotyping

The population history of Southeast (SE) China remains poorly understood due to the sparse sampling of present-day populations and limited modeling with ancient genomic data. We report genome-wide genotyping data from 207 present-day Han Chinese and Hmong-Mien (HM)-speaking She people from Fujian and Taiwan Island, SE China. We coanalyzed 66 Early Neolithic to Iron Age ancient Fujian and Taiwan Island individuals obtained from previously published works to explore the genetic continuity and admixture based on patterns of genetic variations of the high-resolution time transect. We found the genetic differentiation between northern and southern East Asians was defined by a north–south East Asian genetic cline and our studied southern East Asians were clustered in the southern end of this cline. The southeastern coastal modern East Asians are genetically similar to other southern indigenous groups as well as geographically close to Neolithic-to-Iron Age populations, but they also shared excess alleles with post-Neolithic Yellow River ancients, which suggested a southward gene flow on the modern southern coastal gene pool. In addition, we identified one new HM genetic cline in East Asia with the coastal Fujian HM-speaking She localizing at the intersection between HM and Han clines. She people show stronger genetic affinity with southern East Asian indigenous populations, with the main ancestry deriving from groups related to southeastern ancient indigenous rice farmers. The southeastern Han Chinese could be modeled with the primary ancestry deriving from the group related to the Yellow River Basin millet farmers and the remaining from groups related to rice farmers, which was consistent with the northern China origin of modern southeastern Han Chinese and in line with the historically and archaeologically attested southward migrations of Han people and their ancestors. Our estimated north–south admixture time ranges based on the decay of the linkage disequilibrium spanned from the Bronze Age to historic periods, suggesting the recent large-scale population migrations and subsequent admixture participated in the formation of modern Han in SE Asia.     

IL-10 Genetic Polymorphisms Were Associated with Valvular Calcification in Han,Uygur and Kazak Populations in Xinjiang,China

Objective

Valvular calcification occurs via ongoing endothelial injury associated with inflammation. IL-10 is an anti-inflammatory cytokine and 75% of the variation in IL-10 production is genetically determined. However, the relationship between genetic polymorphisms of IL-10 and valvular calcification has not been studied. The objective of this study was to investigate the association between valvular calcification and IL-10 genetic polymorphisms in the Han, Uygur and Kazak populations in China.

Patients and Methods

All of the participants were selected from subjects participating in the Cardiovascular Risk Survey (CRS) study. The single nucleotide polymorphisms (SNPs) rs1800871 and rs1800872 of the IL-10 gene were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Three independent case-control studies involving the Han population, the Uygur population and the Kazak population were used in the analysis.

Results

For the Han and Kazak populations, rs1800871 was found to be associated with valvular calcification in the recessive model, and the difference remained statistically significant following multivariate adjustment (p<0.001, p=0.031, respectively). For the Han, Uygur and Kazak populations, rs1800872 was found to be associated with valvular calcification in the dominant model, and the difference remained statistically significant following multivariate adjustment (p<0.001, p=0.009, and p=0.023,respectively)

Conclusion

Both rs1800871 and rs1800872 of the IL-10 gene are associated with valvular calcification in the Han and Kazak populations in China. Rs1800872 is also associated with valvular calcification in the Uygur population.     

Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci

We have analyzed 105 autosomal polymorphic short tandem repeat (STR) loci for nine East and South-eastern Asian populations (two Japanese, five Han Chinese, Thai, and Burmese populations) and a Caucasian population using a multiplex PCR typing system. All the STR loci are genomewide tetranucleotide repeat markers of which the total number of observed alleles and the observed heterozygosity were 756 and 0.743, respectively, for Japanese populations. Phylogenetic analysis for these allele frequency data suggested that the Japanese populations are more closely related with southern Chinese populations than central and/or northern ones. STRUCTURE program analysis revealed the almost clearly divided and accountable population structure at K=2–6, that the two Japanese populations always formed one group separated from the other populations and never belong to different groups at K≥3. Furthermore, our new allele frequency data for 91 loci were analyzed with those for 52 worldwide populations published by previous studies. Phylogenetic and multidimensional scaling (MDS) analyses indicated that Asian populations with large population size (six Han Chinese, three Japanese, two Southeast Asia) formed one distinct cluster and are closer to each other than other ethnic minorities in east and Southeast Asia. This pattern may be the caviar of comparing populations with greatly differing population sizes when STR loci were analyzed.     

Isolation and characterization of microsatellite loci in the beach pea, Lathyrus japonicus (Fabaceae), in Japan

? Premise of the study: Microsatellite loci were developed for Lathyrus japonicus (Fabaceae) to evaluate genetic diversity, population genetic structure, and demographic patterns of this species in Japan. ? Methods and Results: In total, eight primer sets were identified in Japanese populations of L. japonicus and polymorphisms were evaluated in 83 individuals from three populations, including the northern and southern geographic range in Japan. The number of alleles per locus ranged from four to 20, and gene diversity per locus ranged from 0.636 to 0.935 among three populations. In addition, six of the eight loci could be successfully amplified in L. pratensis. ? Conclusions: These markers will be useful for studies of genetic variations, genetic structure, and gene flow of L. japonicus, which is important to investigate the demographic patterns of this coastal plant. In addition, the primers are useful for further genetic structure analysis of L. pratensis.     

Mitochondrial DNA evidence of southward migration of Manchus in China

The Northeast area of China is a cross region between East Asia and Siberia. Although five populations from this area have been studied in maternal lineage, little is known about the genetics of other populations. In this study, forty-seven Manchu individuals were analyzed using a mitochondrial DNA marker, and fourteen mitochondrial DNA haplogroups, the representative haplogroups of east Eurasian, were identified. All analyses showed that Manchu were close to the neighboring populations such as Mongolian, Korean and northern Han Chinese, and were far from the other populations who lived in the cradle of Manchu, suggesting that the Manchu integrated gradually with natives following its southward migration.     

Use of autosomal loci for clustering individuals and populations of East Asian origin

We studied the genetic relationships among East Asian populations based on allele frequency differences to clarify the relative similarities of East Asian populations with a specific focus on the relationships among the Koreans, the Japanese, and the Chinese populations known to be genetically similar. The goal is to find markers appropriate for differentiating among the specific populations. In this study, no prior data existed for Koreans and the markers were selected to differentiate Chinese and Japanese. We typed, using AB TaqMan assays, single-nucleotide polymorphisms (SNPs) at 43 highly selected mostly independent diallelic sites, on 386 individuals from eight East Asian populations (Han Chinese from San Francisco, Han Chinese from Taiwan, Hakka, Koreans, Japanese, Ami, Atayal, and Cambodians) and one Siberian population (Yakut). We inferred group membership of individuals using a model-based clustering method implemented by the STRUCTURE program and population clustering by using computer programs DISTANCE, NEIGHBOR, LSSEARCH, and DRAWTREE, respectively, calculating genetic distances among populations, calculating neighbor-joining and least-squares trees, and drawing the calculated trees. On average 52% of individuals in the three Chinese groups were assigned into one cluster, and, respectively, 78 and 69% of Koreans and Japanese into a different cluster. Koreans differentiated from the Chinese groups and clustered with the Japanese in the principal component analysis (PCA) and in the best least-squares tree. The majority of Koreans were difficult to distinguish from the Japanese. This study shows that a relatively few highly selected markers can, within limits, differentiate between closely related populations.Electronic Supplementary Material Supplementary material is available for this article at     

Genetic analysis of 30 InDel markers for forensic use in five different Chinese populations

Allele frequencies of 30 insertion/deletion polymorphism (InDel) markers previously selected and validated for forensic purposes were assessed in 419 unrelated individuals originating from five different populations of P.R. China, including Chinese Han, Chinese Hui, Uighur, Mongolians, and Tibetans. Hardy-Weinberg equilibrium tests and linkage disequilibrium analysis were performed; the allele frequency distributions of the 30 InDel markers met the conditions for genetic equilibrium in all five populations and the InDel markers on the same chromosome did not generate any linkage blocking. Analysis of molecular variance indicated that genetic variation among the five populations represents only 4% of the total genetic diversity. We determined the cumulative power of discrimination for each population: 0.99999999999841 in Chinese Han, 0.99999999999690 in Chinese Hui, 0.99999999999709 in Uighur, 0.99999999999772 in Mongolians, and 0.99999999999854 in Tibetans.