Historical sketch of Slovak Haban (Hutterite) population based on autosomal STR analysis

According to the Hutterite chronicles, the Habans arrived from Austrian Tyrol, Switzerland, and northernmost Italy and stayed in four regions of Slovakia (Soboti?te, Vel'ké Leváre, Moravsky Sv?ty Ján, Tren?ín). There are some communities in western Slovakia that retained their Haban cultural identity and still identify themselves as descendents of the Hutterite population with their own specific customs. Slovak Habans are typical founder population with significant social isolation for which high degree of inbreeding is typical. Present study investigated STR polymorphisms as a powerful genetic tool for population genetic studies. The aim was to perform a comparative, population genetic study based on 15 STR loci widely used in forensic genetics, of the Haban population, the Slovak majority population and the population of Tyrol. We analyzed allele frequencies and other statistical parameters in three selected populations in order to identify groups of specific ethnic origin and establish their genetic relationship. The data set included 110 unrelated Habans and 201 unrelated individuals from the Slovak majority population, as well as allelic frequencies for the population of Austrian Tyrol available in the literature. Population pairwise FST values used as a short term genetic distance between populations showed significant differentiation between the Habans and both reference populations (FST=0.0025 and 0.0042 for comparison with the Slovaks and Austrians, respectively; p<10(-3)). The Slovak Hutterites were demonstrated to be genetically distinct and more closely related to their geographic neighbors than to their historical ancestral population, which may be at least partially explained by gene flow between neighboring Haban and Slovak populations.     

Dermatoglyphic analysis of Habans (Hutterites) from Slovakia

Dermatoglyphic traits have been used to assess population structure and affinities of the 91 Habans (Hutterites) and 162 Non-Haban Slovaks. In addition a comparison has been made with other Slovak population samples. Biological distances between individual populations were assessed by means of the Hiernaux distance coefficient. The results show a clear separation of the Habans from the Non-Habans in the same villages as well as from the other Slovak groups. Dermatoglyphic analysis is regarded as noncompatible with the interpretation of the genetic structure.     

Multiple population structure of the giant mottled eel, Anguilla marmorata

The population structure of the giant mottled eel, Anguilla marmorata, was investigated with mitochondrial and microsatellite DNA analyses using 449 specimens from 13 localities throughout the species range. Control region F-statistics indicated the North Pacific (Japan, Taiwan, Philippines, Sulawesi), South Pacific (Tahiti, Fiji, New Caledonia, Papua New Guinea), eastern Indian Ocean (Sumatra), western Indian Ocean (Réunion, Madagascar), Ambon, and Guam regions were significantly different (Phi(ST) = 0.131-0.698, P < 0.05) while only a few differences were observed between localities within the South Pacific. These regions were roughly clustered in the neighbour-joining tree, although Ambon individuals were mainly divided into North and South Pacific groups. Analysis with eight microsatellite loci showed almost identical results to those of the control region, except no genetic difference was observed between the western and eastern Indian Ocean (F(ST) = 0.009, P > 0.05). The Bayesian cluster analysis of the microsatellite data detected two genetic groups. One included four North Pacific localities, and the other included eight localities in the South Pacific, Indian Ocean, and Guam, but Ambon individuals were evenly assigned to these two groups. These results showed that A. marmorata has four genetically different populations (North Pacific, South Pacific, Indian Ocean, Guam region). The North Pacific population is fully panmictic whereas the South Pacific and Indian Ocean populations have a metapopulation structure. Interestingly, Guam was suggested to be inhabited by a reproductive population restricted to that region, and the individuals from the North and South Pacific populations co-exist in Ambon.     

PKU in Slovakia: mutation screening and haplotype analysis

The restriction fragment length polymorphism haplotypes and seven common mutations in the phenylalanine hydroxylase gene were analysed in 49 unrelated Slovak phenylketonuria (PKU) families of Caucasian origin. The predominant mutation in this population sample is R408W, with a frequency of 45.9%. In addition, four other mutations have been identified at relatively high frequencies: IVS12nt1, 10.2%; R158Q, 7.1%; R261Q, 7.1%; R252W, 2.0%. The mutation-haplotype associations correspond to those described in other European populations. The high proportion of mutations (72.4%) amenable to simple rapid detection based on the polymerase chain reaction provides a good basis for direct DNA-diagnosis of PKU in the Slovak population.     

Microsatellite loci in eelgrass Zostera marina reveal marked polymorphism within and among populations

Using an enriched genomic library, we developed seven (CT)n/(GA)n microsatellite loci for eelgrass Zostera marina L. Enrichment is described and highly recommended for genomes in which microsatellites are rare, such as in many plants. A test for polymorphism was performed on individuals from three geographically separated populations (N = 15/population) and revealed considerable genetic variation. The number of alleles per locus varied between five and 11 and the observed heterozygosities for single loci ranged from 0.16 to 0.81 within populations. Mean allele lengths were markedly different among populations, indicating that the identified loci will be useful in studying population structure in Z. marina. As the frequency of the most abundant multilocus genotype within populations was always < 1%, these loci have sufficient resolving power to address clone size in predominantly vegetatively reproducing populations.     

Genetic analysis of twelve X-chromosomal STRs in Japanese and Chinese populations

We investigated the genetic markers of twelve X-STR loci in 670 healthy, unrelated Japanese (438 men and 232 women) from Tokyo and 488 Chinese (263 men and 225 women) from Shenyang, using the Investigator Argus X-12 kit. Allele and haplotype analyses of twelve X-STRs clustered into four linkage groups indicated that they are highly informative for forensic applications in Japanese and Chinese populations. Hardy–Weinberg equilibrium tests demonstrated no significant deviations in the two populations. Among the four closely linked X-STR trios, some haplotype unique to Japanese or Chinese population were detected. Haplotype diversity for each linkage group ranged from 0.9861 to 0.9968, showing high values in each of the study populations. The genetic distances between populations based on the 12 X-STR loci and the phylogenetic tree revealed long genetic distances between Asian and Caucasian populations and between Asian and African population (Moroccan). These results suggest that the twelve X-STR loci will contribute to forensic casework in Japanese and Chinese populations.     

Genetic differentiation among Hemarthria compressa populations in south China and its genetic relationship with H. japonica

Within and among populations genetic variance of twelve Hemarthria compressa populations and one Hemarthria japonica population from China were analyzed using inter simple sequence repeat (ISSR). Twelve primers amplified a total of 165 genomic DNA fragments across a total of 148 individuals of which 156 were polymorphic (94.55%). 75.76% of the bands were unique to each species, while the average genetic distance (GD) between one population of H. japonica and twelve populations of H. compressa was 0.44, which suggest that there was distinct differentiation between these two species. In H. compressa, twelve primers produced 145 bands across 145 individuals. High genetic diversity was observed at species level. The percentage of polymorphic loci (P) was 86.21% and Shannon's information index of diversity (I) was 0.357. In contrast, there were relatively low levels of genetic diversity within population (P=32.93%, I=0.174). Analysis of molecular variance (AMOVA) showed that a considerable proportion of genetic variation (48.02%) resided among populations. The coefficient of gene differentiation (G(ST)=48.6%) also suggested that there was strong genetic differentiation among H. compressa populations in southern China. An indirect estimate of the number of migrants per generation (N(m)=0.264) indicated that gene flow was low among populations of this species. Relative high clonal diversity was found, and all local genotypes were found.     

Genetic structure of the Russian populations of <Emphasis Type="Italic">Pyrenophora tritici-repentis</Emphasis>, determined by using microsatellite markers

The population genetic structure of plant pathogenic fungus Pyrenophora tritici-repentis was examined using microsatellite (SSR) markers. According to the geographical origin of the pathogen populations, they were designated as North Caucasian (S, 33 isolates), northwest (Nw, 39), and Omsk (Om, 43). The populations were analyzed at the nine most polymorphic SSR loci, at which 75 alleles were identified. To characterize the genetic variation within and between populations, the AMOVA algorithm as implemented in the Arlequin v. 3.5 software program was used. The number of alleles per locus ranged from 5 to 12 and their sizes varied within the range from 180 to 400 bp. The mean gene diversity at SSR loci was high for all populations (H = 0.58–0.75). The populations were considerably different in the frequencies of individual alleles of the SSR loci. Most isolates in the populations were represented by unique haplotypes. The within-population variation of the isolates at molecular markers was 86.4%; among the populations, 13.6%. Substantial interpopulation differences were found between the Om and S (F_st = 0.16) and between the Om and Nw (F_st = 0.20) populations, whereas between the S and Nw populations, these differences were small (F_st = 0.05). Thus, it was demonstrated that the population of P. tritici-repentis from Omsk oblast had the independent status of the geographical population; northwest and North Caucasian populations differed in the allelic diversity of SSR loci, and despite the low F_st value (0.05), they also belonged to independent geographical populations.     

A study of conservation genetics in Cupressus chengiana, an endangered endemic of China, using ISSR markers

ISSR markers were used to analyze the genetic diversity and genetic structure of eight natural populations of Cupressus chengiana in China. ISSR analysis using 10 primers was carried out on 92 different samples. At the species level, 136 polymorphic loci were detected. The percentage of polymorphic bands (PPB) was 99%. Genetic diversity (He) was 0.3120, effective number of alleles (Ae) was 1.5236, and Shannon's information index (I) was 0.4740. At the population level, PPB = 48%, Ae = 1.2774, He = 0.1631, and I = 0.2452. Genetic differentiation (Gst) detected by Nei's genetic diversity analysis suggested 48% occurred among populations. The partitioning of molecular variance by AMOVA analysis indicated significant genetic differentiation within populations (54%) and among populations (46%; P < 0.0003). The average number of individuals exchanged between populations per generation (Nm) was 0.5436. Samples from the same population clustered in the same population-specific cluster, and two groups of Sichuan and Gansu populations were distinguishable. A significantly positive correlation between genetic and geographic distance was detected (r = 0.6701). Human impacts were considered one of the main factors to cause the rarity of C. chengiana, and conservation strategies are suggested based on the genetic characters and field investigation, e.g., protection of wild populations, reestablishment of germplasm bank, and reintroduction of more genetic diversity.     

中国新疆野苹果[Malus sieversii(Lebed.)Roem.]群体遗传结构的SSR分析

以中国新疆伊犁地区的巩留县莫合镇库尔德宁、新源县交吾托海、霍城县大西沟和塔城地区的裕民县巴尔鲁克山4个种下居群的109个新疆野苹果实生株系为材料,利用8对苹果SSR引物进行群体遗传结构的研究。结果表明:8对SSR引物在4个居群中可平均扩增出16条带,其中巩留县居群多态性带数百分比最高为89.06%,各位点平均Nei基因多样度为0.257;4个群体共扩增出128个位点,在种级水平及巩留县、新源县、霍城县和裕民县4个居群水平多态性位点百分比分别为100%、88.28%、84.38%、87.50%、78.12%,种级水平Nei基因多样度(H=0.2619)和香农信息指数(I=0.4082)大于种下居群,4个种下居群Nei基因多样度和香农信息指数比较巩留县>霍城县>新源县>裕民县;巩留县居群和新源县居群遗传一致度最大,遗传距离最近;根据基因分化系数(GST=0.064)值,测得的基因流Nm为7.265。UPGMA聚类分析结果表明,巩留县和新源县居群遗传关系最近,霍城县居群次之,裕民县居群远离其他3个居群,巩留县、新源县、霍城县和裕民县4个居群是相对独立的群体,但同时存在部分基因交流。所有参数分析表明,巩留县遗传多样性最丰富,故在制定原位种质保护计划时应优先考虑巩留县居群。     

High frequency of GJB2 mutation W24X among Slovak Romany (Gypsy) patients with non-syndromic hearing loss (NSHL)

Mutations in the GJB2 gene (connexin 26) represent a major cause of autosomal recessive non-syndromic hearing loss (NSHL) worldwide. In most Caucasian populations, the 35delG mutation in this gene was found to account for up to 50% of cases of the genetic non-syndromic childhood deafness. In populations of non-European ethnic background, other GJB2 gene mutations are occasionally common, e.g. 167delT in Ashkenazi Jews, R143W in Africaans and 235delC in Koreans. In this work, DNA samples from 54 unrelated NSHL patients from endogamous and inbred population of Slovak Roms (Gypsies) from Eastern Slovakia were screened for GJB2 mutations. The coding region of the GJB2 gene of patients was sequenced and mutations W24X, R127H, V153I, L90P and V37I were found. In Slovak Romany population, mutation W24X accounts for 23.2%, R127H for 19.4%, 35delG for 8.3%, V153I for 3.7%, L90P for 3.7% and V37I for 0.9% of screened chromosomes. As the W24X mutation was previously found in India and Pakistan, were from the European Romanies originate, it was brought by the European Romnanies from their Indian homeland. The carrier frequency of 35delG was estimated for Slovak non-Romany population to be 3.3%, and for Slovak Romany population to 0.88%. The carrier frequency of W24X varied in different Slovak Romany subpopulations from 0.0% up to 26.1%.     

Persistence of Mhc heterozygosity in homozygous clonal killifish,Rivulus marmoratus: implications for the origin of hermaphroditism

The mangrove killifish Rivulus marmoratus, a neotropical fish in the order Cyprinodontiformes, is the only known obligatorily selfing, synchronous hermaphroditic vertebrate. To shed light on its population structure and the origin of hermaphroditism, major histocompatibility complex (Mhc) class I genes of the killifish from seven different localities in Florida, Belize, and the Bahamas were cloned and sequenced. Thirteen loci and their alleles were identified and classified into eight groups. The loci apparently arose approximately 20 million years ago (MYA) by gene duplications from a single common progenitor in the ancestors of R. marmoratus and its closest relatives. Distinct loci were found to be restricted to different populations and different individuals in the same population. Up to 44% of the fish were heterozygotes at Mhc loci, as compared to near homozygosity at non-Mhc loci. Large genetic distances between some of the Mhc alleles revealed the presence of ancestral allelic lineages. Computer simulation designed to explain these findings indicated that selfing is incomplete in R. marmoratus populations, that Mhc allelic lineages must have diverged before the onset of selfing, and that the hermaphroditism arose in a population containing multiple ancestral Mhc lineages. A model is proposed in which hermaphroditism arose stage-wise by mutations, each of which spread through the entire population and was fixed independently in the emerging clones.     

Genetic variability in natural populations of Arabidopsis thaliana in northern Europe

Ten populations of the model plant Arabidopsis thaliana were collected along a north-south gradient in Norway and screened for microsatellite polymorphisms in 25 loci and variability in quantitative traits. Overall, the average levels of genetic diversity were found to be relatively high in these populations, compared to previously published surveys of within population variability. Six of the populations were polymorphic at microsatellite loci, resulting in an overall proportion of polymorphic loci of 18%, and a relatively high gene diversity for a selfing species (HE = 0.06). Of the overall variability, 12% was found within populations. Two of six polymorphic populations contained heterozygous individuals. Both FST and phylogenetic analyses showed no correlation between geographical and genetic distances. Haplotypic diversity patterns suggested postglacial colonization of Scandinavia from a number of different sources. Heritable variation was observed for many of the studied quantitative traits, with all populations showing variability in at least some traits, even populations with no microsatellite variability. There was a positive association between variability in quantitative traits and microsatellites within populations. Several quantitative traits exhibited QST values significantly less than FST, suggesting that selection may be acting to retard differentiation for these traits.     

Multiplex PCR amplification of 13 microsatellite loci for <Emphasis Type="Italic">Aquila chrysaetos</Emphasis> in forensic applications

The golden eagle (Aquila chrysaetos) is an endangered raptor, which is threatened mainly by illegal egg and nestling robbery. Here we describe a fluorescently labeled, multiplex PCR method using 13 microsatellite markers, which provides a powerful tool for the individual identification and parentage testing of the Golden eagle. This test should be applicable to both forensic analysis and population studies. Fifteen polymorphic loci from A. chrysaetos were cross-amplified. Subsequent PCR condition optimization led to the successful co-amplification of 13 different loci in a single PCR reaction. Fifty samples from wild-living individuals and 89 samples from captive-bred individuals were examined. The results indicated that both populations have similar levels of moderate inbreeding, unsurprising in a small population. This probability of excluding a random individual in parentage analysis was 0.9912 for the wild population and 0.9932 in the captive-bred one in the case that both the individual and its mother were examined together. The probability of identity was estimated to be 3 × 10⁻⁸ for the wild and 4 × 10⁻⁸ for the captive-bred populations. Given the size of the Slovak golden eagle population, this test should therefore be sufficient to reliably identify individual raptors and assess parentage in both conservation studies and forensic analysis.     

Genetic relationships among marine and freshwater populations of the European three-spined stickleback (Gasterosteus aculeatus) revealed by microsatellites

To assess the population genetic structure of the three-spined stickleback, Gasterosteus aculeatus, variability at 18 microsatellite loci was examined in 1724 individuals from 74 locations covering most of the species distribution range in Europe. The results revealed high overall degree of differentiation (F(ST) = 0.21) but contrasting level of divergence and genetic variability between habitat types. Marine populations were genetically relatively uniform even across great geographical distances as compared to substantial differentiation among freshwater populations. Analysis of molecular variance indicated low but significant (2.7%) variation in allele frequencies between geographical regions, but a negligible effect of habitat type (0.2%). The phylogenetic pattern was not explained by habitat type, but a weak signal of populations clustering according to geographical or water system origin was found. The results support the view that three-spined stickleback marine ancestors colonized northern European fresh waters during the postglacial marine submergence c. 10,000 years ago, whereas in the Mediterranean region colonization probably dates back to the Pleistocene. The independent origins of river and lake populations indicate that they originate from multiple colonizations rather than sharing common ancestry. In the continuous marine environment, the low degree of differentiation among populations can be explained by gene flow among subpopulations and large effective population size buffering divergence in neutral markers. In contrast, among postglacially established freshwater populations differentiation appears to be driven by genetic drift and isolation. The stepwise mutations appear to have contributed to the population differentiation in the southern part of the three-spined stickleback distribution range.     

Dissecting the genetic structure of Korean population using genome-wide SNP arrays

Genome-wide SNP arrays have generated unprecedented quantities of data allow the detection of human evolutionary history and dense genome-wide data also enable the identification of distance ancestry among individuals or ethnic groups. To explain wider aspects of the genetic structure of Koreans and the East Asian population, we analyzed 79 individuals from the Korean HapMap project at 555,352 common single-nucleotide polymorphism loci, and compared this data with the worldwide population groups with the 53 ethnic groups from Human Genome Diversity Panel (HGDP-CEPH). Population differentiation (F_ST), Principal Component Analyses, STRUCTURE and ADMIXTURE are examined. In general, all the individual samples studies here were classified into subset of ethnic groups according to their geographical origins. Korean HapMap individuals were grouped together with East Asian populations from HGDP panel. Recently, a sub-population structure within Korean population has been reported. Our result, however, revealed the genetic homogeneity of Korean population. The ADMIXTURE analysis showed that, overall the Korean populations derive 79 % of their genomic ancestry from southern Asia and have relatively little northern Asian ancestry (21 %). The present work, therefore, provide the evidence that the male-biased southern-to-northern migration influenced not only for the genetic make up of the Y chromosome in the Korean population but also, its autosomal composition.     

企鹅珍珠贝不同地理群体遗传多样性的fAFLP 分析

为阐明企鹅珍珠贝(Pteria penguin)不同地理种群的遗传多样性机制, 采用荧光标记扩增片段长度多态性(fAFLP)技术分析了企鹅珍珠贝广西涠洲岛、广东流沙湾和海南黎安3 个不同地理群体的遗传多样性。选取7 对引物组合对90 个个体(每个群体30 个)进行fAFLP 扩增, 结果发现每个个体均能扩增出清晰的、可重复的扩增条带, 每对引物的扩增位点数在100—163 之间, 共得到895 个扩增位点, 多态位点数为865 个; 涠洲岛、流沙湾和黎安群体的多态位点比例分别为70.73%、63.13%、66.82%。Nei 遗传多样性指数为0.1634、0.1558、0.1783, Shannon 遗传多样性指数为0.2635、0.2474、0.2932。3 个群体间遗传相似度在0.9722—0.9824之间, 遗传距离在0.0177—0.0282 之间。根据遗传距离绘制UPGMA 聚类图, 但Mantel 检验结果显示企鹅珍珠贝三群体间的遗传距离与地理距离之间无显著相关。Shannon 遗传多样性指数和AMOVA 分析, 结果均显示企鹅珍珠贝的遗传变异主要来源于群体内个体间, 7.91%的遗传变异来自群体间, 92.09%的遗传变异来自群体内。分析群体的显性基因型频率分布和基因流Nm 发现3 个群体有基本相同的遗传结构, 有明显的基因交流。研究结果表明北海涠洲岛群体、湛江流沙湾群体和海南黎安群体的企鹅珍珠贝种质有较高的多态位点比例, 但未发生显著地理分化。这一结果为我国企鹅珍珠贝的良种选育以及种质资源保护措施的制定提供了参考依据。       

欧洲刺槐种源群体遗传结构和多样性

对来自欧洲和美国的 18个刺槐种源子代进行了等位酶分析。可进行遗传分析的 7个酶系统 (Amy,Fe,L ap,Idh,Mdh,6 Pgd,Skd)中有 14个基因位点 ,其中 12个位点具有多态性。每个多态位点平均等位基因数 (A/L )变化在 1.5 6～ 3.6 7之间 ,平均基因型数 (G/L)变化在 1.6 1～ 7.11之间 ,平均等位基因有效数目 (Ae)变化在 1.0 2～ 2 .5 0之间 ,预期杂合度 (H e)变化在0 .0 2～ 0 .5 6之间。不同种源群体之间也存在较大的遗传差异 ,在 8个德国种源中 ,各群体的 A、Ae、和 H e等相对较小 ,但不同群体间差异较大。各位点等位基因频率在不同种源群体间变化也较大 ,表明德国各种源群体内遗传变异相对较小 ,但群体间差异较大。来自匈牙利和斯洛伐克的 8个种源群则相反 ,各群体的 A、Ae、和 H e等相对较大 ,而不同种源群体间差异则较小 ,各位点等位基因频率在种源群体间变化相对一致 ,表明这两个国家的种源群体内变异较大 ,但不同种源群体间差异较小。欧洲的刺槐种源并未形成明显的地理变异模式 ,而且欧洲的种源和来自原产地的美国种源相比 ,没有发现明显的差异。经过 Hardy-Weinberg平衡检测证明 ,88.4 1%位点符合 H- W遗传平衡 ,表明各群体基因频率和基因型频率保持较高的稳定性 ,且种源内的变异大于种源间变异 ,94 .     

Forensic characteristic and population structure dissection of Shaanxi Han population in the light of diallelic deletion/insertion polymorphism data

The genetic polymorphisms of diallelic deletion/insertion polymorphic (DIP) loci in the Shaanxi Han population are still not clearly characterized. Herein, allele frequencies and forensic application efficiencies for 30 diallelic DIP loci were investigated in 506 unrelated healthy Han individuals from Chinese Shaanxi province. Based on population data of the same 30 diallelic DIP loci, the genetic differentiations, hierarchical clustering relationships and population architectures among Shaanxi Han and other 50 populations were further dissected through genetic and bioinformatics analyses. Results indicated that most of the 30 diallelic DIP loci were relatively high polymorphisms in the Shaanxi Han population; and there were the genetically intimate relationships between Shaanxi Han and the East Asian populations. In summary, this study provided significant insights into genetic background of Shaanxi Han population, and the multiplex amplification of these 30 diallelic DIP loci was appropriate for forensic individual identification and population genetic research in Shaanxi Han population.     

Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies

Mobile elements represent a relatively new class of markers for the study of human evolution. Long interspersed elements (LINEs) belong to a group of retrotransposons comprising approximately 21% of the human genome. Young LINE-1 (L1) elements that have integrated recently into the human genome can be polymorphic for insertion presence/absence in different human populations at particular chromosomal locations. To identify putative novel L1 insertion polymorphisms, we computationally compared two draft assemblies of the whole human genome (Public and Celera Human Genome assemblies). We identified a total of 148 potential polymorphic L1 insertion loci, among which 73 were candidates for novel polymorphic loci. Based on additional analyses we selected 34 loci for further experimental studies. PCR-based assays and DNA sequence analysis were performed for these 34 loci in 80 unrelated individuals from four diverse human populations: African-American, Asian, Caucasian, and South American. All but two of the selected loci were confirmed as polymorphic in our human population panel. Approximately 47% of the analyzed loci integrated into other repetitive elements, most commonly older L1s. One of the insertions was accompanied by a BC200 sequence. Collectively, these mobile elements represent a valuable source of genomic polymorphism for the study of human population genetics. Our results also suggest that the exhaustive identification of L1 insertion polymorphisms is far from complete, and new whole genome sequences are valuable sources for finding novel retrotransposon insertion polymorphisms.