不同株的熊蜂短膜虫与宿主生存的关系

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HUMTH01 allele distribution in four human samples. An interpopulation analysis

The analysis of STR HUMTH01 in four populations (Galicia, SE Spain, Morocco, Cape Verde) was carried out, with up to 8 alleles being found. The frequencies of these alleles determine values of heterozigosity ranging from 0,826 detected in Cape Verde to 0,778 in Morocco. A global comparison of world populations shows clear patterns of differentiation among the main human groups, both by way of the analysis of allele distribution profiles and by the application of a Correspondence Analysis. Caucasian populations are mainly characterised by the highest frequencies in allele 9.3, Mongoloids by a very high frequency of allele 9 and Negroids show the highest frequencies for allele 7 and mainly 8. A significant negative correlation (r=−0,916, p<0,001) found in the relationships between alleles 9 and 9.3 seems to suggest the participation of non-random evolutionary forces in the population dynamics of this marker.     

Population database of STRs in West Africa: a genetic study of TPOX, HUMVWA31/A, HUMTH01, and CYP19

Four tetrameric STRs (TPOX, HUMVWA31/A, HUMTH01, and CYP19) were analysed in a West African population (Cabo Verde). No significant deviations from Hardy–Weinberg proportions were observed, either in conventional or exact tests. Pairwise comparisons confirmed allelic independence for all the combinations of loci. Data is provided for the first time about CYP19 in Black populations. In comparisons between African and Afro‐American populations, significant frequency differences for several alleles at the TH01 and VWA31/A loci were observed. The allele frequencies provided in this study contribute to a better knowledge of the variability of these markers among the main human groups, especially in the context of Subsaharan African populations. This revised version was published online in July 2006 with corrections to the Cover Date.     

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.     

Identification of repeat sequence heterogeneity at the polymorphic short tandem repeat locus HUMTH01[AATG]n and reassignment of alleles in population analysis by using a locus-specific allelic ladder.

An allelic ladder containing amplified sequences of seven alleles of the polymorphic human tyrosine hydroxylase locus, HUMTH01, was constructed and employed as a standard marker. Sequence analysis of each ladder component indicates that fragments differ by integral multiples of the AATG core repeat sequence characteristic of this locus. Individual alleles are designated "5" through "11," according to the number of complete reiterations of the core repeat contained within them. Comparison of the HUMTH01 allelic ladder with DNA samples amplified at this locus revealed core repeat length heterogeneity (i.e., deletions or insertions shorter than one core repeat) within the human population. In particular, a common allele was identified which migrates more quickly than allele 10, but more slowly than allele 9, on electrophoresis through a denaturing polyacrylamide gel. Sequence analysis of this allele, designated "10-1," reveals lack of a single adenine normally present in the seventh copy of the AATG. The allelic ladder was used to reevaluate previously published population data. Results of testing for Hardy-Weinberg equilibrium and population substructure were not altered significantly by these modifications.     

Population genetics of short tandem repeat (STR) loci

To investigate the population genetics of short tandem repeat (STR) polymorphisms in human populations, we have studied the allele frequency distributions of four STR loci (HUMTH01, HUMVWA31, HUMF13A1 and HUMFES) in 16 different population surveys which can be categorised within three broadly defined ethnic groups: Caucasian, Asian (Indian subcontinent), and African (Afro-Caribbean and US black). We have observed that allele frequency distributions of populations within ethnic groups are similar; consequently, genetic distances are an order of magnitude lower than between ethnic groups. Inbreeding coefficients (F-statistics) and calculations of the number of mean heterozygous loci per individual, along with estimates of variance, did not suggest that the populations were substructured. This included a study of an immigrant Asian population known to comprise at least three different sub-groups. Finally, an indication of the discriminating power is given by calculation of likelihood ratios (LR) of each individual tested across all four loci. Approximately 70% of Caucasians give an LR of greater than 10,000; the test is even more discriminating in Afro-Caribbeans-approximately 90% of tests are greater than 10,000.Editor's commentsThe authors present data generated by the move from VNTR to STR loci for human identification. The data they present for samples within major racial groupings address some of the concerns about population substructuring discussed by Balding and Nichols in this volume.     

Microsatellite profiles reveal an unexpected genetic relationship between Asian populations

Allelic frequencies for up to five short tandem repeat systems (HumTH01, HumVWA, HumF13B, HumCD4, HumD21S11) were analyzed in seven population samples from Asia using the polymerase chain reaction and gel electrophoresis. No deviations from Hardy-Weinberg equilibrium were observed. Two new alleles of the CD4 and TH01 loci were detected, and sequenced and their molecular structure is presented. A phylogenetic tree based on Thai, Han Chinese (from the northeast of China), Japanese, German and Ovambo allelic frequencies was constructed and demonstrates the close relationship of the Asian populations. Additionally, allelic frequency data for the VWA and TH01 systems were determined for the south Chinese minorities Bai, Dai and Qiang and for Koreans and compared with the above data. The Bai and Dai populations were clear outliers of the cluster of all other Asians, indicating an unexpected pattern of genetic heterogeneity of the Chinese nation. Two clusters of Asian populations could be established: the Koreans and Japanese together with the Han and Qiang Chinese, and, forming a separate cluster, the Bai and Dai populations. Received: 10 June 1997 / Accepted: 15 March 1998     

HUMF13A01 in autochthonous Basques and in genetically related populations

A population gentics study was carried out on 678 Basque individuals using the short tandem repeat HUMF13A01. Thirteen different alleles were detected. This population is in Hardy-Weinberg equilibrium. The singularity of the Basque population’s HUMF13A01 allele frequencies is displayed in the European context, through some genetic similarities are shown, especially with some neighbouring and culturally related populations, and with other populations with which Basques may have shared ancient common roots, such as the Sardinians.     

Genetic analyses in five western Mediterranean populations: variation at five tetrameric short tandem repeat loci.

A population study of the Balearic (Majorca, Minorca, Ibiza, Chueta) and Valencia populations was carried out using the short tandem repeat loci HUMTHO1, D4S243, HUMF13A1, D18S535, and D12S391. All the populations sampled were found to be in Hardy-Weinberg equilibrium for the five markers analyzed. Several statistical analyses showed a clear displacement of the Chueta and Ibiza populations from the other populations sampled. These results are in agreement with those obtained from the analysis of classical markers and mitochondrial DNA restriction fragment length polymorphisms, as well as with the history of these populations. A comparative study performed with other European populations using three of the five markers selected for this study (HUMTHO1, HUMF13A1, and D12S391) revealed a clear differentiation only of the Chueta population. We detected a tendency for a west-east clinal distribution in the frequency of the HUMTH01*6 allele in the European and Mediterranean area. This distribution could reflect some of the migratory events that have happened throughout that area's history. The forensic usefulness of these markers can be judged by their highly combined power of discrimination (0.999997).     

Genetic polymorphism analysis of 15 STR loci in Chinese Hui ethnic group residing in Qinghai province of China

In the present study, we investigated the diversity distributions of allelic frequencies of 15 short tandem repeats (STRs) loci in a sample of Chinese Hui ethnic group in the Ningxia Hui Autonomous Region. The allelic frequencies of the 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were obtained from 2975 unrelated healthy Hui individuals. The STR genotyping data of all the samples were generated by DNA extraction, multiple amplification, GeneScan and genotype analysis. The genetic distances among different populations were calculated by using Nei's method and a phylogenetic tree was constructed based on the allelic frequencies of the same 15 STR loci using the neighbor-joining method. A total of 185 alleles were observed in the Hui population, with the corresponding allelic frequencies ranging from 0.0002 to 0.5322. Chi-Square tests showed that all STR loci were in Hardy-Weinberg equilibrium. The forensic statistical parameters of all the loci showed high values. The population data in this study were compared with the previously published population data from other ethnics or areas. The Hui population showed significant differences from the Minnan Han, Uigur, Ewenki, Yi, Tibetan, Maonan and Malay ethnic minority groups in some loci, and from the South Morocco population and the Moroccan population in all the loci. Our results are valuable for human individual identification and paternity testing in the Chinese Hui population and are expected to enrich the genetic information resources of Chinese populations.     

基于k-mer组分信息的系统发生树构建方法

随着越来越多基因组的测序完成,基于全基因组的非比对的系统发生分析已成为研究热点。不同的生物物种或个体基因组之间的核酸组分不完全相同。遗传语言-DNA序列的信息很大程度上反映在其k—mer频数中。基于基因组序列k-mer频数的系统发生树则从新的角度为我们提供物种之间的亲缘关系。本文定义基于k-mer,频数的信息参数,并用它表征基因组序列,计算不同基因组之间信息参数的距离,用邻接法对84个病毒构建了系统发生树,发现构建的系统发生树很大程度上与已有的系统发生树相吻合。