Mitochondrial DNA and Y-chromosomal stratification in Iran: relationship between Iran and the Arabian Peninsula

Modern day Iran is strategically located in the tri-continental corridor uniting Africa, Europe and Asia. Several ethnic groups belonging to distinct religions, speaking different languages and claiming divergent ancestries inhabit the region, generating a potentially diverse genetic reservoir. In addition, past pre-historical and historical events such as the out-of-Africa migrations, the Neolithic expansion from the Fertile Crescent, the Indo-Aryan treks from the Central Asian steppes, the westward Mongol expansions and the Muslim invasions may have chiseled their genetic fingerprints within the genealogical substrata of the Persians. On the other hand, the Iranian perimeter is bounded by the Zagros and Albrez mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts, which may have restricted gene flow from neighboring regions. By utilizing high-resolution mitochondrial DNA (mtDNA) markers and reanalyzing our previously published Y-chromosomal data, we have found a previously unexplored, genetic connection between Iranian populations and the Arabian Peninsula, likely the result of both ancient and recent gene flow. Furthermore, the regional distribution of mtDNA haplogroups J, I, U2 and U7 also provides evidence of barriers to gene flow posed by the two major Iranian deserts and the Zagros mountain range.     

Y-chromosomal diversity of the Valachs from the Czech Republic: model for isolated population in Central Europe

Aim

To evaluate Y-chromosomal diversity of the Moravian Valachs of the Czech Republic and compare them with a Czech population sample and other samples from Central and South-Eastern Europe, and to evaluate the effects of genetic isolation and sampling.

Methods

The first sample set of the Valachs consisted of 94 unrelated male donors from the Valach region in northeastern Czech Republic border-area. The second sample set of the Valachs consisted of 79 men who originated from 7 paternal lineages defined by surname. No close relatives were sampled. The third sample set consisted of 273 unrelated men from the whole of the Czech Republic and was used for comparison, as well as published data for other 27 populations. The total number of samples was 3244. Y-short tandem repeat (STR) markers were typed by standard methods using PowerPlex® Y System (Promega) and Yfiler® Amplification Kit (Applied Biosystems) kits. Y-chromosomal haplogroups were estimated from the haplotype information. Haplotype diversity and other intra- and inter-population statistics were computed.

Results

The Moravian Valachs showed a lower genetic variability of Y-STR markers than other Central European populations, resembling more to the isolated Balkan populations (Aromuns, Csango, Bulgarian, and Macedonian Roma) than the surrounding populations (Czechs, Slovaks, Poles, Saxons). We illustrated the effect of sampling on Valach paternal lineages, which includes reduction of discrimination capacity and variability inside Y-chromosomal haplogroups. Valach modal haplotype belongs to R1a haplogroup and it was not detected in the Czech population.

Conclusion

The Moravian Valachs display strong substructure and isolation in their Y chromosomal markers. They represent a unique Central European population model for population genetics.Y-chromosomal variation of Central European populations and the possible appearance of genetic isolates in these populations are of increasing interest to forensic and human population geneticists.Y-chromosomal data for the population of the Czech Republic is still fractional. Kráčmarová et al published a short report on paleolithic and neolithic Y chromosomal haplogroups in the Czech population (1) and Luca et al performed a refined study of the same data (2). Zastera et al published a major study on Czech Y-chromosomal data (3). Other authors have also reported on Czech Y-chromosomal variation, usually with other population data from Europe (4-7). A recent study compared Czechs with other West Slavic populations (8). In this range of reports regarding, genetic variation of possible or confirmed genetic isolates within Central European populations is virtually absent. Here we present the intra-population diversity of such an isolated population, the Moravian Valachs.So far, a limited number of studies that illustrate the variety of Y-chromosomal polymorphisms in the countries and populations supposedly connected or similar to the Moravian Valachs – the supposed isolate – have been published. Rebala et al (9) focused on the Slavic population from Eastern and Central Europe. As historical sources suggest, immigration from Slavic populations was one of the major sources for the emergence of the Valach population of the Czech Republic, therefore the study of Rebala et al (9) is certainly of great interest to us, as well as other studies on southern European Slavic populations (10). Bosch et al (11) analyzed paternal (and maternal) lineages of the Aromuns and other surrounding Balkan populations, thus offering excellent material for their comparison with the Valachs. They clearly documented the differences between Aromuns (ie, isolated populations) and the major populations that surround them, not only in haplogroup and haplotype lineages, but also in intra-population genetic variability.The Valachs (or Wallachs/Vlachs as they are sometimes called) are one of the most distinct ethnographic and cultural subpopulations of Central Europe. Today, they can be found not only in the Czech Republic – in its eastern border mountain ranges and highlands (Beskydy in Moravia) – but also in south-southeast Poland and several parts of Slovakia (far western, northern, and central region). Originally, this group spread from the Maramures region of Romania, roughly following the Carpathian Mountain range. The arrival of the Valachs to the area of today’s Czech Republic took place at the very end of the 15th or beginning of the 16th century (12). The migration was not spontaneous, but rather encouraged and subsidized by the local nobility, and it lasted at least until the end of the 18th century, with immigrants supposedly coming not only from Romania, but also from Ukraine, Poland, and Slovakia (13).Until the beginning of the 20th century, the Moravian Valachs’ way of life was similar to other Romanian ethnic groups in the Balkans, especially the Aromuns (seasonal mountain sheep herding, production of cheese, wool, and leather products). An admixture of the newly-arrived Valachs with autochthonous (Slavic and German) Moravian population also began soon after the arrival of the first immigrants – so we can assume a steady genetic and cultural flow between these two populations. Nonetheless, the core of the Valach settlement was located in a previously uninhabited high altitude region, neighboring with the indigenous population from lowlands. The result of the admixture process was a complete merging of both populations, and the disappearance of any distinction between “new” Valachs and indigenous Moravians during the 18th century, and the creation of one ethnogeographic region with all its properties and people – the Moravian Valachs.Demographic data (13,14) show only a small increase in the Valach population during the 17-18th century. In combination with population depression during and after the Thirty Years'' War (1618-1648), the conditions in the Valach population favored inbreeding, an effect reinforced by isolation-by-distance from the surrounding populations.To investigate how severe this isolation effect was on Y chromosomal polymorphisms in the Moravian Valachs and whether it is still detectable in modern Valach population is the main aim of our study. Another topic of interest was how the intra-population variability and the sampling bias can affect forensic and population analyses performed on these data.     

Y-chromosomal STR haplotype analysis reveals surname-associated strata in the East-German population

In human populations, the correct historical interpretation of a genetic structure is often hampered by an almost inherent inability to differentiate between ancient and more recent influences upon extant gene pools. One method to trace recent population movements is the analysis of surnames, which, at least in Central Europe, can be thought of as traits 'linked' to the Y chromosome. Illegitimacy, extramarital birth and changes of surnames may have substantially obscured this linkage. In order to assess the actual extent of correlation between surnames and Y-chromosomal haplotypes in Central Europe, we typed Y-chromosomal short tandem repeat markers in 419 German males from Halle. These individuals were subdivided into three groups according to the origin of their respective surname, namely German (G), Slavic (S) or 'Mixed' (M). The distribution of the haplotypes was compared by Analysis of Molecular Variance. While the M group was indistinguishable from group G (PhiST=-0.0008, P>0.5), a highly significant difference (PhiST=0.0277, P<0.001) was observed between the S group and the combined G+M group. This surprisingly strong differentiation is comparable to that of European populations of much larger geographic and linguistic difference. In view of the major migration from Slavic countries into Germany in the 19th century, it appears likely that the observed concurrence of Slavic surnames and Y chromosomes is of a recent rather than an early origin. Our results suggest that surnames may provide a simple means to stratify, and thereby to render more efficient, Y-chromosomal analyses of Central Europeans that target more ancient events.     

中国四川汉族人群Y染色体单核苷酸多态性分析

目的 评估Y染色体单核苷酸多态性(single nucleotide polymorphisms,SNPs)遗传标记的法医学应用价值.方法 用等位基因特异性PCR,限制性酶切和直接扩增法检测了161名中国四川汉族人Y染色体上10个SNPs位点M9,M15,M45,M89,M95,M122,M134,M145,M173和P25的多态性.结果 有8个位点发现遗传多态性,多态性频率0.988/0.012～0.752/0.248.个人识别能力0.094～0.373,累积个人识别能力为0.8308,M122和M134在中国四川汉族人群中的多态性最高.按照国际Y染色体学会的命名原则,10个位点命名了9种单倍组型,单倍组型频率1.2%～52.2%,其中75.2%的中国四川汉族人主要是K*(XO2a,O3,P),O3*(XO3e)和O3e 3种单倍组型.结论 该研究获得了中国四川汉族人群Y染色体的10个SNPs位点的多态性频率分布及其构建的9种单倍组型,为Y-SNPs做为法医遗传学个人识别和亲子鉴定的遗传标记奠定了基础.     

Y-chromosomal evidence for a limited Greek contribution to the Pathan population of Pakistan

Three Pakistani populations residing in northern Pakistan, the Burusho, Kalash and Pathan claim descent from Greek soldiers associated with Alexander's invasion of southwest Asia. Earlier studies have excluded a substantial Greek genetic input into these populations, but left open the question of a smaller contribution. We have now typed 90 binary polymorphisms and 16 multiallelic, short-tandem-repeat (STR) loci mapping to the male-specific portion of the human Y chromosome in 952 males, including 77 Greeks in order to re-investigate this question. In pairwise comparisons between the Greeks and the three Pakistani populations using genetic distance measures sensitive to recent events, the lowest distances were observed between the Greeks and the Pathans. Clade E3b1 lineages, which were frequent in the Greeks but not in Pakistan, were nevertheless observed in two Pathan individuals, one of whom shared a 16 Y-STR haplotype with the Greeks. The worldwide distribution of a shortened (9 Y-STR) version of this haplotype, determined from database information, was concentrated in Macedonia and Greece, suggesting an origin there. Although based on only a few unrelated descendants, this provides strong evidence for a European origin for a small proportion of the Pathan Y chromosomes.     

Analysis of Y-chromosomal biallelic polymorphisms in Sichuan Han of Chinese population]

OBJECTIVE: To evaluate the forensic utility of Y-single nucleotide polymorphisms (SNPs) markers. METHODS: Allele-specific PCR, restriction enzyme digestion or direct PCR were performed to examine 10 different SNP loci on Y chromosome, namely M9, M15, M45, M89, M95, M122, M134, M145, M173 and P25 in 161 Chinese Han males. RESULTS: A total of 8 of the 10 SNPs are reported to be polymorphic in Chinese. The gene diversity for the loci showing polymorphism ranged from 0.988/0.012-0.752/0.248, with a power of discrimination 0.094-0.373. Loci M122 and M134 were the most polymorphic markers in Chinese Hans. Nine different haplogroups with frequencies from 1.2% to 51.6% were observed and 3 of the haplogroups-K*(x O2a, O3, P), O3*(x O3e) and O3e were found in 75.2% of Chinese Hans. CONCLUSION: A comprehensive gene diversity data of Y chromosome and haplogroups were obtained in Sichuan Han population, which will be served as the base for using these Y-SNP markers in forensic medicine and individual identification in Sichuan Hans.     

Mitochondrial DNA polymorphism in the Vietnamese population

The mitochondrial DNA variation was screened in a sample of 50 unrelated individuals of the Vietnamese population originating from Hanoi. A combination of long and standard PCR and restriction endonuclease digests with the enzymes HpaI, BamHI, HaeII, MspI, AvaII and HincII were used to reveal mtDNA variation. Twenty enzyme morphs were detected, three of which (HaeII-13^Viet, MspI-19^Viet and MspI-20^Viet) are new and are produced by a single mutational event in already known enzyme morphs. Ten already known and four new mitotypes [93^Viet (1-1-2-4-1), 94^Viet (2-1-13^Viet-1-1), 95^Viet (2-1-13^Viet-19^Viet-1) and 96^Viet (1-1-2–20^Viet-12)] were found in the Vietnamese population. The 9-bp deletion occurring in the COII/tRNA^Lys region of the mitochondrial genome was also analysed and 10 samples were found to have this deletion. The comparison of the Vietnamese with other East Asian populations showed a close genetic relationship of the population under investigation with other Orientals. However, the Vietnamese population can be differentiated by the significantly higher frequency of the enzyme morph HincII-5 and by seven new markers. These results strongly support the hypothesis of a dual ethnic origin of the Vietnamese population from the Chinese and Thai–Indonesian populations based on HLA markers and linguistic evidence.     

HLA profile of the Mexican Mestizo population

The HLA—A, B and C profile of 665 Mexican Mestizos was studied by microcytotoxicity testing for 30 HLA specificities. Antigen, gene and haplotype frequencies were calculated, and results were compared to those of the three other series of HLA profiles in Mexican Mestizos available in the literature: one from Mexico-City, one from Los Angeles, California, USA, and a recent one from San Antonio, Texas, USA. Comparing the antigen frequencies of our series with those of the other study from Mexico-City, significant differences were only found in three antigens of the HLA-B locus. On the other hand, comparison of either series from Mexico-city with the Los Angeles or the San Antonio studies yielded discrepancies in several specificities of both HLA-A and B loci, most notably the consistent absence of A25 in Mexican Mestizos living in Mexico-City. The presence of this specificity in the Mexican Mestizo Population living in these two American cities could have resulted from input of Caucasian and Black genes over several generations. Differences in haplotype frequency were observed comparing the two series from Mexico-City and the series from San Antonio. Comparison of haplotype frequency with the Los Angeles series was not possible.     

Mitochondrial DNA polymorphism in the Vietnamese population.

The mitochondrial DNA variation was screened in a sample of 50 unrelated individuals of the Vietnamese population originating from Hanoi. A combination of long and standard PCR and restriction endonuclease digests with the enzymes HpaI, BamHI, HaeII, MspI, AvaII and HincII were used to reveal mtDNA variation. Twenty enzyme morphs were detected, three of which (HaeII-13Viet, MspI-19Viet and MspI-20Viet) are new and are produced by a single mutational event in already known enzyme morphs. Ten already known and four new mitotypes [93Viet (1-1-2-4-1), 94Viet (2-1-13Viet-1-1), 95Viet (2-1-13Viet-19Viet-1) and 96Viet (1-1-2-20Viet-12)] were found in the Vietnamese population. The 9-bp deletion occurring in the COII/tRNALys region of the mitochondrial genome was also analysed and 10 samples were found to have this deletion. The comparison of the Vietnamese with other East Asian populations showed a close genetic relationship of the population under investigation with other Orientals. However, the Vietnamese population can be differentiated by the significantly higher frequency of the enzyme morph HincII-5 and by seven new markers. These results strongly support the hypothesis of a dual ethnic origin of the Vietnamese population from the Chinese and Thai-Indonesian populations based on HLA markers and linguistic evidence.     

Cadmium concentrations in blood samples from an East Greenlandic population

An analysis for cadmium was made of 101 human blood samples from the district of Angmagssalik, East Greenland, and 29 from East Greenlanders living temporarily in Copenhagen. No relationship could be found between concentrations of blood cadmium and ethnic origin (Eskimos--Danes), sex, age or amount of seal eaten. Only smoking habits were reflected, as a median of 2.2 micrograms/l was found in smokers and 1.1 in non-smokers. Since analyses of organs from seals have suggested that the WHO provisional, tolerable weekly intake is exceeded by a factor as high as 10 as a result of seal eating, it is surprising that seal eating is without any effect on the blood concentration.     

Determination of population origin: a comparison of autosomal SNPs,Y-chromosomal and mtDNA haplogroups using a Malagasy population as example

Y-chromosomal and mitochondrial DNA (mtDNA) polymorphisms have been used for population studies for a long time. However, there is another possibility to define the origin of a population: autosomal single-nucleotide polymorphisms (SNPs) whose allele frequencies differ considerably in different populations. In an attempt to compare the usefulness of these approaches we studied a population from Madagascar using all the three mentioned approaches. Former investigations of Malagasy maternal (mtDNA) and paternal (Y chromosome) lineages have led to the assumption that the Malagasy are an admixed population with an African and Asian-Indonesian heritage. Our additional study demonstrated that more than two-third of the Malagasy investigated showed clearly a West African genotype regarding only the autosomal SNPs despite the fact that 64% had an Asian mtDNA and more than 70% demonstrated an Asian-Indonesian heritage in either mtDNA or Y-chromosomal haplogroup or both. Nonetheless, the admixture of the Malagasy could be confirmed. A clear African or Asian-Indonesian heritage according to all the three DNA approaches investigated was only found in 14% and 1% of male samples, respectively. Not even the European or Northern African influences, detected in 9% of males (Y-chromosomal analysis) and 11% of samples (autosomal SNPs) were consistent. No Malagasy in our samples showed a European or Northern African origin in both categories. So, the analysis of autosomal SNPs could confirm the admixed character of the Malagasy population, even if it pointed to a greater African influence as detectable by Y-chromosomal or mtDNA analysis.     

Characterization of new HLA-A and -B alleles from Kazakhstan

Eight novel alleles, two HLA-A and six HLA-B, are described in Kazakh individuals.     

神经前体细胞表达发育调控样基因rs4149601多态性与新疆哈萨克族人群中心性肥胖的关联研究

目的 研究神经前体细胞表达发育调控样基因rs4149601多态性与新疆哈萨克族人群中心性肥胖的相关性.方法 采取以人群为基础的横断面病例-对照研究方法,采用TaqMan聚合酶链反应对新疆哈萨克族856名自然人群(男性364名、女性492名;其中肥胖478例、对照378名)的rs4149601多态性进行分型,分析其与新疆哈萨克族人群肥胖的相关性.结果 共有853名的基因型分型成功,在总体女性新疆哈萨克族自然人群中,rs414960l多态性的基因型、等位基因在肥胖组及对照组分布差异有统计学意义(P＜0.05).在校正了年龄、吸烟、饮洒和性别等影响因素后,Logistics回归分析显示GG基因型仍与新疆哈萨克族人群中心性肥胖相关(OR=1.479,95%CI:1.103～1.983,P=0.009);协方差分析结果提示携带GG基因型者的腰围高于AA携带者+AG携带者(P=0.028).结论 神经前体细胞表达发育调控样基因的rs4149601多态性与新疆哈萨克族人群中心性肥胖相关,GG基因型可能是哈萨克族人群中心性肥胖的易感因素.     

Metacarpophalangeal pattern profile analysis of a sample drawn from a North Wales population

Sexual dimorphism and population differences were investigated using metacarpophalangeal pattern profile (MCPP) analysis. Although it is an anthropometric technique, MCPP analysis is more frequently used in genetic syndrome analysis and has been under-used in the study of human groups. The present analysis used a series of hand radiographs from Gwynedd, North Wales, to make comparisons, first, between the sexes within the sample and then with previously reported data from Japan. The Welsh sexes showed MCPP analyses that indicated size and shape differences but certain similarities in shape were also evident. Differences with the Japanese data were more marked. MCPP analysis is a potentially useful anthropometric technique but requires further statistical development.     

Metacarpophalangeal pattern profile analysis of a sample drawn from a North Wales population

Sexual dimorphism and population differences were investigated using metacarpophalangeal pattern profile (MCPP) analysis. Although it is an anthropometric technique, MCPP analysis is more frequently used in genetic syndrome analysis and has been under-used in the study of human groups. The present analysis used a series of hand radiographs from Gwynedd, North Wales, to make comparisons, first, between the sexes within the sample and then with previously reported data from Japan. The Welsh sexes showed MCPP analyses that indicated size and shape differences but certain similarities in shape were also evident. Differences with the Japanese data were more marked. MCPP analysis is a potentially useful anthropometric technique but requires further statistical development.

Geschlechtsdimorphismen und Bevölkerungsunterschiede wurden mit der Metacarpophalangeal- Analyse des Musterprofils (MCPP) untersucht. Obgleich es eine anthropometrische Technik ist, wird die MCPP-Analyse häufiger für die Analyse genetischer Syndrome verwendet und ist bei der Untersuchung menschlichen Gruppen unterrepräsentiert. Bei der durchgeführte Analyse werden eine Reihe von Handröntgenbildern von Gwynedd, Nordwales, verwendet, um zuerst einen Vergleich zwischen den Geschlechtern innerhalb der Stichprobe durchzuführen und dann diese mit früher erstellten nischen Daten zu vergleichen. Die MCPP-Analysen weisen auf Größen- und Formunterschiede bei den walisischen Geschlechtern hin, aber auch bestimmte Ähnlichkeiten in der Form waren vorhanden. Die Unterschiede zu den japanischen Daten waren deutlicher. Die MCPP-Analyse ist eine potentiell nützliche anthropometrische Technik, die aber statistisch weiterentwickelt werden muß.

Les différences entre populations et le dimorphisme sexuel, sont étudiés au moyen d'une analyse du profil phalangométacarpien (PPM). Bien qu'il s'agisse d'une technique anthropométrique, l'analyse du PPM est plus fréquemment utilisée dans l'analyse de syndrome génétique et n'a que peu été employée pour l'étude de groupes humains. La présente étude utilise une série de radiographies de la main provenant de Gwynedd (nord du pays de Galles), pour comparer en premier lieu les deux sexes de l'échantillon, puis pour comparer les données galloises avec celles d'une étude antérieure effectuée au Japon. Les deux sexes gallois montrent des analyses du PPM qui indiquent des différences de forme et de format, mais qui montrent également à l'évidence certaines similarités de forme. Les différences avec les données japonaises sont plus marquées. L'analyse du PPM est une technique anthropométrique potentiellement utile, mais qui requiert plus de développement statistique.     

Spirometric reference values for children and adolescents from Kazakhstan

BACKGROUND: Spirometric parameters are influenced by several factors and many reference data are available in the literature. However, no spirometric data are available for children and adolescents from Central Asia. AIM: The study aimed to calculate spirometric reference curves on the basis of anthropometry, ethnicity (Kazakh vs. Russian) and living environment (urban vs. rural). SUBJECTS AND METHODS: Spirometry (FEV1, FVC and FEF25-75%) was performed and anthropometric measurements taken for 1926 male and 1967 female Kazakh children aged 7-18 years. RESULTS: Height explained almost all the variance of forced vital capacity (FVC) and forced expiratory volume in 1 s (FEV1) for both sexes, while age and inspiratory circumference contributed slightly to the prediction. Moreover, FVC and FEV1 were greater in Russians than in Kazakhs and ethnicity did enter the prediction model for these parameters. The living environment had a marginal effect on spirometry. In fact, forced expiratory flow 25-75% (FEF25-75%) was slightly higher in urban than in rural females, FVC was slightly higher in rural than in urban males, while FEV1 was not affected. Finally, among several spirometric equations available in the literature, those performing better in our children were obtained in developed countries. CONCLUSION: Anthropometry was the most important predictor of spirometry. Age and ethnicity were also predictors, while the contribution of the living environment was more limited.     

Spirometric reference values for children and adolescents from Kazakhstan

Background: Spirometric parameters are influenced by several factors and many reference data are available in the literature. However, no spirometric data are available for children and adolescents from Central Asia.

Aim: The study aimed to calculate spirometric reference curves on the basis of anthropometry, ethnicity (Kazakh vs. Russian) and living environment (urban vs. rural).

Subjects and methods: Spirometry (FEV1, FVC and FEF25–75%) was performed and anthropometric measurements taken for 1926 male and 1967 female Kazakh children aged 7–18 years.

Results: Height explained almost all the variance of forced vital capacity (FVC) and forced expiratory volume in 1?s (FEV1) for both sexes, while age and inspiratory circumference contributed slightly to the prediction. Moreover, FVC and FEV1 were greater in Russians than in Kazakhs and ethnicity did enter the prediction model for these parameters. The living environment had a marginal effect on spirometry. In fact, forced expiratory flow 25–75% (FEF25–75%) was slightly higher in urban than in rural females, FVC was slightly higher in rural than in urban males, while FEV1 was not affected. Finally, among several spirometric equations available in the literature, those performing better in our children were obtained in developed countries.

Conclusion: Anthropometry was the most important predictor of spirometry. Age and ethnicity were also predictors, while the contribution of the living environment was more limited.     

Fertility and mortality profile of an urban and rural population

A comparative study of fertility and mortality between the rural and urban components of a population of 472 families in Meerut, India, is presented using data for 1981-1982. The results show higher rates of fertility, mortality, and infant mortality in rural areas.