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O Semino

Publications and source records attributed to O Semino.

At least 19 recordsLinked to original sources

A signal, from human mtDNA, of postglacial recolonization in Europe.

Mitochondrial HVS-I sequences from 10,365 subjects belonging to 56 populations/geographical regions of western Eurasia and northern Africa were first surveyed for the presence of the T-->C transition at nucleotide position 16298, a mutation which has previously been shown to characterize haplogroup V mtDNAs. All mtDNAs with this mutation were then screened for a number of diagnostic RFLP sites, revealing two major subsets of mtDNAs. One is haplogroup V proper, and the other has been termed "pre*V," since it predates V phylogenetically. The rather uncommon pre*V tends to be scattered throughout Europe (and northwestern Africa), whereas V attains two peaks of frequency: one situated in southwestern Europe and one in the Saami of northern Scandinavia. Geographical distributions and ages support the scenario that pre*V originated in Europe before the Last Glacial Maximum (LGM), whereas the more recently derived haplogroup V arose in a southwestern European refugium soon after the LGM. The arrival of V in eastern/central Europe, however, occurred much later, possibly with (post-)Neolithic contacts. The distribution of haplogroup V mtDNAs in modern European populations would thus, at least in part, reflect the pattern of postglacial human recolonization from that refugium, affecting even the Saami. Overall, the present study shows that the dissection of mtDNA variation into small and well-defined evolutionary units is an essential step in the identification of spatial frequency patterns. Mass screening of a few markers identified using complete mtDNA sequences promises to be an efficient strategy for inferring features of human prehistory.

Africa, Northern↗

The 49a,f haplotype 11 is a new marker of the EU19 lineage that traces migrations from northern regions of the Black Sea.

Previous studies on human Y-chromosome polymorphisms in the European populations highlighted the high frequency of the 49a,f/TaqI haplotype 11 and of the Eu19 (M17) lineage in Eastern Europe. To better understand the origin and the evolution of the Eu19, and its relationship with 49a,f Ht11, this study surveyed 2,235 individuals (mainly from Europe and the Middle East) for the 49a,f Ht11 and for many biallelic markers defining the Eu19 lineage. As previously described, the highest frequency of Eu19 was found in Eastern Europe. All the Eu19 Y-chromosomes turned out to be 49a,f Ht11 or its derivatives, the distribution of which suggests that the Eu19/49a,f Ht11 emerged in Ukraine, probably in a Palaeolithic population. Thereafter, the spread of this lineage toward Europe, Asia, and India occurred at different waves over a few thousands years. At present this seems to indicate the influence of the Ukraine Palaeolithic groups in the gene pool of modern populations. For the first time it is possible to make inferences about the evolution of some haplotypes of the 49a,f system. In spite of its unknown molecular base, this is one of the first most informative polymorphisms of the Y chromosome.

Alleles↗

Y chromosome binary markers to study the high prevalence of males in Sardinian centenarians and the genetic structure of the Sardinian population.

We have analyzed a sample of 40 centenarians and 116 young controls from Sardinia, with a set of new Y chromosome binary markers, to evaluate if Y chromosome genes are involved in the high prevalence of males among centenarian Sardinians (1/2 vs. 1/4 in other populations studied). The results indicate that none of the seven lineages that account for >97% of the Y chromosome diversity in Sardinia provide an advantage with respect to the extreme longevity. However, our results, although based on the male-specific Y chromosome polymorphisms, give a clear profile of the pattern of genetic variability in Sardinia. Indeed they indicate that the Sardinian population had two main founder populations that have evolved in isolation for at least the last 5,000 years. These findings set the stage for future studies on longevity and other complex traits in Sardinia.

Aged↗

The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective.

A genetic perspective of human history in Europe was derived from 22 binary markers of the nonrecombining Y chromosome (NRY). Ten lineages account for >95% of the 1007 European Y chromosomes studied. Geographic distribution and age estimates of alleles are compatible with two Paleolithic and one Neolithic migratory episode that have contributed to the modern European gene pool. A significant correlation between the NRY haplotype data and principal components based on 95 protein markers was observed, indicating the effectiveness of NRY binary polymorphisms in the characterization of human population composition and history.

Alleles↗

MtDNA and Y chromosome polymorphisms in Hungary: inferences from the palaeolithic, neolithic and Uralic influences on the modern Hungarian gene pool.

Magyars imposed their language on Hungarians but seem not to have affected their genetic structure. To better investigate this point, we analysed some mtDNA and Y chromosome polymorphisms in a sample of the Hungarian Palóc who, for historical reasons, could have retained genetic traces of Magyars more than other groups. In addition, we examined a mixed sample from Budapest. About 100 individuals were tested for the markers defining all the European and Asian mtDNA haplogroups and about 50 individuals for some Y chromosome markers, namely the 12f2 and 49a,f/TaqI RFLPs, the YAP insertion, the microsatellites YCAIIa, YCAIIb, DYS19 and the Asian 50f2/C deletion. In the mtDNA analysis only two subjects belonged to the Asian B and M haplogroups. The Y chromosome analyses showed that the Palóc differed from the Budapest sample by the absence of YAP+ allele and by the DYS19 allele distribution; that the proto-European 49a,f Ht 15 and the neolithic 12f2-8Kb were rather uncommon in both groups; that there is a high prevalence of the 49a,f Ht 11 and the YCAII a5-b1; and that the Asian 50f2/C deletion is absent. These results suggest that the influence of Magyars on the Hungarian gene pool has been very low through both females and males and the Hungarian language could be an example of cultural dominance. Alternative explanations are discussed. An expansion centred on YAP-, 49a,f Ht 11 is revealed by the median network based on compound haplotypes. 49a,f Ht 11 could represent either a paleolithic marker of eastern Europe which underwent expansion after the last glacial period, or a marker of the more recent spread of the Yamnaia culture from southern Ukraine.

Alu Elements↗

Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa.

The out-of-Africa scenario has hitherto provided little evidence for the precise route by which modern humans left Africa. Two major routes of dispersal have been hypothesized: one through North Africa into the Levant, documented by fossil remains, and one through Ethiopia along South Asia, for which little, if any, evidence exists. Mitochondrial DNA (mtDNA) can be used to trace maternal ancestry. The geographic distribution and variation of mtDNAs can be highly informative in defining potential range expansions and migration routes in the distant past. The mitochondrial haplogroup M, first regarded as an ancient marker of East-Asian origin, has been found at high frequency in India and Ethiopia, raising the question of its origin. (A haplogroup is a group of haplotypes that share some sequence variations.) Its variation and geographical distribution suggest that Asian haplogroup M separated from eastern-African haplogroup M more than 50,000 years ago. Two other variants (489C and 10873C) also support a single origin of haplogroup M in Africa. These findings, together with the virtual absence of haplogroup M in the Levant and its high frequency in the South-Arabian peninsula, render M the first genetic indicator for the hypothesized exit route from Africa through eastern Africa/western India. This was possibly the only successful early dispersal event of modern humans out of Africa.

Africa↗

Further characteristics of proto-European y chromosomes.

We examined a set of populations mainly from Europe but also from the Middle East and North Africa for the three Y-linked microsatellites YCAII, DYS19 (about 1300 individuals) and DYS392 (about 350 individuals). Three markers (YCAII a5-b1 Ht, DYS19-190 bp and DYS392-254 bp) show decreasing gradients of frequency from western Europe towards the Middle East which parallel that of the proto-European 49a,f/TaqI Ht 15. Indeed, a strong linkage disequilibrium between these markers and the 49a,f Ht15 is observed. We therefore suggest that the 49a,f/TaqI Ht15, YCAII a5-b1 Ht, DYS19-190 bp and DYS392-254 bp Y chromosome could represent a component of the proto-European gene pool. This European specific compound haplotype distinctively characterises western Europeans and its very high incidence in these populations (particularly in the Basques) is discussed.

Europe↗

Y-chromosome specific YCAII, DYS19 and YAP polymorphisms in human populations: a comparative study.

Two hypervariable Y-specific markers, the YCAII and DYS19 STRs, and the more stable Y Alu Polymorphism (YAP) have been analysed in about 1400 individuals of 21 different populations, mainly from Europe but also from the Middle East, Africa and Asia. On the basis of the frequency distributions of these three Y-markers we compare, using different statistical analyses, their power in detecting population genetic structure and in distinguishing closely related groups. The pattern of populations' genetic affinities inferred from the three markers considered altogether suggests a strong genetic structure that, with a few exceptions, broadly corresponds to the linguistic relatedness and/or geographic location of the sampled populations.

Alleles↗

Different genetic components in the Ethiopian population, identified by mtDNA and Y-chromosome polymorphisms.

Seventy-seven Ethiopians were investigated for mtDNA and Y chromosome-specific variations, in order to (1) define the different maternal and paternal components of the Ethiopian gene pool, (2) infer the origins of these maternal and paternal lineages and estimate their relative contributions, and (3) obtain information about ancient populations living in Ethiopia. The mtDNA was studied for the RFLPs relative to the six classical enzymes (HpaI, BamHI, HaeII, MspI, AvaII, and HincII) that identify the African haplogroup L and the Caucasoid haplogroups I and T. The sample was also examined at restriction sites that define the other Caucasoid haplogroups (H, U, V, W, X, J, and K) and for the simultaneous presence of the DdeI10394 and AluI10397 sites, which defines the Asian haplogroup M. Four polymorphic systems were examined on the Y chromosome: the TaqI/12f2 and the 49a,f RFLPs, the Y Alu polymorphic element (DYS287), and the sY81-A/G (DYS271) polymorphism. For comparison, the last two Y polymorphisms were also examined in 87 Senegalese previously classified for the two TaqI RFLPs. Results from these markers led to the hypothesis that the Ethiopian population (1) experienced Caucasoid gene flow mainly through males, (2) contains African components ascribable to Bantu migrations and to an in situ differentiation process from an ancestral African gene pool, and (3) exhibits some Y-chromosome affinities with the Tsumkwe San (a very ancient African group). Our finding of a high (20%) frequency of the "Asian" DdeI10394AluI10397 (++) mtDNA haplotype in Ethiopia is discussed in terms of the "out of Africa" model.

Black People↗

Human genetic affinities for Y-chromosome P49a,f/TaqI haplotypes show strong correspondence with linguistics.

Numerous population samples from around the world have been tested for Y chromosome-specific p49a,f/TaqI restriction polymorphisms. Here we review the literature as well as unpublished data on Y-chromosome p49a,f/TaqI haplotypes and provide a new nomenclature unifying the notations used by different laboratories. We use this large data set to study worldwide genetic variability of human populations for this paternally transmitted chromosome segment. We observe, for the Y chromosome, an important level of population genetics structure among human populations (FST = .230, P < .001), mainly due to genetic differences among distinct linguistic groups of populations (FCT = .246, P < .001). A multivariate analysis based on genetic distances between populations shows that human population structure inferred from the Y chromosome corresponds broadly to language families (r = .567, P < .001), in agreement with autosomal and mitochondrial data. Times of divergence of linguistic families, estimated from their internal level of genetic differentiation, are fairly concordant with current archaeological and linguistic hypotheses. Variability of the p49a,f/TaqI polymorphic marker is also significantly correlated with the geographic location of the populations (r = .613, P < .001), reflecting the fact that distinct linguistic groups generally also occupy distinct geographic areas. Comparison of Y-chromosome and mtDNA RFLPs in a restricted set of populations shows a globally high level of congruence, but it also allows identification of unequal maternal and paternal contributions to the gene pool of several populations.

DNA Probes↗

Pre-Caucasoid and Caucasoid genetic features of the Indian population, revealed by mtDNA polymorphisms.

About 70 individuals from Punjab were examined for some mtDNA polymorphisms, namely, the RFLPs of the six classical enzymes (HpaI, BamHI, HaeII, MspI, AvaII, and Hin-cII) and for the sites AluI(7,025), DdeI(10,394), and AluI(10,397). The AluI(7,025) polymorphic site was also investigated in 96 Indians from Uttar Pradesh and Andhra Pradesh and in 163 Mediterranean Caucasoids. Moreover, 30 Indian DdeI(10,394)Alu(10,397) (++) mtDNAs were typed by the "high-resolution restriction analysis" with 14 endonucleases to estimate their divergence time. The results obtained are the following: (1) The RFLPs analysis has displayed some Caucasoid types as in Indians of Uttar Pradesh; (2) the AluI(7,025) (-) allele, which defines the most frequent Caucasoid-specific lineage (haplogroup H), ranges from 18% to 45% in the Mediterranean Caucasoids, whereas it has shown low frequencies in Punjab (6.0%) and in Uttar Pradesh (1.8%) and was not found in Andhra Pradesh; (3) the DdeI(lO,394)AluI(10,397) (+ +) haplotype, which although previously was considered an East Asian marker (haplogroup M) and was found very frequently in India, is also frequent in Punjab (27%); this frequency is, however, much lower than in Uttar Pradesh (49%) and in Andhra Pradesh (74%), and a gradient decreasing from south to north is therefore observed; (4) the divergence time of the Indian DdeI(10,394)AluI(10,397) (++) mtDNAs has been estimated to be 30,250-60,500 years, a value that is compatible with that of the homologous East Asian lineage. These results strongly support the hypothesis that the DdeI(10,394)AluI(10,397) (++) haplotype predated the Indo-European invasion and probably the split between proto-Indians and proto-Orientals. Its frequency cline well reflects the major influence of Indo-Europeans in the north and in the center of India.

DNA, Mitochondrial↗

Evolutionary correlation between control region sequence and restriction polymorphisms in the mitochondrial genome of a large Senegalese Mandenka sample.

We present here the first comparative analysis at the population level between Restriction Fragment Length Polymorphism (RFLP) and control region sequence polymorphism in a large and homogeneous Senegalese Mandenka sample. Eleven RFLP haplotypes and 60 different sequences are found in 119 individuals, revealing that a very high level of mtDNA diversity can be maintained in a small population. A sequence neighbor-joining tree and an analysis of molecular variance show that sequences associated with a given restriction haplotype are evolutionarily highly correlated: sequencing generally leads to the subtyping of RFLP haplotypes. Evolutionary relationships among RFLP haplotypes inferred from restriction site differences are in good agreement with those inferred from sequence data. A single difference is observed and is likely due to a single restriction homoplasy having occurred in the control region. Selective neutrality tests on both RFLP and sequence data accept the hypotheses of mtDNA neutrality and population equilibrium. The deep coalescence times (exceeding 50,000 yr) of sequences associated with the two most frequent restriction haplotypes confirm that the Niokolo Mandenka population has not passed through a recent bottleneck and that gene flow is maintained among West African populations despite ethnic differences.

Base Sequence↗

A recombination event in the closely linked plasminogen and apolipoprotein(a) gene loci.

Genetic studies as well as in situ hybridisation data have strongly demonstrated that the genes coding for apoprotein(a) and plasminogen are linked and localised to chromosome 6 at band 6q26-27. We describe in this report the presence of a recombination event in a region of approximately 50 kb of DNA separating the two genes. The recombination was found in an Italian family, in which a mutation affecting both plasminogen plasma level and activity of plasminogen activity has been detected. Polymerase chain reaction and sequencing analysis showed the presence of a mutation different from those previously reported in two Japanese families.

Adult↗

MtDNA polymorphisms in a sample of Czechoslovaks and in two groups of Italians.

Mitochondrial DNA (mtDNA) variation was investigated in a group of 185 unrelated individuals (64 Czechoslovaks, 99 Northern and 28 Central Italians) using total blood DNA and the six restriction enzymes HpaI, BamHI, HaeII, MspI, AvaII and HincII. Among the 25 patterns (morphs) found, two morphs for HaeII, one for MspI and one for AvaII were new and each was represented by a single individual from Northern Italy. They account for four of the five new types encountered in this survey, being the fifth type characterized by the presence of the very rare morph HaeII-13. The populations analysed confirm the Caucasoid characteristics of certain polymorphisms. A review of the European data available so far is reported.

Czechoslovakia↗

Genetic studies in Cameroon: mitochondrial DNA polymorphisms in Bamileke.

In two population samples of 77 Bamileke (Bantu sensu lato) and 18 Bakaka (Bantu sensu stricto) from southwestern Cameroon, the mtDNA RFLPs for the HpaI, HaeII, MspI, AvaII, and HincII enzymes were studied. Two of the MspI morphs had not been reported before. Six new types were found, four of which represent new combinations of previously described morphs. The AvaII morph 3 was found in association with the "African" HpaI morph 3. This finding is in line with previous observations in Negroids and demonstrates the usefulness of this combination as an indicator of black African ancestry. Two differences were noted between the groups: a lower frequency of HpaI morph 3 and a higher frequency of HaeII morph 4 in the Bakaka with respect to the Bamileke (0.44 versus 0.62 and 0.17 versus 0.03, respectively). The importance of these differences could not be evaluated because the Bakaka sample was too small. Nevertheless, because the Bamileke show a relatively low frequency of mtDNA type 1 (2.1.1.1.-) and high frequencies of mtDNA types 2 (3.1.1.1.3.-) and 7 (3.1.1.1.1.-), they can be placed with the other Negroids so far examined, but they are closer to the Senegalese than to the Bantu from South Africa. In comparing the Bamileke and the Bantu, mtDNA type 3 (3.1.1.2.2.-) appears particularly discriminative because it is present in all the Bantu subgroups examined but not in the Bamileke. mtDNA type 39 (2.1.4.1.1.-), which was observed only in the Bamileke, might be considered likewise discriminative, although to a lesser degree.

Adult↗

mtDNA and Y-chromosome polymorphisms in four Native American populations from southern Mexico.

mtDNA sequence variation was examined in 60 Native Americans (Mixtecs from the Alta, Mixtecs from the Baja, Valley Zapotecs, and Highland Mixe) from southern Mexico by PCR amplification and high-resolution restriction endonuclease analysis. Four groups of mtDNA haplotypes (haplogroups A, B, C, and D) characterize Amerind populations, but only three (haplogroups A, B, and C) were observed in these Mexican populations. The comparison of their mtDNA variation with that observed in other populations from Mexico and Central America permits a clear distinction among the different Middle American tribes and raises questions about some of their linguistic affiliations. The males of these population samples were also analyzed for Y-chromosome RFLPs with the probes 49a, 49f, and 12f2. This analysis suggests that certain Y-chromosome haplotypes were brought from Asia during the colonization of the Americas, and a differential gene flow was introduced into Native American populations from European males and females.

DNA, Mitochondrial↗

The common, Near-Eastern origin of Ashkenazi and Sephardi Jews supported by Y-chromosome similarity.

About 80 Sephardim, 80 Ashkenazim and 100 Czechoslovaks were examined for the Y-specific RFLPs revealed by the probes p12f2 and p49a,f on TaqI DNA digests. The aim of the study was to investigate the origin of the Ashkenazi gene pool through the analysis of markers which, having an exclusively holoandric transmission, are useful to estimate paternal gene flow. The comparison of the two groups of Jews with each other and with Czechoslovaks (which have been taken as a representative source of foreign Y-chromosomes for Ashkenazim) shows a great similarity between Sephardim and Ashkenazim who are very different from Czechoslovaks. On the other hand both groups of Jews appear to be closely related to Lebanese. A preliminary evaluation suggests that the contribution of foreign males to the Ashkenazi gene pool has been very low (1% or less per generation).

Adult↗