MS205 minisatellite diversity in Basques: evidence for a pre-Neolithic component

A number of studies have suggested that Basques might be a relic of Mesolithic Europeans who escaped much of the homogenization brought about by the Neolithic expansion. In an attempt to add new insights into this hypothesis, MS205 minisatellite diversity has been investigated by Minisatellite Variant Repeat (MVR) analysis in a sample of >100 autochthonous individuals from the Basque Country, along with 24 Castilian (N. Spain) and 23 individuals from the United Kingdom. These populations were examined in the context of the available world database for MS205 alleles. To deduce the similarities among populations, we have applied a phylogenetic approach that takes into account similarity between alleles. The variability of these populations seems to be a subset of the greater and presumably older African diversity, as has been suggested previously for non-Africans. Within non-Africans, Basques seem to cluster with other Northern European populations; however, some apparently Basque-specific alleles can be dated back to post-Aurignacian times, supporting the continuity of some lineages of this population since the Upper Paleolithic period.     

The dihydroxyacetonephosphate pathway for biosynthesis of ether lipids in Leishmania mexicana promastigotes

Microsatellites can be highly unstable and show a high level of polymorphism between individuals. Here we present the analysis of the CAG trinucleotide repeat polymorphism at the SBMA locus in 57 phenotypically normal individuals rigorously assigned to the Spanish Basque population. Results are compared with 100 Spanish non-Basque individuals who were already analyzed by us (175 alleles). This is the first study undertaken in these populations for this marker. In addition, we compared our results with those published for other populations. Relative allele frequencies showed differences between the samples and no unimodal distribution. The expected heterozygosity in the Basque sample was slightly lower than in the non-Basque sample. Conformity with Hardy-Weinberg equilibrium was verified by three tests. When compared with published data, the predominant alleles appear to be the same in the various populations. There are more differences between Basques and other Caucasoid samples than between non-Basques and Caucasoid samples. Population relationships were also examined by dendrograms based on genetic distances. The results obtained showed some peculiarities in the Basque population. The high degree of similarity with other dendrograms based on different markers and the efficiency of this STR marker in differentiating closely related populations, support the potential usefulness of microsatellites as tools for human population studies.     

Global patterns of linkage disequilibrium at the CD4 locus and modern human origins

Haplotypes consisting of alleles at a short tandem repeat polymorphism (STRP) and an Alu deletion polymorphism at the CD4 locus on chromosome 12 were analyzed in more than 1600 individuals sampled from 42 geographically dispersed populations (13 African, 2 Middle Eastern, 7 European, 9 Asian, 3 Pacific, and 8 Amerindian). Sub-Saharan African populations had more haplotypes and exhibited more variability in frequencies of haplotypes than the Northeast African or non-African populations. The Alu deletion was nearly always associated with a single STRP allele in non-African and Northeast African populations but was associated with a wide range of STRP alleles in the sub-Saharan African populations. This global pattern of haplotype variation and linkage disequilibrium suggests a common and recent African origin for all non-African human populations.     

Distribution and prevalence of Anguillicola crassus (Nematoda) in eels Anguilla anguilla of the rivers Rhine and Naab, Germany

The distribution of apolipoprotein E (apo E) polymorphism was examined in 11 population groups not previously studied for this system. There is a marked difference in phenotype and gene frequency between the populations of England and Spain. The south European populations of Basques and Spanish non-Basques showed greater similarity to the populations of South Asia. The study clearly indicates that the distribution of apo E alleles does match with regions showing a high mortality rate of coronary heart disease. The data presented also indicate that authochthon groups such as Basques in Europe and tribals in India may throw better light on the role of apolipoproteins in the regulation of lipid levels in disease.     

GM and KM immunoglobulin allotypes in a Spanish Pyrenean population: Val d'Aran

Four hundred and thirteen unrelated individuals (202 autochthonous and 211 non-autochthonous) of Val d'Aran (Catalan Pyrenees) have been analysed for the GM and KM immunoglobulin genetic system using the inhibition haemagglutination method. This population was defined by eight GM haplotypes (GM*3 23 5*, GM*3 5*, GM*1,17 21,28, GM*1,2,17 21,28, GM*1,17 5*, GM*1,17 5,6,11,24, GM*1,17 10,11,13,15 and GM*1,17 10,11,13,15,16) inferred from the 17 observed phenotypes. The Val d'Aran population frequencies conform to Hardy-Weinberg expectations. The frequencies of phenotypes and haplotypes show a definite homogeneity between the autochthonous and non-autochthonous people of Val d'Aran and 11 other Pyrenean populations (Mauléon, Macaye, St. Jean Pied de Port, Vallée de L'Ouzom, Gavarnie, Barèges, Luz St. Sauveur, Esparros, Camurac, Capcir and Pays de Sault) that have already been studied for the same allotypes. A factorial correspondence analysis was performed for the 12 autochthonous Pyrenean populations, showing a high frequency of the GM*3 23 5* haplotype in the three Pyrenean regions (Western, Central and Eastern), while the GM*1,17 21,28 haplotype is mainly found in the Central region, GM*3 5* in the Eastern and Western zones, and the GM*1,2,17 21,28 is mainly present in the Central and Eastern populations. The results show a relative regional homogeneity, so there is no evidence of a frequency gradient in the Pyrenean populations for the GM and KM genetic systems. It may, however, be noticed that the Central Pyrenean populations form a group, with one population (Vallée de l'Ouzom) isolated from the rest, probably because of its particular model of inheritance by which the heritage is passed to the first born without sex consideration. It has been possible to point out some differences in the genetic structure of the autochthonous and non-autochthonous Val d'Aran population and to place the autochthonous Aranese group among its Pyrenean neighbours.     

Immunoglobulin allotypes and estimation of genetic admixture among populations of Kinnaur District, Himachal Pradesh, India

Four regional populations of the Kanet (Puh, Kalpa, Sangla, and Nachar) and an endogamous group of Koli from Kinnaur District, Himachal Pradesh, India, were studied to determine the extent of genetic variation of immunoglobulin allotypes (GM, KM, and AM) and the genetic contribution from ancestral populations of Tibet and northwest India. Haplotype GM*A G showed a higher frequency in the Kanet (40-60%)-a frequency that is more comparable to Asian populations-whereas in the Koli a lower frequency was observed, which is nearer the values for populations from northwest India. The IG haplotype data suggest that the Kanet population of Kinnaur District and the northeastern population of Nepal have different European origins than the more central population of India, represented by a sample from Delhi. The present results suggest that the populations of Kinnaur District are of admixed origin with contributions of Tibetan genes of 87.3%, 51.3%, 49.9%, 40.0%, and 9.5% in the Puh, Kalpa, Sangla, and Nachar Kanet and the Koli, respectively. The genetic distance obtained from 19 loci (9 blood groups, 8 biochemical markers, GM, and KM) showed an inverse relationship between the distance of the hybrid population from the parental gene pool. The Puh Kanet, nearest the Tibetan border, had the highest proportion of Tibetan genes but showed the lowest genetic distance with Tibetans. As the geographic distance of the other regional populations of the Kanet increases from the border of Tibet, genetic distance compared with the parental Tibetan population increases and the proportion of Tibetan admixture decreases. In the Kinnaur District admixture seems to contribute largely to the present-day observed high level of genetic differentiation.     

When Memory Shifts Toward More Typical Category Exemplars: Accentuation Effects in the Recollection of Ethnically Ambiguous Faces.

In 4 studies, the authors examined the impact of categorization on the recollection of ethnically ambiguous faces. Participants were presented with faces lying at various locations on mixed-race continua (i.e., Caucasian-North African and Caucasian-Asian faces were used as source images in a morphing program). In all studies, the prevalence of exclusive ethnic features in a face distorted participants' recollections of the face toward faces more typical of the category. Specifically, the recollection of 30% North African (or 30% Asian) faces shifted toward Caucasian source faces, whereas the recollection of 70% North African (or 70% Asian) faces shifted toward North African (Asian) source faces. Memory distortions did not emerge for extremely ambiguous (50%) faces and proved larger on mixed-race than same-race continua (Studies 3 and 4). Memory distortions also emerged with high levels of confidence. The authors elaborate on the theoretical and practical implications of these findings. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Polymorphic admixture typing in human ethnic populations

A panel of 257 RFLP loci was selected on the basis of high heterozygosity in Caucasian DNA surveys and equivalent spacing throughout the human genome. Probes from each locus were used in a Southern blot survey of allele frequency distribution for four human ethnic groups: Caucasian, African American, Asian (Chinese), and American Indian (Cheyenne). Nearly all RFLP loci were polymorphic in each group, albeit with a broad range of differing allele frequencies (delta). The distribution of frequency differences (delta values) was used for three purposes: (1) to provide estimates for genetic distance (differentiation) among these ethnic groups, (2) to revisit with a large data set the proportion of human genetic variation attributable to differentiation within ethnic groups, and (3) to identify loci with high delta values between recently admixed populations of use in mapping by admixture linkage disequilibrium (MALD). Although most markers display significant allele frequency differences between ethnic groups, the overall genetic distances between ethnic groups were small (.066-.098), and < 10% of the measured overall molecular genetic diversity in these human samples can be attributed to "racial" differentiation. The median delta values for pairwise comparisons between groups fell between .15 and .20, permitting identification of highly informative RFLP loci for MALD disease association studies.     

Clustering of Caucasian Leber hereditary optic neuropathy patients containing the 11778 or 14484 mutations on an mtDNA lineage

Leber hereditary optic neuropathy (LHON) is a type of blindness caused by mtDNA mutations. Three LHON mtDNA mutations at nucleotide positions 3460, 11778, and 14484 are specific for LHON and account for 90% of worldwide cases and are thus designated as "primary" LHON mutations. Fifteen other "secondary" LHON mtDNA mutations have been identified, but their pathogenicity is unclear. mtDNA haplotype and phylogenetic analysis of the primary LHON mutations in North American Caucasian patients and controls has shown that, unlike the 3460 and 11778 mutations, which are distributed throughout the European-derived (Caucasian) mtDNA phylogeny, patients containing the 14484 mutation tended to be associated with European mtDNA haplotype J. To investigate this apparent clustering, we performed chi2-based statistical analyses to compare the distribution of LHON patients on the Caucasian phylogenetic tree. Our results indicate that, unlike the 3460 and 11778 mutations, the 14484 mutation was not distributed on the phylogeny in proportion to the frequencies of the major Caucasian mtDNA haplogroups found in North America. The 14484 mutation was next shown to occur on the haplogroup J background more frequently that expected, consistent with the observation that approximately 75% of worldwide 14484-positive LHON patients occur in association with haplogroup J. The 11778 mutation also exhibited a moderate clustering on haplogroup J. These observations were supported by statistical analysis using all available mutation frequencies reported in the literature. This paper thus illustrates the potential importance of genetic background in certain mtDNA-based diseases, speculates on a pathogenic role for a subset of LHON secondary mutations and their interaction with primary mutations, and provides support for a polygenic model for LHON expression in some cases.     

HLA gene and haplotype frequencies in the North American population: the National Marrow Donor Program Donor Registry

BACKGROUND: As of May 1, 1995, the National Marrow Donor Program had a donor registry consisting of over 1.35 million HLA-typed volunteers recruited from most major cities and states in the United States. This registry represents the largest single HLA-typed pool of normal individuals in the world. METHODS: We analyzed the HLA-A, -B, -DR locus phenotypes of the National Marrow Donor Program donors in order to estimate gene and haplotype frequencies for major racial groups of the United States: Caucasian American, Asian American, African American, Latin American, and Native American. The large size of the database allowed us to calculate the frequencies of relatively rare antigens and haplotypes with more accuracy than previous studies. RESULTS: We observed 89,522 distinguishable HLA-A, -B phenotypes in 1,351,260 HLA-A, -B-typed donors and 302,867 distinguishable HLA-A, -B, -DR phenotypes in 406,503 HLA-A, -B, -DR-typed donors. Gene and haplotype frequencies differed remarkably among the five racial groups, with African Americans and Asian Americans having a large number of haplotypes that were specific to their racial groups, whereas Caucasian Americans, Latin Americans, and Native Americans shared a number of common haplotypes. CONCLUSIONS: These data represent an important resource for investigators in the fields of transplantation and population genetics. The gene and haplotype frequencies can be used to aid clinicians in advising patients about the probability of finding a match within a specific ethnic group, or to determine donor recruitment goals and strategies. The information is also a valuable resource for individuals who are interested in population genetics, selection and evolution of polymorphic human genes, and HLA-disease association.     

Anomalous behaviour of the 5' insulin gene polymorphism allele 814: lack of association with Type I diabetes in Basques. GEPV-N Group. Basque-Navarre Endocrinology and Paediatrics

A susceptibility locus (IDDM2) for Type I (insulin-dependent) diabetes mellitus has been identified as allelic variation at a variable number of tandem repeats polymorphic region upstream of the human insulin gene. In Caucasian populations, individuals homozygous for the short length alleles (26 to 63 repeats: class I) have a two- to fivefold increased risk of developing the disease, while the long alleles (more than 140 repeats: class III) are dominantly protective. Recent evidence has shown that class I alleles are not equally predisposing, and in particular, the 42-repeat allele (allele 814) can be protective when paternally inherited. We have assessed the contribution of IDDM2 to disease in a group of Basque families with Type I diabetes. As in other Caucasoid populations, we found that class I alleles, as a whole, are associated with an increased risk of developing the disease. Using a polymerase chain reaction-based assay to more accurately resolve the different sizes of individual class I alleles, we identified 14 different variants and observed that allele 814 has an anomalous behaviour in Basques, being the only class I allele that does not have an increased frequency in the diabetic alleles group. These findings provide additional support for the recently published allele-specific effects of IDDM2 in Type I diabetes pathogenesis.     

Different forces drive the evolution of the Acp26Aa and Acp26Ab accessory gland genes in the Drosophila melanogaster species complex

The Acp26Aa and Acp26Ab genes that code for male accessory gland proteins are tandemly arranged in the species of the Drosophila melanogaster complex. An approximately 1.6-kb region encompassing both genes has been sequenced in 10, 24, and 18 lines from Spain, Ivory Coast, and Malawi, respectively; the previously studied 10 lines from North Carolina have also been included in the analyses. A total of 110 nucleotide and 4 length polymorphisms were detected. Silent variation for the whole Acp26A region was slightly higher in African than in non-African populations, while for both genes nonsynonymous variation was similar in all populations studied. Based on Fst estimates no major genetic differentiation was detected between East and West Africa, while in general non-African populations were strongly differentiated from both African populations. Comparison of polymorphism and divergence at synonymous and nonsynonymous sites revealed that directional selection acting on amino acid replacement changes has driven the evolution of the Acp26Aa protein in the last 2.5 myr.     

Decreased Na/K ATPase ouabain binding sites in red blood cells of patients with insulin-dependent diabetes and healthy north African control subjects: relationship with diabetic neuropathy

Like other degenerative complications occurring during diabetes, development of neuropathy is determined mainly by the duration of disease and quality of control. However, there may be some predisposing factors. Activity of Na/K ATPase has been implicated in the pathophysiology of diabetic neuropathy. A decrease in the activity of this enzyme has been observed in red blood cells of poorly controlled diabetic patients and healthy North African subjects who are predisposed to diabetic neuropathy. This study was performed to characterize abnormalities of Na/K ATPase activity in these two populations. For this purpose we measured enzyme activity (hydrolysis of ATP) and the number of enzyme units (number of binding sites for ouabain) in the red blood cells of three groups of men, i.e., healthy Caucasian subjects, healthy North African subjects and Caucasian insulin-dependent diabetic patients. The level of Na/K ATPase activity and the number of enzyme units were about 30% lower in the red blood cells of diabetic patients and North African subjects, than in healthy Caucasian controls. In healthy North African subjects predisposed to neuropathy in case of development of diabetes, the decrease in enzymatic activity was correlated with a decrease in the number of enzyme units. This correlation was not observed in diabetic patients. We speculate that the constitutional decrease in Na/K ATPase activity in healthy North African subjects corresponds to a quantitative defect, whereas the acquired decrease in diabetic patients corresponds to a qualitative defect probably related to the structure of the lipid membrane.     

Knowledge of the utilization of preventive practices through a telephone survey

OBJECTIVES: To determine knowledge and use of preventive practices (cervical cytology, mammography and taking blood pressure) through a telephone survey. DESIGN: Crossover study. SETTING: Billabona Health Centre (Guipúzcoa). PARTICIPANTS: People over 15 in the Health Centre's catchment area. MAIN RESULTS: The sample size was 800 people. It reached 80% telephone coverage with a reply rate of 86.09% (278 men and 273 women). 76.5% of women stated they had heard of cervical cytology; and 80.2% mammography. 87.5% had had their blood pressure taken on some occasion. CONCLUSIONS: Both cervical cytology and mammography are well-known preventive procedures, although they could always be improved, whereas taking blood pressure is a widespread practice in all age-groups.     

The genetic relationship between the Finns and the Finnish Saami (Lapps): analysis of nuclear DNA and mtDNA

The genetic relationships between two Finno-Ugric-speaking populations, the Finns and the Finnish Saami (Lapps), were studied by using PCR for six nuclear-DNA marker loci, mitochondrial restriction-site polymorphism, and sequence variation of a 360-bp segment of the mitochondrial control region. The allele frequencies of each of the nuclear-DNA marker loci and the frequencies of mtDNA restriction haplotypes were significantly different between the populations. The Saami showed exceptionally low variation in their mtDNA restriction sites. The 9-bp deletion common in East Asian populations was not observed, nor did the haplotype data fit into the haplogroup categorization of Torroni et al. The average number of nucleotide substitutions from the mtDNA haplotype data indicated that the Finnish Saami may be closer to the Finns than to the other reference populations, whereas nuclear DNA suggested that the Finns are more closely related to the European reference populations than to the Finnish Saami. The similarity of the Finns to the other Europeans was even more pronounced according to the sequence data. We were unable to distinguish between the Finns and either the Swiss or Sardinian reference populations, whereas the Finnish Saami clearly stood apart. The Finnish Saami are distinct from other Circumarctic populations, although two of the lineages found among the Saami showed closer relationship to the Circumarctic than to the European lineages. The sequence data indicated an exceptionally high divergence for the Saami mtDNA control lineages. The distribution of the pairwise nucleotide differences in the Saami suggested that this population has not experienced an expansion similar to what was indicated for the Finns and the reference populations.     

Circular unidimensional scaling: A new look at group differences in interest structure.

The fit of J. L. Holland's (1959, 1997) RIASEC model to U.S. racial-ethnic groups was assessed using circular unidimensional scaling. Samples of African American, Asian American, Caucasian American. and Hispanic American high school students and employed adults who completed either the UNIACT Interest Inventory (K. B. Swaney, 1995) or the Strong Interest Inventory (L. W. Harmon. J. C. Hansen, F. H. Borgen. & A. L. Hammer. 1994) were obtained from published sources. Two circumplex models were evaluated: a quasi-circumplex model with unconstrained distances between adjacent types and a circulant model constrained to equal distances. Results indicate that a quasi-circumplex model was a good fit with all samples; however, the circulant model may be more appropriate for Asian Americans and Caucasian Americans than for other groups. Circulant model results suggest that distinctions made between Holland's types may be less salient for some groups and that additional work is needed to produce interest measures with improved structural validity. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Mitochondrial DNA haplotype frequencies in natural and experimental populations of Drosophila subobscura

The evolution of Drosophila subobscura mitochondrial DNA has been studied in experimental populations, founded with flies from a natural population from Esporles (Majorca, Balearic Islands, Spain). This population, like other European ones, is characterized by the presence of two very common (>96%) mitochondrial haplotypes (called I and II) and rare and endemic haplotypes that appear at very low frequencies. There is no statistical evidence of positive Darwinian selection acting on the mitochondrial DNA variants according to Tajima's neutrality test. Two experimental populations, with one replicate each, were established with flies having a heterogeneous nuclear genetic background, which was representative of the composition of the natural population. Both populations were started with the two most frequent mitochondrial haplotypes, but at different initial frequencies. After 13 to 16 generations, haplotype II reached fixation in three cages and its frequency was 0.89 by generation 25 in the fourth cage. Random drift can be rejected as the force responsible for the observed changes in haplotype frequencies. There is not only statistical evidence of a linear trend favoring a mtDNA (haploid) fitness effect, but also of a significant nonlinear deviation that could be due to a nuclear component.     

Allele-specific population structure of Drosophila melanogaster alcohol dehydrogenase at the molecular level

The history of the Drosophila melanogaster alcohol dehydrogenase (ADH) Fast/Slow polymorphism was studied by recording molecular variation and inversion polymorphism in 233 chromosomes from European and African populations. Silent molecular variation in the Slow allele was very different between standard chromosomes and chromosomes bearing the In(2L)t inversion. Within populations, inverted Slow haplotypes were more variable than standard Slow haplotypes. Between populations, geographical structure was almost nonexistent for inverted Slow haplotypes and highly significant for standard Slow. All Fast haplotypes occurred on standard chromosomes. They showed little variation within and between populations. They were highly significantly closer to standard Slow haplotypes from Europe. These results suggest that the current range of Fast and In(2L)t Slow haplotypes is recent and that an older genetic differentiation between populations was followed by allele-specific gene flow.     

A single genetic origin for the common prothrombotic G20210A polymorphism in the prothrombin gene

The polymorphism G20210A in the 3' untranslated region of the prothrombin gene is associated with an increased level of factor II activity and confers a twofold to fivefold increase in the risk for venous thromboembolism. Among Caucasian populations, the prevalence of factor II G20210A heterozygotes is 1% to 6%, whereas in non-Caucasian populations it is very rare or absent. The aim of the present study was to discern whether factor II G20210A originated from a single or recurrent mutational events. Allele frequencies of four dimorphisms spanning 16 of 21 kb of the factor II gene were determined in 133 unrelated Caucasian subjects of Jewish, Austrian, and French origins who bore factor II G20210A (10 homozygotes and 123 heterozygotes) and 110 Caucasian controls. Remarkable differences in the allele frequencies for each dimorphism were observed between the study groups (P = .0007 or less), indicating strong linkage disequilibrium and suggesting a founder effect. Indeed, a founder haplotype was present in 68% of 20210A mutant alleles and only in 34% of 20210G normal alleles (P < .0001). These data strongly support a single origin for factor II G20210A that probably occurred after the divergence of Africans from non-Africans and of Caucasoid from Mongoloid subpopulations.     

Sclerosing cholangitis, race and sex

BACKGROUND: Primary sclerosing cholangitis develops in 3-10% of patients with ulcerative colitis, and may be associated with an increased cancer risk. Ulcerative colitis is probably less common in people of African origin than in populations of European descent. AIMS AND METHODS: To review the records of all patients under regular follow up for ulcerative colitis at St Bartholomew's Hospital (London, UK), a tertiary referral centre, prompted by discovering a cluster of cases with common features. RESULTS AND CONCLUSIONS: Among 166 patients with ulcerative colitis under regular follow up, only four (all women) are of African or Caribbean genetic origin, and three of these have developed sclerosing cholangitis within three years of presentation with colitis, compared with four of 162 patients of European or Asian descent (odds ratio 119, 95% confidence interval 8-3837; p = 0.0002). This cluster, which is not explained by common HLA DR or DQ type, suggests that Africans and Afro-Caribbeans, especially women, may be at increased risk of sclerosing cholangitis. This may reflect genetic influences on the development of enteric and hepatobiliary inflammatory disease.