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F Calafell

Publications and source records attributed to F Calafell.

70 records · Page 4Linked to original sources

Identification of a base pair substitution at the tetranucleotide tandem repeat locus DHFRP2 (AAAC)n in a worldwide survey.

An allele heterogeneity in a short tandem repeat at the human dihydrofolate reductase pseudogene (DHFRP2) was detected using non-denaturing gel electrophoresis and ethidium bromide staining. Sequence analysis of the allele, designated 9A, revealed the C to A substitution in the 8th AAAC repeat. A survey of 16 worldwide human populations showed that this mutation was spread through five continents at a relatively high frequency (up to p = 0.19 in Europeans). Some statistical parameters of forensic interest were also calculated (h, PD, EC and PIC) for this polymorphism. This type of heterogeneity stresses the complexity of STR variation.

Alleles↗

Geographic homogeneity and non-equilibrium patterns of mtDNA sequences in Tuscany, Italy.

The geographical distribution of 49 mtDNA sequences from 22 localities in Southern Tuscany, Italy, was studied by molecular analysis of variance, by a new spatial autocorrelation statistic specifically designed for sequence data and by reconstructing genealogies of haplotypes. All these methods indicated a high homogeneity of populations. Nevertheless, genetic variability showed significant departure from equilibrium expectations, in agreement with the predicted effects of a population expansion. We suggest that a past population expansion that was probably associated with a migrational wave and with local gene flow between localities prevented spatial structuring in Southern Tuscany.

Analysis of Variance↗

Gene mapping in Gypsies identifies a novel demyelinating neuropathy on chromosome 8q24.

Founder effect and linkage disequilibrium have been successfully exploited to map single gene disorders, and the study of isolated populations is emerging as a major approach to the investigation of genetically complex diseases. In the search for genetic isolates ranging from Pacific islands to Middle East deserts, the 10 million Gypsies resident in Europe have largely escaped the attention of geneticists. Because of their geographical ubiquity, lack of written history and the presumed social and cultural nature of their isolation, Gypsies are construed as not meeting the criteria for a well defined founder population. Gypsy society has a complex structure with subdivisions and stratifications that are incomprehensible to the surrounding populations. Marginalization by the health care systems in most countries results in a lack of information on causes of morbidity and mortality and little is known about hereditary disorders or the population genetic characteristics of Gypsies. This study is the first example of mapping a disease gene in endogamous Gypsy groups. Using lod score analysis and linkage disequilibrium, we have located a novel demyelinating neuropathy to a narrow interval on chromosome 8q24. We show that the disease, occurring in Gypsy groups of different identity and history of migrations, is caused by a single mutation whose origin predates the divergence of these groups.

Adolescent↗

Geographic variation in human mitochondrial DNA control region sequence: the population history of Turkey and its relationship to the European populations.

The hypervariable segment I of the control region of the mtDNA (positions 16024-16383) was amplified from hair roots by PCR and sequenced in 45 unrelated individuals from Anatolia (Asian Turkey). Forty different sequences were found, defined by 56 variable positions, of which only one involves a transversion. The neighbor-joining tree of Kimura's distance matrix for all sequences shows four main clusters. Cluster D was found to be the most statistically robust of the four, and all the sequences in it shared a mutation that is present only in European and West Asian populations. The variability in cluster D could have originated between 37,000 and 107,000 years ago. No branch is unexpectedly long, denoting the absence of sequences that diverged much before the others. The pairwise difference distribution is bell-shaped, in accordance with a population expansion occurring roughly 35,000 to 100,000 years ago. When compared to other Caucasoid populations through the pairwise difference distribution, there is a pattern from the Middle East (older expansion) to the various European populations, with Turkey in an intermediate position; when Turkish sequences are compared through a neighbor-joining tree on a genetic distance matrix of populations, this position is again evidenced. Although there is a very low level of genetic divergence among Caucasoid populations as shown by mtDNA control region sequences, a geographic pattern of genetic variation emerges, denoting a stepping-stone position of Turkey between the Middle East and Europe, which is in agreement with the hypothesis of a replacement of Neanderthals by modern humans, which could be related to the Upper Paleolithic cultural expansion.

Base Sequence↗

From Asia to Europe: mitochondrial DNA sequence variability in Bulgarians and Turks.

Two hypervariable sequence segments in the control region of mitochondrial DNA were determined in samples of Bulgarians and Turks. The Turkish sample presented a higher degree of internal diversity, in terms of total number of variable nucleotides, as well as in the average pairwise nucleotide difference. Pairwise difference distributions were built for both samples, yielding smooth bell shapes in agreement with the Rogers and Harpending model. The Bulgarian and Turkish data were compared with several European and W. Asian Caucasoid populations (Basques, Tuscans, Sardinians, British, Middle Easterners and Indians). Mean pairwise differences suggest that a demographic expansion occurred sequentially in the Middle East, through Turkey, to the rest of Europe (Bulgaria included). Current mutation rate estimates date this expansion in times ranging between 50,000 and 100,000 years ago and, thus, would correspond to the arrival of anatomically modern humans in Europe. Sequence trees for segment I show that European and Middle Eastern sequences derived from the reference sequence. Coalescence times for segment I sequences agree with those predicted by pairwise distributions. Genetic trees were constructed between populations and revealed an extreme homogeneity between European samples.

Base Sequence↗

High mitochondrial sequence diversity in linguistic isolates of the Alps.

Segment I of the control region of mtDNA (360 bases) was sequenced in seven samples, each of 10 individuals inhabiting villages in the eastern Italian Alps (South Tyrol and Trentino). Three linguistic groups, German, Italian, and Ladin, were represented by two samples each; the seventh sample comes from an isolated group of German origin, the Mocheni, who are linguistically distinct and geographically separated from the bulk of the German speakers. Seventy-four polymorphic sites were identified, defining 63 different haplotypes. Mocheni and Ladin speakers tend to form two clusters in the evolutionary trees inferred from sequences. Analysis of molecular variance shows significant differentiation within samples, among them, and among linguistic groups. Genetic differences between the Ladins and the other groups are not much smaller than between Europeans and some Africans; variation is large within groups, as well, with the exception of only the Mocheni. In the evolutionary trees where the four alpine groups are compared with other European populations, Mocheni and especially Ladins appear as clear outliers. Romansch-speaking Swiss, who are linguistically related to Ladins, are not genetically similar to them, for this segment of DNA. Because the time elapsed since colonization of the Alps (< or = 12,000 years) is short in mutational terms, the only model accounting for the observed relationships between mtDNA variation and linguistic identity seems one in which a population ancestral to Ladin speakers was already differentiated long before the Alps were settled and the current linguistic affiliations were established. For the Mocheni, the results are consistent with a simpler episode of allele loss, from an original genetic pool common to the ancestors of the current German speakers.

DNA, Mitochondrial↗

Human mitochondrial DNA variation and the origin of Basques.

The hypervariable segment I of the control region of the mtDNA (positions 16024-16383) was PCR-amplified from mouth scrape and hairs and sequenced in 45 unrelated individuals of pure matrilineal Basque descent. Twenty-seven different sequences were found, of which 21 are unique to the Basques. The allelic partition observed, together with resampling experiments, suggested that much more variation remained to be discovered. The mean pairwise difference in number of nucleotides between individuals was 3-15, a very low value. Moreover, the number of steps for the most parsimonious tree is very low compared to the number of different sequences. Both findings suggest that the Basque population was founded by a few lineages that diverged in a short time span. The number of nucleotide differences between individuals was shown not to be influenced by the distance between their birthplaces, thus validating the sampling strategy used a posteriori. The pairwise difference distribution agreed well with the three-parameter model proposed by Rogers & Harpending (1992). The parameter estimates found for the Basques implied that a demographic expansion (or perhaps two, given the bimodal shape of the distribution) took place sometime between 14500 and 42000 BP which is in agreement with archaeological data. Our sample was compared to other populations for which D-loop sequences were available through the Nei & Miller (1990) distance. In a neighbour-joining tree, all the Caucasoid samples, including the Basques, appeared tightly clustered, whereas African samples were the most distant to the Caucasoids and also the most heterogeneous. Although classical markers, such as blood groups and protein polymorphisms, clearly separate the Basques (and the Sardinians) from other European populations, this distinctiveness was not found using D-loop sequences.

Base Sequence↗

Do Basque- and Caucasian-speaking populations share non-Indo-European ancestors?

Genetic evidence is consistent with the view that the Indo-European languages were propagated in Europe by the diffusion of early farmers. The existence of phylogenetic relationships between European populations speaking other languages has been proposed on linguistic and archaeological grounds, and is here tested by analyzing allele frequencies at ten polymorphic protein and blood group loci. Genetic distances between speakers of Basque and Caucasian languages are compared with those between controls, i.e. contiguous populations speaking Indo-European and Altaic. Although some statistical tests show an excess of genetic similarity between Basque and South Caucasian speakers, most results do not support their common origin. If the Basques and the Caucasian-speaking populations share common ancestors, recent evolutionary phenomena must have caused divergence between them, so that their gene frequencies do not appear more similar now than those of random pairs of populations separated by the same geographic distance.

Biological Evolution↗

Principal component analysis of gene frequencies and the origin of Basques.

The genetic peculiarity of the Basque population has long been noted. We aim to describe Basque distinctiveness in space and assess the internal Basque heterogeneity. All these aspects are relevant to the question of the origin of Basques. After a thorough literature search, a data base was created containing all the available data on gene frequencies in the Iberian Peninsula and France. Twenty-nine systems, comprising 71 alleles, were used to carry out a principal component (PC) analysis. The results show a sharp peak in the first PC in the Basque area, which remains even when the geographic scope is widened to include western Europe. As demonstrated by "wombling" analysis, the steeper slope in the first PC is found to the east of the Basque area, along the Pyrenees. Measures of genetic heterogeneity (such as FST values) within the Basque country, as compared to those for non-Basques, do not show a particular internal substructuration in the Basque population. The genetic results support a scenario in which the Basques are the product of in situ differentiation around the time of the Last Glacial Maximum (18,000 B.P.), in agreement with archaeological and linguistic data. Isolation from the surrounding populations has allowed the differentiation to last for millennia, but has erased the differences existing among Basques.

Alleles↗

Mountains and genes: population history of the Pyrenees.

The Pyrenees Mountains rise between France and Spain. At their western end live the Basques, one of the oldest populations in Europe. All the available genetic information (gene frequencies of blood groups, serum proteins, red cell enzymes, and HLA antigens) on Pyrenean populations has been gathered and subjected to two kinds of analysis: a discrete approach, in which eight separate populations have been defined according to linguistic and geographic criteria to compute genetic distances between them; and a continuous principal components analysis on gene frequencies interpolated to a regular grid. In the first approach the Pyrenean samples have also been compared to other Western European populations. Our results show that the Basque population is most genetically differentiated with respect to other Pyrenean and Western European populations. There is a strong genetic gradient along the mountain range (i.e., in an east-west direction); thus the mountains have not acted as barriers to gene flow. A Catalan-speaking sample, the Cerdanya, is slightly detached from its neighbors and seems closer to other European populations. This genetic picture together with linguistic, paleoanthropological, and archeological data points to a Mesolithic (or older) differentiation of the Cantabrian ancestors of the Basques. Moreover, the Basque genetic features are found in the northern slope of the Pyrenees far beyond the present Basque linguistic boundaries, in accordance with the most recent hypotheses on Pyrenean historical linguistics. The genetic consequences of the arrival of the first Indo-European-speaking peoples in the Iberian Peninsula are also studied; no clear genetic trace has been left of that population movement, except perhaps for the Cerdanya, an eastern valley that affords a passage between north and south.

Algorithms↗

Multivariate approach to matrimonial mobility in Catalonia.

Matrimonial mobility in Catalonia was studied using 1986 census data. Comarca (a geographic division) of birth was used as the population unit, and a measure of affinity (a statistical distance) between comarques in spouse geographic origin was defined. This distance was analyzed with multivariate methods drawn from numerical taxonomy to detect any discontinuities in matrimonial mobility and gene flow between comarques. Results show a three-level pattern of gene flow in Catalonia: (1) a strong endogamy within comarques; (2) a 100-km matrimonial circle around every comarca; and (3) the capital, Barcelona, which attracts migrants from all over Catalonia. The regionalization in matrimonial mobility follows the geographically clear-cut groups of comarques almost exactly.

Family↗

Human mitochondrial DNA sequence variation in the Moroccan population of the Souss area.

BACKGROUND: Various populations have contributed to the present-day gene pool of Morocco, including the autochthonous Berber population, Phoenicians, Sephardic Jews, Bedouin Arabs and sub-Saharan Africans. OBJECTIVE: The primary objective of the study was to complete a genetic description of the Berber-speaking population in the Souss region of southern Morocco, based on mitochondrial DNA (mtDNA) sequence analysis. SUBJECTS AND METHODS: The first hypervariable segment of the mtDNA control region was sequenced in a sample of 50 individuals from the Souss Valley, and the results compared with the extensive body of data available on mtDNA sequence variation in Europe and sub-Saharan Africa. RESULTS: Thirty-four different sequences were found: an estimated 68% of the sequences occurred throughout Europe, West Asia and North Africa, 26% originated in sub-Saharan Africa, and 6% belonged to the North African specific haplogroup U6. The Souss Valley mtDNA sequences indicated the presence of two populations which expanded at different times: the West Eurasian sequences in the Souss sample had a smaller average number of pairwise differences than pairs of sub-Saharan sequences. CONCLUSION: Detailed knowledge of the possible geographic origin of each sequence facilitated an interpretation of both internal diversity parameters and between-population relationships. The sub-Saharan admixture in the Souss Valley matched the south-north cline of sub-Saharan influence in North Africa, also evident in the genetic distances of North African populations to Europeans and sub-Saharan Africans.

Africa South of the Sahara↗

Population history of Corsica: a linguistic and genetic analysis.

Genetic and linguistic differentiations within Corsica were analysed and compared; the genetic relationships of Corsica to other Mediterranean populations were also studied. Lexical distances between 49 Corsican localities were computed from a standard word list; trees built from these distances were compared with average linkage and neighbour-joining trees of genetic distances. Our lexical distance results confirmed the north/south dialectal subdivision of Corsican speeches described by linguists. No clear results were achieved with genetic distances because of the low number of loci for which data were available. Nevertheless, a tight northern cluster clearly emerged. When compared to other Mediterranean populations, Corsica showed a certain degree of differentiation, although not so marked as that of Sardinia. Corsica presented genetic affinities with Campania, Sicily, Liguria, Provence and Latium, while distances with Tuscany and Sardinia were larger. These results can be interpreted as a reflection of the prehistoric isolation of Corsica and the relative contribution to the island gene pool of prehistoric and historic invaders and immigrants from several populations.

Blood Group Antigens↗

Blood biochemistry reflects seasonal nutritional and reproductive constraints in the eurasian badger (Meles meles).

Physiological responses to nutritional and reproductive constraints were explored in a wild population of Eurasian badgers (Meles meles) inhabiting Wytham Woods, Oxfordshire, United Kingdom. We compared seasonal blood levels of lipid and protein compounds to variables describing the sex, age, body condition, wounds, testes position, and flea abundance of the badgers. We found seasonal variations in albumin/globulins and urea/creatinine ratios matched by differences in body condition. High creatinine, urea, and triglycerides levels were obtained in animals in poor nutritional condition and with low levels of body fat. The maintenance of urea/creatinine ratios indicates that the badger does not demonstrate a stage of protein conservation in periods of food scarcity during the summer or periods of cold weather. Hypercholesterolaemia, especially in fat animals, was confirmed. We also offer baseline levels of metabolites commonly used in clinical biochemistry for their further use in the analysis of the status and the management of wild badger populations.

Adipose Tissue↗

Allele frequencies for 20 microsatellites in a worldwide population survey.

20 microsatellite polymorphisms: HUMHPRT, HUMD3S1358, HUMTH01, HUMACPP, HUMVWF, HUMD16S310, HUMD4S243, HUMTPO, HUMFES/FPS, HUMF13A1, HUMDHFRP2, HUMD11S2010, HUMD13S767, HUMD9S926, HUMD2S1328, HUMD14S306, HUMD18S848, HUMD5S818, HUMD7S820 and HUMFGA were analyzed in a worldwide survey covering five continents and allele frequencies are given. There is a high heterogeneity in allele frequencies among continents. A neighbor-joining tree based on Fst distance shows a pattern of differentiation that may reflect the role of drift in the development of genetic differences among humans. The variation found between continents confirms the usefulness of tetranucleotide microsatellites in human genetic variation studies.

Alleles↗

Nicaraguan population data on LDLR, GYPA, D7S8, HBGG, GC and HLA-DQA1 loci.

Nicaraguans have become the most numerous and fastest increasing minority in Costa Rica: at present they represent around 6% of the total population of the country. We have analyzed the allele and genotype frequencies of six PCR-based genetic markers (LDLR, GYPA, HBGG, D7S8, GC, and HLA-DQA1) in 100 unrelated Nicaraguans living in Costa Rica. All loci studied were in Hardy-Weinberg equilibrium. Some statistical parameters of forensic interest were also calculated (h, PD and CE). Allele frequencies of the markers HLA-DQA1 and GYPA were found to be significantly different between the populations of Nicaragua and Costa Rica. Nevertheless, genetic distances showed that Nicaragua is close to other Hispanic-admixed populations like those from Argentina, Chile, Colombia, Costa Rica, and USA Hispanics. The loci set was assessed to be useful for paternity testing and individual identification in the Nicaraguan population residing in Costa Rica.

Adult↗