Environmental factors modulated ancient mitochondrial DNA variability and the prevalence of rheumatic diseases in the Basque Country.

Among the factors that would explain the distribution of mitochondrial lineages in Europe, climate and diseases may have played an important role. A possible explanation lies in the nature of the mitochondrion, in which the energy generation process produces reactive oxygen species that may influence the development of different diseases. The present study is focused on the medieval necropolis of San Miguel de Ereñozar (13th-16th centuries, Basque Country), whose inhabitants presented a high prevalence of rheumatic diseases and lived during the Little Ice Age (LIA). Our results indicate a close relationship between rheumatic diseases and mitochondrial haplogroup H, and specifically between spondyloarthropathies and sub-haplogroup H2. One possible explanation may be the climate change that took place in the LIA that favoured those haplogroups that were more energy-efficient, such as haplogroup H, to endure lower temperatures and food shortage. However, it had a biological trade-off: the increased risk of developing rheumatic diseases.

The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa.

After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Pestera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.

Temporal mitochondrial DNA variation in the Basque Country: influence of post-neolithic events.

The Basque population has been considered an outlier in a large number of genetic studies, due to its hypothesized antiquity and greater genetic isolation. The present paper deals with an analysis of the mtDNA variability of the historical population of Aldaieta (VI-VII c. AD; Basque Country) which, together with genetic data existing for other prehistoric populations of the Basque Country (4,500-5,000 YBP), permits an appraisal of the hypotheses proposed for the origin of the genetic differentiation of the Basque population. Given that this is an aDNA study, application has been made both of standard precautions, to avoid contamination, and of authentication criteria (analysis of duplicates, replication in an independent laboratory, quantification of target DNA, sequencing and cloning of PCR products). The variability of the mtDNA haplogroups of the historical population of Aldaieta falls within the range of the present-day populations of Europe's Atlantic fringe, whereas the prehistoric populations of the Basque Country display clear differentiation in relation to all others. Consequently, we suggest that between 5,000-1,500 YBP approximately, there may have been gene flow amongst the western European populations that homogenised mtDNA lineages.

Structuring the genetic heterogeneity of the Basque population: a view from classical polymorphisms.

In this study we analyze 18 classical polymorphisms (ABO, Rh, MNSs, Lewis, P, Duffy, Kell, ADA, ESD, PGM1, PGD, AK1, ACP1, GLO1, HP, GC, TF, and PI) in over 2000 autochthonous individuals from 14 natural districts in three provinces of the Basque Country (Alava, Guipuzcoa, and Biscay). Heterogeneity analysis via the chi2 test and a calculation of F(ST) indicate that there is significant genetic heterogeneity between the Basque districts. The R matrix informs us that this heterogeneity is not significantly concentrated in a single district or in the districts of a single province, but is rather distributed among several districts belonging to the three provinces analyzed. We undertake to assess the influence of various historical, geographical, and cultural factors on the genetic structure of the Basque population. Analysis suggests that allele distribution is geographically patterned in the Basque Country. The gradient distributions observed in the case of some alleles (ABO*O, RH*cDE, RH*cde, MNS*MS, and ACP1*C) on the basis of Moran's autocorrelation coefficient I, along with the influence of the two main travel routes through the Basque Country (western route through Bilbao and eastern route through Vitoria), suggest that the gene flow tends toward the coast. As regards other factors considered (administrative division, repopulation processes, linguistic heterogeneity, and north vs. south cultural heterogeneity), we detected only a certain influence exerted by an old tribal differentiation (2000 B.P.), which would diminish with the passage of time.

An mtDNA analysis in ancient Basque populations: implications for haplogroup V as a marker for a major paleolithic expansion from southwestern europe.

mtDNA sequence variation was studied in 121 dental samples from four Basque prehistoric sites, by high-resolution RFLP analysis. The results of this study are corroborated by (1) parallel analysis of 92 bone samples, (2) the use of controls during extraction and amplification, and (3) typing by both positive and negative restriction of the linked sites that characterize each haplogroup. The absence of haplogroup V in the prehistoric samples analyzed conflicts with the hypothesis proposed by Torroni et al., in which haplogroup V is considered as an mtDNA marker for a major Paleolithic population expansion from southwestern Europe, occurring approximately 10,000-15,000 years before the present (YBP). Our samples from the Basque Country provide a valuable tool for checking the previous hypothesis, which is based on genetic data from present-day populations. In light of the available data, the most realistic scenario to explain the origin and distribution of haplogroup V suggests that the mutation defining that haplogroup (4577 NlaIII) appeared at a time when the effective population size was small enough to allow genetic drift to act-and that such drift is responsible for the heterogeneity observed in Basques, with regard to the frequency of haplogroup V (0%-20%). This is compatible with the attributed date for the origin of that mutation (10,000-15, 000 YBP), because during the postglacial period (the Mesolithic, approximately 11,000 YBP) there was a major demographic change in the Basque Country, which minimized the effect of genetic drift. This interpretation does not rely on migratory movements to explain the distribution of haplogroup V in present-day Indo-European populations.

Analysis of 6 short tandem repeat loci in Navarre (northern Spain).

A genetic study was performed on a sample of 146 autochthonous individuals from the province of Navarre (northern Spain) to test for 6 STR systems: CSF1PO, TPOX, TH01, F13A1, FES/FPS, and VWA31/A. The Navarre population has a series of allele frequencies that are at the extreme end of the European range of variation and that are in most cases similar to those found in the Basque population of the provinces of Alava, Biscay, and Guipuzcoa. This similarity is corroborated by correspondence analysis, in which the population of Navarre is at one end of the first axis with the Basque sample close to it and the remaining European populations far removed. In tree-type representations the Navarre population is grouped with the Basque series at 1 end. Even so, the comparison of allele frequency distributions by the chi-square heterogeneity test indicates that these 2 groups are statistically different. Our results together with the cultural relationship that exists between all the Basque-speaking provinces and the genetic heterogeneity described in earlier studies between the Basque provinces of Alava, Biscay, and Guipuzcoa (Aguirre et al. 1989; Manzano, Orue et al. 1996; Manzano, Aguirre et al. 1996) lead us to believe that the Navarre population lies within the heterogeneous Basque genetic map.

Genetic diversity in northern Spain (Basque Country and Cantabria): GM and KM variation related to demographic histories.

Genetic diversity in Northern Spain (SW Europe) was assessed through the analysis of the GM and KM immunoglobulin markers in 505 individuals using a set of 17 allotypes, including the G2M(23) allotype which has been infrequently used before now. The individuals were representative of three anthropologically well-defined populations belonging to two geographically and archaeologically distinct areas in the Basque Country (Guipúzcoa and Alava provinces) and to the mountainous region of Montes de Pas in the province of Cantabria. Gene frequency distributions indicated a high genetic divergence between Montes de Pas and the Basque Country, and a relative degree of heterogeneity between the two Basque regions. The genetic differentiation of Montes de Pas, which is consistent with previous classical polymorphism analyses, suggests a considerable genetic variation range within the Iberian Peninsula, possibly higher than that often polarised around the Basque versus non-Basque variation. Analyses of genetic structure show that the major differentiation of Montes de Pas could be related to the historically documented mixed origin of this population. The moderate genetic distances between regions in the Spanish Basque Country could be explained by differential systematic pressures acting through a stronger gene flow in the South than in the more isolated Northern areas. The comparisons with neighbouring populations from the French Pyrenees suggest that the present genetic variation revealed by lg polymorphisms in SW Europe can be related to historical demographic processes including gene flow and/or low population sizes.

The deltaccr5 mutation conferring protection against HIV-1 in Caucasian populations has a single and recent origin in Northeastern Europe.

The chemokine receptor CCR5 is encoded by the CMKBR5 gene located on the p21.3 region of human chromosome 3, and constitutes the major co-receptor for the macrophage-tropic strains of HIV-1. A mutant allele of the CCR5 gene, Delta ccr5 , was shown to provide to homozygotes with a strong resistance against infection by HIV. The frequency of the Delta ccr5 allele was investigated in 18 European populations. A North to South gradient was found, with the highest allele frequencies in Finnish and Mordvinian populations (16%), and the lowest in Sardinia (4%). Highly polymorphic microsatellites (IRI3.1, D3S4579 and IRI3.2, D3S4580 ) located respectively 11 kb upstream and 68 kb downstream of the CCR5 gene deletion were used to determine the haplotype of the chromosomes carrying the Delta ccr5 variant. A strong linkage disequilibrium was found between Delta ccr5 and specific alleles of the IRI3.1 and IRI3.2 microsatellites: >95% of the Delta ccr5 chromosomes carried the IRI3.1-0 allele, while 88% carried the IRI3.2-0 allele. These alleles were found respectively in only 2 or 1.5% of the chromosomes carrying a wild-type CCR5 gene. From these data, it was inferred that most, if not all Delta ccr5 alleles originate from a single mutation event, and that this mutation event probably took place a few thousand years ago in Northeastern Europe. The high frequency of the Delta ccr5 allele in Caucasian populations cannot be explained easily by random genetic drift, suggesting that a selection advantage is or has been associated with homo- or heterozygous carriers of the Delta ccr5 allele.

Genetic polymorphisms of the Basques from Gipuzkoa: genetic heterogeneity of the Basque population.

A random sample of 586 Basque individuals from the province of Gipuzkoa was studied for 16 genetic systems: A1A2B0, Rh, MNSs, P, Lewis, Duffy, Kell, GC, TF, AAT, ACP, AK, ADA, ESD, HP and PGM1. The results of this study indicate that the Basque population of Gipuzkoa presents certain differential values with respect to other Basque series, such as maximum values for RH*cde, AK*2 and PGM1*2+ and minimum for PGM1*1-, while the remaining alleles are located within the range of values found in the Basque population to date. It is suggested that there is intraprovincial heterogeneity, as described for Bizkaia by Aguirre et al. in 1991, and the existence of heterogeneity within the Basque population on an inter-provincial level, backing up previous studies in this respect (by Aguirre et al. in 1989 and Manzano et al. 1993).

The "Basqueness" of the Basques of Alava: a reappraisal from a multidisciplinary perspective.

The genetic and linguistic peculiarity of the Basque population is well known. Analysis of the studies published to date on the Basque population reveals that these studies refer basically to the provinces of Vizcaya and Labourd, both in the Northern part of the Basque Country. Multidisciplinary information indicates that the landscape differences of the Basque Country could have conditioned differential population biodynamics in the Atlantic and Mediterranean parts of the Basque area. In order to evaluate this possibility, this study focuses on the genetic constitution of the Basque population of Alava (in the South of the Basque Country) through the analysis of several red-cell systems. The data obtained in this genetic study and those from archaeology, linguistics, ethnography, and skeletal biology suggest that within the "Basque population" there may be at least two distinct groups: an "Atlantic" group and a "Mediterranean" one, divided mainly by the watershed. This geographical feature could have led to a greater genetic isolation of the Northern slopes, with the South more open to population contact. This is reflected nowadays in the different cline distribution detected for most systems in the Alava Basques in comparison with other Basque and Iberian Peninsula series studied to date.

HLA-DQA1 in autochthonous Basques: description of a genocline for the DQA1*0201 allele in Europe.

A total of 250 autochthonous Basque individuals were tested in the HLA-DQA1 system, and the allele frequency distribution found was significantly different from that of any other European population. The differences centre mainly on the alleles DQA1*0201 and DQA1*0501: for the former the Basques have the highest frequency described anywhere in the world (f = 0.210) and for the latter they have the lowest frequency in Europe (f = 0.204). For the allele DQA1*0201 a genocline is also described in Europe with the Basques and Finno-Ugric populations basically at the extremes. The genocline reflects the isolation of the Basque population since prehistoric times, and supports existing linguistic, archaeological and genetic data.

Genetic typing with HUMTH01, HUMVWA31A and HUMFES/FPS short tandem repeat loci, D1S80 variable number tandem repeat locus and HLA-DQ alpha of recent and from XII-XIII centuries spongy bone.

The genetic analysis of ancient populations through DNA from bone remains, requires use of short sized loci that can be amplified by polymerase chain reaction (PCR) for which the short tandem repeat (STR) loci are most suitable. These techniques can also be applied to genetic identification in forensic casework. In this study three STR loci, HUMFES/FPS, HUMTH01, and HUMVWA31A, were selected to estimate their usefulness when applied to recent and ancient spongy bone DNA typing. In addition, loci D1S80 and HLA DQ alpha were also tested in the analysis of recent spongy bone DNA. The recent remains studied were constituted by ten spongy bone samples of postmortem material from one individual buried for 1 year. The ancient remains are composed by 8 spongy bone samples from the heads of left femurs from a XII-XIII Centuries Basque Country population. Adequate amplification and typing results could only be obtained with cetyltrimethyl ammonium bromide (CTAB)-extracted DNA, without any further purification after precipitation. Genotypes of the one year post-mortem material and those of his son and his wife were obtained at the D1S80, HLA-DQ alpha, and STR loci. In all these systems, no exclusion was observed, with a combined probability of paternity of 0.9997. This demonstrates the reliability of the obtained results. The genetic typing of HUMTH01 in spongy bone from the XII-XIII Centuries Basque Country individuals was also performed. This will allow the genetic analysis of ancient bone remains and therefore, to carry out evolutionary population studies.

Alpha-2-HS-glycoprotein gene frequencies in Basques.

The genetic polymorphism of human alpha 2-HS-glycoprotein (AHSG) was analyzed in a sample of 736 native individuals from the three provinces of the Basque Autonomous Community (Guipúzcoa, Vizcaya and Alava). The Basque population shows the highest frequency of the allele AHSG*3 described to date in European populations. The same is not true for the frequency of allele AHSG*2, which fits well into the genocline described in Europe, in accordance with the adaptive hypothesis.

New contribution to the genetics of the Basques: heterogeneity in the esterase D subtype distribution.

A random sample of 1,491 individuals from three Basque provinces was studied for the red-cell esterase D (ESD) polymorphism by means of isoelectric focusing. The following allele frequencies were observed: Vizcaya, ESD*1 = 0.933, ESD*2 = 0.058, ESD*5 = 0.009; Guipuzcoa, ESD*1 = 0.938, ESD*2 = 0.053, ESD*5 = 0.009; and Alava, ESD*1 = 0.894, ESD*2 = 0.088, ESD*5 = 0.018. The Basques from Vizcaya and Guipuzcoa display the lowest values for allele ESD*5 of any European population studied to date. The value obtained for this allele in the Basque population of Alava is significantly higher than those found in the other two Basque samples. This, together with the fact that Basques from Alava display the lowest ESD*1 frequency of any Basque series, suggests that there are genetic differences between Basque provinces.

Serum protein polymorphisms (GC, TF, and PI subtypes) in the Basque population of Alava.

Group-specific component (GC), transferrin (TF) and alpha-1-antitrypsin (PI) polymorphisms have been studied in the Basque population of Alava. The following gene frequencies were found: GC*1S = 0.525, GC*1F = 0.109, GC*2 = 0.366; TF*C1 = 0.793, TFC*2 = 0.171, TF*C3 = 0.032, TF*B = 0.003; PI*M1 = 0.611, PI*M2 = 0.164, PI*M3 = 0.101, PI*M4 = 0.019, PI*S = 0.101, PI*T = 0.003, PI*Z = 0.002. These results show that there is heterogeneity within the Basque population. In comparison with other populations from the Iberian Peninsula, the Basques from Alava show significant differences only for the PI system.

Genetic polymorphism of inter-alpha-trypsin inhibitor (ITI) in the Basque Country (northern Spain).

The genetic polymorphism of inter-alpha-trypsin inhibitor (ITI) was analyzed in 2 samples of 554 residents and 303 autochthonous healthy unrelated individuals from the Basque Country (northern Spain), by isoelectric focusing on miniaturized polyacrylamide gels followed by immunoblotting. The allele frequencies were ITI*1 = 0.586, ITI*2 = 0.402 and ITI*3 = 0.012 in residents and ITI*1 = 0.548, ITI*2 = 0.449 and ITI*3 = 0.003 in the autochthonous population. These allele frequencies were compared with those reported in other European populations.