HLA-DQA1 and HLA-DQB1 genes in Tsachilas Indians from Ecuador: new insights in population analysis by Human Leukocyte Antigens.

Human Leucocyte Antigen (HLA) loci are widely known for their role in the generation of immune responses and are often considered to be effective in reconstructing human relationships. This is due to the high degree of polymorphism and the rarity of recombination observed at HLA loci. In this study, we have made an attempt to support the potential of HLA class II loci by analysing DQA1 and DQB1 in 52 Ecuadorians with ties to the Tsachilas community. Little is known about this populations either ethnologically or historically: they are considered retaining much of the ancient Chibchan culture in spite of the lack of significant genetic characterization. A total of 21 alleles were observed, with very low heterozygosity. The obtained data were then assessed for relationship reconstruction. The compiled database of 63 populations was segregated and resolved in clusters corresponding to the ethnogeographic distribution of the populations. This analysis of Central and Southern Amerindians allowed us to support a historical hypothesis related to the origin and migration of Ecuadorian people. Indeed, the relationships with neighbour human groups, especially Cayapas and Colombians, could shed light on the genetic similarity within ancient Chibchan culture that was dispersed by tribes coming up the Barbacoas. This indicates that if an appropriate analysis was to be carried out on a set of populations representative of different geographic locations, and that analysis was properly interpreted, then there would be a high possibility that HLA class II loci could infer accurate assessments, as revealed by uniparental markers.

Genetic response to an environmental pathogenic agent: HLA-DQ and onchocerciasis in northwestern Ecuador.

The aim of this study is to explore human leukocyte antigen (HLA)-DQ variability in two populations (Cayapas Amerindians and Afro-Ecuadorians) who live near one another along the Cayapa River and who are exposed to the same environmental stresses, such as infection by Onchocerca volvulus. HLA-DQA1 and HLA-DQB1 of 149 unrelated individuals (74 Cayapas and 75 Afro-Ecuadorians) have been analyzed. HLA high-resolution molecular typing was performed by sequence-based typing, sequence-specific oligonucleotides hybridization and sequence-specific primer (SSP) amplification. The comparison between affected (cases) and unaffected people (controls) in both populations shows the key role of several HLA-DQA1 alleles in susceptibility and protection against onchocerciasis. In both populations, there is strong evidence related to the protective role of DQA1*0401 against onchocerciasis. Alleles HLA-DQA1*0102 and *0103 seem to represent risk factors in Afro-Ecuadorians, while HLA-DQA1*0301 is only a suggestive susceptibility allele in Cayapas. These findings represent new positive/negative associations with onchocerciasis in South America, whereas previous findings pertained only to African populations.

Growth variation, final height and secular trend. Proceedings of the 17th Aschauer Soiree, 7th November 2009.

Growth and body height have always been topics interesting to the public. In particular, the stupendous increase of some 15-19cm in final adult height during the last 150 years in most European countries (the "secular trend"), the concomitant changes in body and head proportions, the tendency towards early onset of sexual maturation, the changes in the age when final height is being reached, and the very recent trend in body mass index, have generated much scientific literature. The marked plasticity of growth in height and weight over time causes problems. Child growth references differ between nations, they tend to quickly become out of date, and raise a number of questions regarding fitting methods, effects caused by selective drop-out, etc. New findings contradict common beliefs about the primary importance of nutritional and health related factors for secular changes in growth. There appears to be a broad age span from mid-childhood to early adolescence that is characterised by a peculiar insusceptibility. Environmental factors that are known to influence growth during this age span appear to have only little or no impact on final height. Major re-arrangements in height occur at an age when puberty has almost been completed and final height has almost been reached, implying that factors, which drive the secular trend in height, are limited to early childhood and late adolescence.

Estrogen receptor alpha polymorphisms and fertility in populations with different reproductive patterns.

The estrogen receptor (ER) plays an important role in mediating estrogen action on target tissues. ER-alpha, the most abundant, is found in all human reproductive tissues and studies on alpha-ER knockout mice have highlighted its role in reproduction. ER-alpha gene (ESR1) polymorphisms have been associated with a variety of disorders including human infertility. In this study, we examined the association of ESR1 PvuII and XbaI polymorphisms with fertility in two populations with different reproductive patterns and precisely in a sample of healthy Italian men and women (n=178) and in a sample of healthy African-Ecuadorian women (n=57). ESR1 xx and ppxx genotypes among the Italian men were found to be associated with an above-median number of children (P=0.01 and P=0.004, respectively). ESR1 pp genotype among the Italian women showed a tendency to be associated with a lower number of abortions (P=0.04), whereas ESR1 pp and ppxx genotypes among African-Ecuadorian women were associated with a higher number of children (P=0.02 and P=0.03, respectively). These results are consistent with previous observations indicating a role of ESR1 genotypes in human infertility and give insight into the complex interactions between genotypes and reproductive behaviours in human populations.

An analysis of peroxisome proliferator-activated receptor gamma (PPAR-gamma 2) Pro12Ala polymorphism distribution and prevalence of type 2 diabetes mellitus (T2DM) in world populations in relation to dietary habits.

BACKGROUND AND AIM: The human peroxisome proliferator-activated receptor gamma (PPAR-gamma) is involved in lipid storage, glucose homeostasis and adipocyte differentiation. The Ala allele of the Pro12Ala polymorphism has been associated with a protective effect against T2DM. Ala allele frequencies are known for many populations, but data are absent for other interesting human groups. METHODS AND RESULTS: We examined samples from Ethiopia, Benin, Ecuador and Italy. In addition, we performed an analysis of the Pro12Ala polymorphism distribution in world populations, also in relation to T2DM prevalence and the diet lipid content. In the European populations, the Ala allele frequencies are distributed according to a latitudinal trend, with the highest in the northern and central European populations and the lowest in the Mediterranean populations. Considering the world populations, a significant inverse relationship between Ala frequency and T2DM prevalence was observed mainly in populations where energy from lipids exceeded 30% of the total energy intake. CONCLUSION: Northern Europe's cold climate has been hypothesised to have played a role in contributing to the present pattern. Moreover our analysis appears to confirm, at a population level, the protective effect of Ala allele against T2DM, already observed in case-control studies, but only in populations with a diet rich in lipids.

COL1A2 (type I collagen) polymorphisms in the Colorado Indians of Ecuador.

BACKGROUND: EcoRI, MspI and RsaI restriction fragment length polymorphisms (RFLPs) of the COL1A2 (type I collagen) gene are proving to be extremely informative markers for describing human populations; therefore they hold considerable potential for anthropogenetic research. AIM: The objective of this study was to characterize at the DNA level the Colorado Indians from Ecuador, for whom only blood group frequency information is available, and to investigate their relationships with the Cayapa-another Ecuadoran Native American group belonging to the same linguistic affiliation-and other world populations. SUBJECTS AND METHODS: Colorado Indians (n = 80) were analysed for the three anthropologically informative RFLPs of the COL1A2 gene. To better define the genetic relationship between this group and other populations, principal component analysis (PCA) was performed and genetic distances were estimated. Population genetic structure was tested through analysis of molecular variance (AMOVA) by comparing haplotype frequencies. RESULTS: COL1A2 allele and haplotype frequencies showed a certain degree of heterogeneity between the two Chibchan populations of Ecuador. The AMOVA test detected a significant level of differentiation (Fst = 0.034, p = 0.0049) between Colorado and Cayapa Indians. PC and genetic distance analyses showed a clear-cut separation between African and non-African populations; within the latter, the two Native American groups were differentiated from each other. CONCLUSIONS: The present findings suggest the presence of a low level of genetic relatedness between the Colorado and the Cayapa, despite their supposed common ethnogenesis. This confirms what has been inferred from other genetic data about the high degree of heterogeneity among Native Americans, even within the same linguistic branch, thus supporting the existence of genetic sub-structure within the central and southern American populations.

Apolipoprotein E polymorphism and fertility: a study in pre-industrial populations.

Human apolipoprotein E is the most important supplier of the cholesterol precursor for steroid hormone production in steroidogenic tissues and therefore could play a role in the regulation of steroid hormone function and influence human reproduction. This hypothesis has been confirmed by studies describing a differential fertility associated with common apolipoprotein (APOE) genotypes in two European populations. In the present investigation the impact of APOE genetic variation on fertility was studied in two Ecuadorian populations, African-Ecuadorians (57 women) and Cayapa Indians (27 women). In addition some biodemographic variables concerning women's fertility were investigated (124 African-Ecuadorian women; 40 Cayapa women) to better understand the APOE-fertility relationships in these pre-industrial populations. General fertility rates in both populations were very high (6.5 and 6.2 for the African-Ecuadorians and for the Cayapa respectively). When considering only women near the end of reproductive life (>/=40 years), a more marked difference was observed between the two groups (9.1 versus 7.7, P=0.09). In both communities, the highest number of children was found to be associated with the e*4/e*3 genotype; the e*4/e*3 genotype frequency (0.50) in the African-Ecuadorian women with 9-17 children was about three times that of the women with 0-8 children (0.14) (P=0.02). The present findings are at variance with those observed in European populations, where e*3/e*3 was the genotype associated with the highest reproductive efficiency. A possible explanation for this inconsistency could be due to the different functional properties associated with the e*3 and e*4 alleles and to genotype interactions with environmental factors including reproductive strategies.

New data on the world distribution of paraoxonase (PON1 Gln 192 --> Arg) gene frequencies.

The physiological role of human paraoxonase (PON), a serum enzyme that hydrolyzes organophosphate insecticides and nerve agents, is not clear. Of the three genes in the paraoxonase gene family, PON1 shows a polymorphism, Gln 192 --> Arg, governed by two common alleles named *Q and *R. These determine two different isoforms associated, respectively, with lower and higher activity towards paraoxon, a toxic metabolic product of the insecticide parathion. The *R allele has often been found associated with an increased risk of coronary heart disease. As human populations tend towards greater exposure to environmental changes, including changes in dietary habits and contact with insecticides or other toxic substances, health risks will change as well. In studying the prevention of these newly emerging risks, it could be important to know the distribution of the two alleles in the various world populations. In this paper we report on the genotype and allele frequencies of this polymorphism in different populations, most of which have never been examined for this polymorphism. Samples were taken from mainland Italy, Sardinia, Ethiopia, Benin, and Ecuador. The *R allele frequencies for the samples were: 0.313, 0.248, 0.408, 0.612, and 0.789, respectively. The data show a large variability in allele frequencies, and, in particular, that PON1 allele distribution depends on membership to different geographic populations.

Genetic variation atapolipoprotein E locus in Ethiopia: an E5 variant corresponds to two different mutant alleles: E*5 (Glu212Lys) and E*5 (Gln204Lys; Cys112Arg).

A previous investigation on apolipoprotein E polymorphism in the Ethiopian population highlighted the presence of a further variant allele named E*5 in addition to the three common alleles. The variant is considered rare elsewhere but has a frequency of more than 1% in this population. Now characterized by gene sequencing and restriction isotyping in many members of the families of the original carriers, the variant isoform has actually been found to be determined by two different gene mutations. Effectively rare in Ethiopians, one of the two, E5 (Gln204Lys, Cys 112Arg), has never been described before. The other, E5 (Glu212Lys), previously described in a subject of Turkish origin, is present at the polymorphic level only in the Ethiopian population. No subjects bearing these variants had anomalous lipid or apolipoprotein patterns. In the course of the present investigation both have been found to occur as rare variants in the southern Italian population as well. The occurrence of the two variants in the populations of Ethiopia and of the Mediterranean basin could be explained by taking into account the relevant Caucasoid contribution to the Ethiopian gene pool.

Analysis of three RFLPs of the COL1A2 (Type I Collagen) in the Amhara and the Oromo of Ethiopia.

BACKGROUND: The present composition of the Ethiopian population is the result of a complex and extensive intermixing of different peoples of North African, Near and Middle Eastern, and south-Saharan origin. The two main groups inhabiting the country are the Amhara, descended from Arabian conquerors, and the Oromo, the most important group among the Cushitic people. With the exception of some surveys on the general Ethiopian populations, little is known about the degree of genetic differentiation between the Amhara and the Oromo. AIM: The study seeks to investigate the genetic structure of these two heterogeneous Ethiopian populations and to characterize their relationships with other African and Mediterranean peoples. SUBJECTS AND METHODS: Amhara and Oromo individuals (n = 171) were analysed for three RFLPs (restriction fragment length polymorphisms) of the COL1A2 gene. To better define the genetic relationship between the two Ethiopian groups, and also between African and non-African peoples, genetic distances among Amhara, Oromo and other populations were estimated using the COL1A2 allele and haplotype frequencies, and the allele frequencies of 16 additional classical markers. RESULTS: chi(2) analysis applied to the COL1A2 allele and haplotype frequencies showed a small but statistically significant degree of heterogeneity between the two Ethiopian populations. Combining the information obtained from the three RFLP markers, a significant level of differentiation (Fst = 0.0147, p = 0.036) was also detected between Amhara and Oromo. The genetic distance analysis showed the separation between African and non-African populations, with the Amhara and Oromo located in an intermediate position. This pattern is consistent with the location of the two Ethiopian groups in other genetic analysis and with cultural data. CONCLUSIONS: The present findings suggest the presence of a differential level of genetic relatedness with south-Saharan peoples in the two Ethiopian groups, which could reflect their different history and seems to indicate the existence of genetic sub-structure within the country.

Genetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome.

The geographic structure of Y-chromosome variability has been analyzed in native populations of South America, through use of the high-frequency Native American haplogroup defined by the DYS199-T allele and six Y-chromosome-linked microsatellites (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), analyzed in 236 individuals. The following pattern of within- and among-population variability emerges from the analysis of microsatellite data: (1) the Andean populations exhibit significantly higher levels of within-population variability than do the eastern populations of South America; (2) the spatial-autocorrelation analysis suggests a significant geographic structure of Y-chromosome genetic variability in South America, although a typical evolutionary pattern could not be categorically identified; and (3) genetic-distance analyses and the analysis of molecular variance suggest greater homogeneity between Andean populations than between non-Andean ones. On the basis of these results, we propose a model for the evolution of the male lineages of South Amerindians that involves differential patterns of genetic drift and gene flow. In the western part of the continent, which is associated with the Andean area, populations have relatively large effective sizes and gene-flow levels among them, which has created a trend toward homogenization of the gene pool. On the other hand, eastern populations-settled in the Amazonian region, the central Brazilian plateau, and the Chaco region-have exhibited higher rates of genetic drift and lower levels of gene flow, with a resulting trend toward genetic differentiation. This model is consistent with the linguistic and cultural diversity of South Amerindians, the environmental heterogeneity of the continent, and the available paleoecological data.

Red cell enzyme polymorphisms in Friuli Venezia Giulia (northeast Italy).

Seven erythrocyte enzyme polymorphisms (ACP1, ADA, ESD, GLO1, PGD, PGM1 and PGM2) were investigated in a sample of 673 unrelated adult individuals from Friuli Venezia Giulia (or Friuli) and Istria. The gene frequencies found in the four provincial samples of Friuli and Istria fall within the range previously reported for Italy, showing a genetic homogeneity among the considered samples. However, comparisons with data from ex-Yugoslavian samples--using the chi 2 test--showed rather marked differences, probably due to a real different genetic structure of the compared samples. A significant association was found assuming a linear relation between the ADA*2 allele frequencies and longitude (r = +0.5503) and between the PGD*C frequencies and latitude (r = -0.6483), suggesting the existence of a clinal trend for these allele frequencies in Italy. These results seem to disagree with foregoing conclusions stated by other authors, probably because these studies were carried out in an area either rather narrow from the geographical point of view or affected by small size migration movements.

Apolipoprotein B signal peptide polymorphism distribution among south Amerindian populations.

We report the distribution of the APOB signal peptide polymorphism in 5 native populations of South America: 2 samples of Mataco and 1 sample each of Pilagá and Toba from the Argentinian Chaco and 1 sample of Ache from the Paraguay forest. A randomly selected subsample of a previously studied sample from the Cayapa of Ecuador (Scacchi et al. 1997) was reanalyzed to investigate probable differences attributable to sampling, laboratory techniques, or interobserver error. The polymorphism observed in the signal peptide region of the APOB gene among native populations of South America exhibits the same range of variation found among geographic continental populations, confirming the high genetic heterogeneity of South Amerindians. Extremes in the allele prevalences were found among the Mataco and Ache, populations not far apart geographically. The small differences in genotype and allele frequencies between the subsample of the Cayapa analyzed here and the original Cayapa sample and between the 2 Mataco samples were not statistically significant and most likely were due to sampling error.

mtDNA history of the Cayapa Amerinds of Ecuador: detection of additional founding lineages for the Native American populations.

mtDNA variation in the Cayapa, an Ecuadorian Amerindian tribe belonging to the Chibcha-Paezan linguistic branch, was analyzed by use of hypervariable control regions I and II along with two linked regions undergoing insertion/deletion mutations. Three major maternal lineage clusters fit into the A, B, and C founding groups first described by Schurr and colleagues in 1990, whereas a fourth lineage, apparently unique to the Cayapa, has ambiguous affinity to known clusters. The time of divergence from a common maternal ancestor of the four lineage groups is of sufficient age that it indicates an origin in Asia and supports the hypothesis that the degree of variability carried by the Asian ancestral populations into the New World was rather high. Spatial autocorrelation analysis points out (a) statistically significant nonrandom distributions of the founding lineages in the Americas, because of north-south population movements that have occurred since the first Asian migrants spread through Beringia into the Americas, and (b) an unusual pattern associated with the D lineage cluster. The values of haplotype and nucleotide diversity that are displayed by the Cayapa appear to differ from those observed in other Chibchan populations but match those calculated for South American groups belonging to various linguistic stocks. These data, together with the results of phylogenetic analysis performed with the Amerinds of Central and South America, highlight the difficulty in the identification of clear coevolutionary patterns between linguistic and genetic relationships in particular human populations.

Genetic population structure of two African-Ecuadorian communities of Esmeraldas.

The genetic structure of two African-Ecuadorian communities, Rio Cayapas and Viche (Esmeraldas province, northwest Ecuador), was studied on the basis of ACP1, ADA, AK1, CA2, ESD, GLO1, G6PD, PGD, and PGM1 subtypes and thermostability, PGM2, HBbeta, F13A, F13B, ORM1, AHSG, C6, C7, and APOC2 gene frequency, and migration data on 255 individuals. The fixation index of Wright (F(ST)), correspondence, and genetic distance analysis were applied to compare the genetic relationships between these communities and other American populations of African ancestry. F(ST) values from the migration data and surname origins suggest that Rio Cayapas is genetically more isolated and shows less mobility and admixture than does Viche. The genetic admixture estimates indicate a large contribution of African genes to the gene pool of both communities (74.3% to 58.4%), whereas the proportion of the Amerindian component differs significantly (14.5% in Rio Cayapas to 27.6% in Viche).

An investigation of human apolipoproteins B and E polymorphisms in two African populations from Ethiopia and Benin.

Three polymorphisms (XbaI, EcoRI, and Ins/Del) of the apolipoprotein B (APOB) gene and the polymorphism of apolipoprotein E (APOE) were investigated in two population samples of Amhara and Oromo origin from Ethiopia, and in two population samples of Bariba and Berba origin from Benin. No heterogeneity was observed within each major group. The cumulated frequencies of the APOB X+, R+, and D alleles for the Ethiopia and the Benin groups were 0.268 and 0.133, 0.958 and 0.818, 0.206 and 0.223, respectively. Regarding APOE, the cumulated allele frequencies of Ethiopia and Benin were 0.031 and 0.103 for epsilon*2 allele, 0.811 and 0.742 for epsilon*3, and 0.143 and 0.155 for epsilon*4, respectively. APOE typing performed at the protein level only in the Ethiopians revealed a variant allele, epsilon*5, found at the polymorphic level both in the Amhara and in the Oromo (cumulated frequency: 0.015). A tentative explanation for the higher frequencies of epsilon*4 and epsilon*5 alleles was sought in relation to the lifestyle and ethnicity of the two populations. Am. J. Hum. Biol. 11:297-304, 1999. Copyright 1999 Wiley-Liss, Inc.

Biodemography in Siena, Italy.

Data were obtained on surnames of the parents and places of birth of the parents and grandparents of children in Siena, Italy. Isonymy and total inbreeding coefficient, and their random and non-random components, are 0.005, 0.00125, 0.00019 and 0.00106, respectively. Isonymy and inbreeding figures are similar to those of other medium-sized Italian towns, while higher values have been reported for Italian villages and Italian ethnic minorities. City endogamy, and endogamy of Contrada for grandparents have the same values (44.1 and 44.8%, respectively), but for parents, endogamy of Contrada is lower than city endogamy (15.2 and 33.4%, respectively). The difference between the extent of Contrada endogamy expected at random and observed in the parents' generation does not seem to affect the genetic structure of the present population. However, the bulk of marriage migration (more than 70%) is short range, with people coming from Tuscany. There is no statistical difference in marital migration between males and females.

Genetic history of the population of Sicily.

We investigated the genetic heterogeneity of 2354 individuals from the 9 provinces of Sicily. The genetic markers we used were HP, GC, TF, PI, and AK1 plus other previously tested polymorphisms, for a total of 24 independent markers. Distinct multivariate statistics were applied to verify the claimed genetic distinctiveness between extant eastern and western Sicilian populations. Our hypothesis stated that any diversity found between the two subpopulations would represent the signature of early colonization of the island by Greek and Phoenician peoples. Correspondence analysis showed that there was no clear geographic clustering within Sicily. The genetic distance matrix used for identifying the main genetic barriers revealed no east-west differences within the island's population, at least at the provincial level. FST estimates proved that the population subdivision did not affect the pattern of gene frequency variation; this implies that Sicily is effectively one panmictic unit. The bulk of our results confirm the absence of genetic differentiation between eastern and western Sicilians, and thus we reject the hypothesis of the subdivision of an ancient population in two areas.

HLA class II allele and haplotype frequencies in Ethiopian Amhara and Oromo populations.

HLA class II alleles were identified in 181 healthy unrelated Ethiopian children of both sexes and in 350 European controls from the South of France. The Ethiopian individuals belonged to the two major ethnic groups of the country: Oromo (N=83) and Amhara (N=98). In both panels, genetic polymorphism of HLA class II alleles was analysed for the first time by molecular typing of DRB1, DQA1 and DQB1 loci. Allelic and phenotypic frequencies were compared with those of European controls and other African populations. Construction of HLA class II three-locus haplotypes was also performed. The study revealed some differences between the two groups. Characteristic features of Central and North African populations appeared on the Ethiopian HLA genotypes. Surprisingly, DRB1*11 presented one of the lowest gene frequencies in both Ethiopian ethnic groups in contrast to Europeans and West Africans. Furthermore, this decrease was more marked than those observed using serological techniques in other geographically close East African countries. Oromo and Amhara only showed minor differences in spite of their different origins and histories. One significant difference consisted of a lower DRB1*01 gene frequency in Oromo as reported in most West African people. Some new or rare haplotypes were also observed in the Oromo group. Our results underline the distinctive features of the Ethiopian populations among the few HLA genotyping data available for East African groups and emphasise the major interest of such investigations in this region of Africa.