First analysis of ancient burned human skeletal remains probed by neutron and optical vibrational spectroscopy

Burned skeletal remains are abundant in archaeological and paleontological sites, the result of fire or of ancient funerary practices. In the burning process, the bone matrix suffers structural and dimensional changes that interfere with the reliability of available osteometric methods. Recent studies showed that these macroscopic changes are accompanied by microscopic variations are reflected in vibrational spectra. An innovative integrated approach to the study of archaeological combusted skeletal remains is reported here, where the application of complementary vibrational spectroscopic techniques-INS (inelastic neutron scattering), FTIR (Fourier transform infrared), and micro-Raman-enables access to the complete vibrational profile and constitutes the first application of neutron spectroscopy to ancient bones. Comparison with data from modern human bones that were subjected to controlled burning allowed identification of specific heating conditions. This pioneering study provides archaeologists and anthropologists with relevant information on past civilizations, including regarding funerary, burial, and cooking practices and environmental settings.

East of the Andes: The genetic profile of the Peruvian Amazon populations

OBJECTIVES

Assuming that the differences between the Andes and the Amazon rainforest at environmental and historical levels have influenced the distribution patterns of genes, languages, and cultures, the maternal and paternal genetic reconstruction of the Peruvian Amazon populations was used to test the relationships within and between these two extreme environments.

MATERIALS AND METHODS

We analyzed four Peruvian Amazon communities (Ashaninka, Huambisa, Cashibo, and Shipibo) for both Y chromosome (17 STRs and 8 SNPs) and mtDNA data (control region sequences, two diagnostic sites of the coding region, and one INDEL), and we studied their variability against the rest of South America.

RESULTS

We detected a high degree of genetic diversity in the Peruvian Amazon people, both for mtDNA than for Y chromosome, excepting for Cashibo people, who seem to have had no exchanges with their neighbors, in contrast with the others communities. The genetic structure follows the divide between the Andes and the Amazon, but we found a certain degree of gene flow between these two environments, as particularly emerged with the Y chromosome descent cluster's (DCs) analysis.

DISCUSSION

The Peruvian Amazon is home to an array of populations with differential rates of genetic exchanges with their neighbors and with the Andean people, depending on their peculiar demographic histories. We highlighted some successful Y chromosome lineages expansions originated in Peru during the pre-Columbian history which involved both Andeans and Amazon Arawak people, showing that at least a part of the Amazon rainforest did not remain isolated from those exchanges.

16(th) IHIW: population global distribution of killer immunoglobulin-like receptor (KIR) and ligands

In the last fifteen years, published reports have described KIR gene-content frequency distributions in more than 120 populations worldwide. However, there have been limited studies examining these data in aggregate to detect overall patterns of variation at regional and global levels. Here, we present a summary of the collection of KIR gene-content data for 105 worldwide populations collected as part of the 15th and 16th International Histocompatibility and Immunogenetics Workshops, and preliminary results for data analysis.

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.

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.

Immunoglobulin enhancer HS1,2 polymorphism: a new powerful anthropogenetic marker

The human HS1,2 enhancer of the immunoglobulin (Ig) heavy chain 3' enhancer complex plays a central role in the regulation of Ig maturation and production. Four common alleles HS1,2-A*1, *2, *3, *4 are directly implicated with the transcription level and at least one of them, HS1, 2-A*2, seems to be related to immune disorders, such as coeliac disease, herpetiform dermatitis and Berger syndrome. Given their clinical significance it is of interest to know the distribution of HS1,2-A variants in populations from different continents, as well as to determine whether the polymorphism is associated to specific evolutionary factors. In this paper we report the distribution of the HS1,2-A polymorphism in 1098 individuals from various African, Asian and European populations. HS1,2-A*3 and HS1,2-A*4 alleles are at their highest frequencies among Africans, and HS1,2-A*2 is significantly lower in Africans in comparison with both Europeans and, to a lesser extent, Asians. Analysis of molecular variance of the allele frequencies indicates that the HS1,2-A polymorphism can be considered as a reliable anthropogenetic marker.

Increased frequency of the immunoglobulin enhancer HS1,2 allele 2 in coeliac disease

BACKGROUND

Coeliac disease (CD) is characterized by increased immunological responsiveness to ingested gliadin in genetically predisposed individuals. This genetic predisposition is not completely defined. A dysregulation of immunoglobulins (Ig) is present in CD: since antiendomysium antibodies (anti-EMA) are of the IgA class. One polymorphic enhancer within the locus control region (LCR) of the immunoglobulin heavy chain cluster at the 3' of the C alpha-1 gene was investigated. The correlation of the penetrance of the four different alleles of the HS1,2-A enhancer of the LCR-1 3' to C alpha-1 in CD patients compared to a control population was analysed.

METHODS

A total of 115 consecutive CD outpatients, on a gluten-free diet, and 248 healthy donors, age- and sex-matched, from the same geographical area were enrolled in the study. HS1,2-A allele frequencies were investigated by nested polymerase chain reaction (PCR).

RESULTS

The frequency of allele 2 of the enhancer HS1,2-A gene was increased by 30.8% as compared to the control frequency. The frequency of homozygosity for allele 2 was significantly increased in CD patients. Crude odds ratio (OR) showed that those with 2/2 and 2/4 (OR 2.63, P < 0.001 and OR 2.01, P = 0.03) have a significantly higher risk of developing the disease. In contrast, allele 1/2 may represent a protective genetic factor against CD (OR 0.52, P = 0.01).

CONCLUSIONS

These data provide further evidence of a genetic predisposition in CD. Because of the Ig dysregulation in CD, the enhancer HS1,2-A may be involved in the pathogenesis.

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.

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.

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.

DNA analyses of the remains of the Prince Branciforte Barresi family

The five skeletons found buried in the church of Militello di Catania, Sicily, were tentatively identified by morphological analysis and historical reports as the remains of Prince Branciforte Barresi, two of his children, his brother and another juvenile member of the family (sixteenth and seventeenth centuries). In order to attempt to clarify the degree of relationships of the five skeletons, sex testing and mitochondrial DNA (mtDNA) sequence analysis of the hypervariable segments I and II (HV1 and HV2) of control region were performed. Moreover, the 9 bp-deletion marker of region V (COII/tRNAlys) was examined. Molecular genetic analyses were consistent with historical expectations, although they did not directly demonstrate that these are in fact the remains of the Prince and his relatives, due to the impossibility of obtaining DNA from living maternal relatives of the Prince.

Genetic variability and linkage disequilibrium within the HLA-DP region: analysis of 15 different populations

In order to understand the forces governing the evolution of the genetic diversity in the HLA-DP molecule, polymerase chain reaction (PCR)-based methods were used to characterize genetic variation at the DPA1 and DPB1 loci encoding this heterodimer on 2,807 chromosomes from 15 different populations including individuals of African, Asian, Amerindian, Indian and European origin. These ethnically diverse samples represent a variety of population substructures and include small, isolated populations as well as larger, presumably admixed populations. Ten DPA1 and 39 DPB1 alleles were identified and observed on 87 distinct DP haplotypes, 34 of which were found to be in significant positive linkage disequilibrium in at least one population. Some haplotypes were found in all ethnic groups while others were confined to a single ethnic group or population. Strong positive global linkage disequilibrium (Wn) between DPA1 and DPB1 was present in all 15 populations. The African populations displayed the lowest values of Wn whereas the Amerindian populations displayed near absolute disequilibrium. Analysis of the distribution of haplotypes using the normalized deviate of the Ewens-Watterson homozygosity statistic, F, suggests that DP haplotypes encoding the functional heterodimer are subject to much lower degrees of balancing selection than other loci within the HLA region. Finally, neighbor joining tree analyses demonstrate the power of haplotype diversity for inferring the relationships between the different populations.

Combined use of biallelic and microsatellite Y-chromosome polymorphisms to infer affinities among African populations

To define Y-chromosome haplotypes, we studied seven biallelic polymorphic sites. We combined data with those from four dinucleotide-repeat polymorphisms, to establish Y-chromosome compound superhaplotypes. Eight biallelic haplotypes that matched the dendrogram proposed by other investigators were identified in 762 Y chromosomes from 25 African populations. For each biallelic site, coalescence time of lineages carrying the derived allele was estimated and compared with previous estimates. The "ancestral" haplotype (haplotype 1A) was observed among Ethiopians, "Khoisan" (!Kung and Khwe), and populations from northern Cameroon. Microsatellite distributions within this haplotype showed that the Khoisan haplotypes 1A are widely divergent from those of the other two groups. Populations from northern Africa and northern Cameroon share a haplotype (i.e., 1C), which is not observed in other African populations but represents a major Eurasian cluster. Haplotypes 1C of northern Cameroon are clearly distinct from those of Europe, whereas haplotypes 1C of northern African are well intermingled with those of the other two groups. Apportionment of diversity for the Y-chromosomal biallelic haplotypes was calculated after populations were clustered into different configurations. Despite some correspondence between language affiliation and genetic similarity, geographic proximity seems to be a better predictor of genetic affinity.

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).

World distribution of the T833C/844INS68 CBS in cis double mutation: a reliable anthropological marker

Mild hyperhomocysteinemia is associated to mutations either in cystathionine beta-synthase (CBS) or in 5,10-methylenetetrahydrofolate reductase (MTHFR) genes. In 1995, Sebastio et al. characterized a 68 bp insertion in cis with the most common CBS mutation (T833C) detected in homocystinuric patients. Recently, this double mutation has been detected in Italian and North-American controls. Compared to a group of patients affected by coronary artery disease, North-American controls showed not statistically significant difference. Moreover, Italian controls displayed a microheterogeneity in the mutant allele frequency distribution depending on their geographical origin (North or South of Italy). Aim of our study was to evaluate the prevalence of the double in cis mutation in different populations. We studied 377 healthy subjects belonging to various human groups. Genomic DNA, extracted from peripheral blood samples, was amplified using specific primers; PCR fragments were digested with Bsr I restriction enzyme to detect the double mutation. Our data show a significant heterogeneity among the populations studied, therefore this mutation turned out to be a reliable anthropogenetic marker. The distribution of the double mutation will contribute, with other DNA polymorphisms, to evaluate the genetic admixture of mixed populations such as Afro-Americans.

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.

GM and KM allotypes in nine population samples of Sicily

Serum samples of 864 unrelated healthy male and female individuals belonging to nine provinces of Sicily were types for Glm (1,2,3,17), G3m (5,10,11,13,14,15,16,21), and KM (1). With the exception of the Trapani sample these samples are characterized by the presence of five GM haplotypes: GM*1,17;21,26; GM*1,2,17;21,26; GM*1,3;5,10,11,13,14,26; GM*3;5,10,13,14,26; and GM*1,17;10,11,13,15,16. The interpopulation variability in the distribution of these haplotypes is considerable, which is especially due to haplotypes GM*1,3;5,10,11,13,14,26, and GM*3;5,10,13,14,26. However, no clear-cut clustering of the samples according to historical or geographical facts could be shown. Comparisons with other Italian populations reveal the considerable genetic difference of the Sicilians, which is in particular caused by the presence of the haplotypes GM*1,3;5,10,11,13,14,26, and GM*1,17;10,11,13,15,16. These haplotypes are quite uncommon in Europeans and may reflect gene flow from the Middle East. The KM phenotype and allele frequencies also show a considerable interpopulation variability among the nine Sicilian samples, but as for GM no distinction between eastern and western provinces of Sicily is present.

Apolipoprotein B and E genetic polymorphisms in the Cayapa Indians of Ecuador

Three DNA polymorphisms (XbaI, EcoRI, and Ins/Del) of the apolipoprotein B (APOB) gene and the CfoI polymorphism of the APOE gene were investigated in a sample of 96 Cayapa Indians from Ecuador. The frequencies of the X+ (0.182), R+ (1.000), and Del alleles (0.432) at the three APOB sites were found to be higher than and to differ significantly from those reported for East Asians. No comparisons could be made between the Cayapa and other native Americans because of the lack of data on these sites. We observed in our sample that, like native American populations but unlike East Asians, the APOE allele frequencies were characterized by the absence of the APOE*2 allele and by a high frequency of the APOE*4 allele (0.280). Besides a probable drift effect, the high APOE*4 value was tentatively attributed to an effect of selection. Because this allele enhances the absorption of cholesterol by the intestine, it could confer an advantage to carriers in an unfavorable environment (i.e., diet poor in cholesterol).

Prevalence of factor V Leiden mutation in non-European populations

A difference in the prevalence of venous thromboembolism (TE) in major human groups has been described and an uneven distribution of FV Leiden mutation over the world has recently been reported. We investigated FV Leiden mutation in 584 apparently healthy subjects mostly from populations different from those previously investigated: 170 Europeans (Spanish, Italians), 101 sub-saharan Africans (Fon, Bariba, Berba, Dendi), 115 Asians (Indonesians, Chinese, Tharus), 57 Amerindians (Cayapa), 84 Afroamericans (Rio Cayapa, Viche), and 57 Ethiopians (Amhara, Oromo). The mutation was detected in only 1/115 Asian (Tharu) and in 5/170 Europeans (4 Italians, 1 Spanish). These data confirm that in non-Europeans the prevalence of FV mutation is at least 7 times lower than in Europeans and provide indirect evidence of a low prevalence not only of the FV Leiden gene but also of other genes leading to more severe thrombophilia. Finally, findings from the literature together with those pertaining to this study clearly show a marked heterogeneity among Europeans.

Biodemography and genetics of the Berba of Benin

Genetic structure of the Berba of Benin was studied on the basis of biodemographic data and ABO, RH, MNS, KEL, JK, FY, ACP1, ADA, AK1, CA2, ESD, GLO1, G6PD, PGD, PGM1 (subtypes and thermostability), PGM2, PGP, SODA, HB alpha, HB beta, HB delta, BF, C3, and HP gene frequencies. Comparisons were carried out with other populations of Benin and of sub-Saharan Africa. Correspondence analysis revealed genetic differentiation among the three main groups of populations who inhabit sub-Saharan Africa: Bushmen-Hottentots, Pygmies, and Negroes. The genetic differentiation of the Negroes in relation to their linguistic affiliation and geographic localization was evident. The first group included the populations belonging to the Bantoid subfamily of the Nigritic linguistic stock living in southern Africa; in the second subcluster the populations of central-eastern Africa were localized, and the third subcluster included the populations living in the West.

Allele and haplotype frequency distribution of the EcoRI, RsaI, and MspI COL1A2 RFLPs among various human populations

The EcoRI, RsaI, and MspI RFLPs (restriction fragment length polymorphisms) of the COL1A2 gene, one of the two genes that encode for the polypeptides of type I collagen, have been studied in four West African and two Asian populations to evaluate their potential effectiveness as anthropological markers. All three RFLPs were in Hardy-Weinberg equilibrium. The comparisons between present data on two of the major human groups and those on Europeans and Amerindians show a considerable heterogeneity for each of the three RFLPs under study. EcoRI, in particular, appears to be highly effective in distinguishing Africans, Europeans, and Asians from each other. As expected, the analysis at the haplotype level considerably improves the discriminating efficiency of these three markers by creating a clear-cut distinction between Tharus and Indonesians, the two Asian populations of the present survey. In fact, even though these two populations exhibit the same frequencies for the RsaI and MspI alleles, the frequency of the MspI(-) allele among the RsaI(-) chromosomes is 0.5 +/- 0.14 in the Indonesian sample and 0 + 0.04 in the Tharu sample.

Genetic heterogeneity among the Hindus and their relationships with the other "Caucasoid" populations: new data on Punjab-Haryana and Rajasthan Indian states

The genetic structure of Rajasthan Hindus and Punjab-Haryana Hindus and Sikhs has been studied for ABO, RH, APOC2, C6, C7, F13A, F13B, HP, ORM1, ACP1, ADA, AK1, ESD, GLO1, PGD, PGM1 subtyping, and PGP. This is the first genetic survey on Hindus of Rajasthan. Furthermore, many of these markers have never been studied on Hindus before (APOC2, C6, C7, F13A, F13B, ORM1, PGP). These data, together with those previously available for Hindus, have been utilized to analyze the within-Hindus genetic heterogeneity by RST statistic and correspondence analysis. The genetic relationships of Hindus to other Causcasoid populations were also investigated. In the first analysis, two eastern states (Orissa and Andhra Pradesh) were found to be quite separate from each other and clearly distinct from the northwestern and western states. Out of the markers which could not be utilized in this analysis, PGM1 subtyping turned out to discriminate between the Dravidian-speaking and the Indo-Aryan-speaking Hindus. The second analysis shows a clear-cut separation of Hindus from Europeans, with Near Eastern and Middle Eastern populations genetically in an intermediate position.

HLA class II linkage disequilibrium and haplotype evolution in the Cayapa Indians of Ecuador

DNA-based typing of the HLA class II loci in a sample of the Cayapa Indians of Ecuador reveals several lines of evidence that selection has operated to maintain and to diversify the existing level of polymorphism in the class II region. As has been noticed for other Native American groups, the overall level of polymorphism at the DRB1, DQA1, DQB1, and DPB1 loci is reduced relative to that found in other human populations. Nonetheless, the relative evenness in the distribution of allele frequencies at each of the four loci points to the role of balancing selection in the maintenance of the polymorphism. The DQA1 and DQB1 loci, in particular, have near-maximum departures from the neutrality model, which suggests that balancing selection has been especially strong in these cases. Several novel DQA1-DQB1 haplotypes and the discovery of a new DRB1 allele demonstrate an evolutionary tendency favoring the diversification of class II alleles and haplotypes. The recombination interval between the centromeric DPB1 locus and the other class II loci will, in the absence of other forces such as selection, reduce disequilibrium across this region. However, nearly all common alleles were found to be part of DR-DP haplotypes in strong disequilibrium, consistent with the recent action of selection acting on these haplotypes in the Cayapa.

HLA-B alleles of the Cayapa of Ecuador: new B39 and B15 alleles

Recent data suggest that HLA-B locus alleles can evolve quickly in native South American populations. To investigate further this phenomenon of new HLA-B variants among Amerindians, we studied samples from another South American tribe, the Cayapa from Ecuador. We selected individuals for HLA-B molecular typing based upon their HLA class II typing results. Three new variants of HLA-B39 and one new variant of HLA-B15 were found in the Cayapa: HLA-B*3905, HLA-B*3906, HLA-B*3907, and HLA-B*1522. A total of thirteen new HLA-B alleles have now been found in the four South American tribes studied. Each of these four tribes studied, including the Cayapa, had novel alleles that were not found in any of the other tribes, suggesting that many of these new HLA-B alleles may have evolved since the Paleo-Indians originally populated South America. Each of these 13 new alleles contained predicted amino acid replacements that were located in the peptide binding site. These amino acid replacements may affect the sequence motif of the bound peptides, suggesting that these new alleles have been maintained by selection. New allelic variants have been found for all common HLA-B locus antigenic groups present in South American tribes with the exception of B48. In spite of its high frequency in South American tribes, no evidence for variants of B48 has been found in all the Amerindians studied, suggesting that B48 may have unique characteristics among the B locus alleles.

Genetic history of the population of Puglia (southern Italy)

Nine-hundred and twenty-two individuals belonging to the five provinces of Puglia were typed for nine erythrocyte genetic markers (ACP1, ADA, AK1, ESD, GLO1, PGD, PGM1, PGM2, and SODA). Genetic heterogeneity within Puglia was investigated on the basis of allele frequencies of the above mentioned markers plus ABO*A, ABO*B, ABO*O, and RH*D, by the (chi 2 test and Rst statistic. The analyses revealed no differences at the provincial level. Furthermore, correspondence and genetic distance analyses were applied to look for a statistical difference within Puglia from different standpoints, as well as between Puglia, the rest of Italy and other European and Near and Middle Eastern populations whose genetic history is most likely related. Southern and central Italian, Greek and Aegean populations appeared very homogeneous and quite differentiated from the rest of Europe, both continental (including northern Italy) and south-eastern, stressing the major impact of the heavy Greek colonization on the genetic pools of the circum-Mediterranean people.

EcoRI, RsaI, and MspI RFLPs of the COL1A2 gene (type I collagen) in the Cayapa, a Native American population of Ecuador

EcoRI, RsaI, and MspI RFLPs of the COL1A2 gene were analyzed, using the polymerase chain reaction technique, for the first time in a native American population: the Cayapa of Ecuador. These polymorphisms recently turned out to be good anthropological markers, both at the allele and at the haplotype frequency level. These data underline the well-known genetic affinity between the Cayapa and Asian populations. Moreover, our data on DNA polymorphisms agree with the indication of extremely low, if any, gene flow into the Cayapa gene pool from the neighboring black community, as already suggested not only by cultural data but also by protein polymorphisms.

Genetic relationships among the Native American populations

Red cell antigen data were used to investigate the genetic relationship among the Native American populations and their affinities with Siberian and Eastern Asian populations. Correspondence analysis showed a clear subdivision of all the Native American populations into three clear-cut clusters corresponding to the three linguistic families (identified by Greenberg)--Amerind, Na-Dene and Eskimo-Aleut. This result, as well as the close genetic resemblance between the Eskimos and the Asian populations, support the conclusion that the Americas were populated during at least three distinct and subsequent migration waves of people coming from Asia.

Polynesian mitochondrial DNAs reveal three deep maternal lineage clusters

The 4000-year-old human population expansion into Remote Oceania has been studied from a variety of genetic perspectives. Here, we report the discovery that Polynesians, traditionally considered to be a single cohesive linguistic and cultural unit, exhibit at least three distinct mitochondrial DNA (mtDNA) groups that probably shared a common maternal ancestor more than 85,000 years ago. The major lineage groups were first identified by PCR amplification of the mitochondrial region V deletion marker, known to be present at high frequency in Polynesian populations. Sequence analysis of mtDNA hypervariable control regions reveals a surprising number of lineages in Polynesia. We also note high sequence divergence between lineage groups deleted and not deleted in region V. Major group I lineages are common in Remote Oceania and include about 95% of the Native Hawaiian, 90% of the Samoan, and 100% of the Tongan donors in our sample. They contain the region V deletion and generally share three control region transition substitutions. This group also contains non-Polynesian individuals, such as Indonesians, Native Americans, Micronesians, Malaysians, Japanese, and Chinese. The group I Polynesians differ by 4.4% in sequence identity from major lineage group II Polynesians, who do not have the region V deletion and who share among themselves four distinct single-base substitutions. Group II individuals are seen at low frequency (< 10%) in Hawaii, Samoa, and the Cook Islands and may represent the predominant maternal lineage group of Papuan Melanesia. Major lineage group III, not found in Hawaii, tentatively links Samoa to Indonesia. Our observation of deep maternal genetic branches in Polynesia today confirms the notion that during the colonization of the Pacific, mainland Asian immigrants mixed with Melanesian peoples already inhabiting Near Oceania and carried a complex assortment of maternal genotypes derived from two distinct geographic sources to isolated island archipelagoes.

Linkage disequilibrium at the human phosphoglucomutase 1 locus

By considering the four common PGM1 alleles as haplotypes, that is, combinations of mutations at two polymorphic intragenic sites (1/2 and A/B), we investigated the levels of linkage disequilibrium in 142 human population samples. These groups showed considerable diversity in their disequilibrium (Drel) and heterogeneity. In all the populations the disequilibrium was found to be due to an excess of 1A and 2B haplotypes, although this direction is the opposite of that expected according to the proposed phylogeny of the system. Natural selection could be one of the major causes for such a disequilibrium direction.

Analysis of HLA class II haplotypes in the Cayapa Indians of Ecuador: a novel DRB1 allele reveals evidence for convergent evolution and balancing selection at position 86

PCR amplification, oligonucleotide probe typing, and sequencing were used to analyze the HLA class II loci (DRB1, DQA1, DQB1, and DPB1) of an isolated South Amerindian tribe. Here we report HLA class II variation, including the identification of a new DRB1 allele, several novel DR/DQ haplotypes, and an unusual distribution of DPB1 alleles, among the Cayapa Indians (N = 100) of Ecuador. A general reduction of HLA class II allelic variation in the Cayapa is consistent with a population bottle-neck during the colonization of the Americas. The new Cayapa DRB1 allele, DRB1*08042, which arose by a G-->T point mutation in the parental DRB1*0802, contains a novel Val codon (GTT) at position 86. The generation of DRB1*08042 (Val-86) from DRB1*0802 (Gly-86) in the Cayapa, by a different mechanism than the (GT-->TG) change in the creation of DRB1*08041 (Val-86) from DRB1*0802 in Africa, implicates selection in the convergent evolution of position 86 DR beta variants. The DRB1*08042 allele has not been found in > 1,800 Amerindian haplotypes and thus presumably arose after the Cayapa separated from other South American Amerindians. Selection pressure for increased haplotype diversity can be inferred in the generation and maintenance of three new DRB1*08042 haplotypes and several novel DR/DQ haplotypes in this population. The DPB1 allelic distribution in the Cayapa is also extraordinary, with two alleles, DPB1*1401, a very rare allele in North American Amerindian populations, and DPB1*0402, the most common Amerindian DPB1 allele, constituting 89% of the Cayapa DPB1.(ABSTRACT TRUNCATED AT 250 WORDS)

Genetic characterization of the Cayapa Indians of Ecuador and their genetic relationships to other Native American populations

One-hundred sixty-four Cayapa Indians living in the Esmeraldas Province (northwest Ecuador) were studied for several erythrocyte genetic markers (ACP1, ADA, AK1, CA2, ESD, GLO1, G6PD, PGD, PGM1 subtyping and thermostability, PGM2, SODA, and HB). The Cayapa show allele frequencies typical of those of South American Indians. The absence of the CA2*2, G6PD*A, G6PD*A-, HBB*S, and HBB*C alleles and the low PGM1*1A and PGM1*2A and high PGM1*1B allele frequencies indicate that very little (no more than 2%), if any, genetic admixture has occurred with the black community living in the same area. Correspondence analysis was used to study the genetic relationships between the Cayapa and other linguistically defined Amerind populations and between the Amerinds and the other two native American groups, the Na-Dene and Eskimo-Aleut. The results of this analysis, obtained on the basis of some erythrocyte and serum markers and some blood group systems, show (1) the close affinity between the Cayapa and other South American populations, (2) the absence in the Amerind group of a clear-cut correspondence between linguistic classification and genetic relatedness, and (3) the evident distinctiveness of the Amerinds from other native American people.

The Cayapa Indians of Ecuador: a population study of seven protein genetic polymorphisms

The Cayapa Indians are a population of 3600 individuals living in Ecuador, along the Cayapas River and its tributaries. They are thought to have migrated from the Andes, north of Quito, and settled in the Cayapas area five centuries ago as a consequence of Inca expansion and of the Spanish conquest. In order to study the genetic structure of the Cayapa and their relationships with other native American peoples, and to enquire on the possibility of admixture from nearby Black communities, we have investigated a sample of 139 individuals for seven plasma genetic markers (F13A, F13B, ORM1, AHSG, C6, C7 and APOC2) by isoelectric focusing and immunoblotting. The following gene frequencies have been found: F13A*1 = 0.824, F13A*2 = 0.176; F13B*1 = 0.126, F13B*3 = 0.874; ORM1*1 = 0.554, ORM1*2 = 0.446; AHSG*1 = 0.275, AHSG*2 = 0.725; C6*A = 0.131, C6*B = 0.814, C6*A21 = 0.055; C7*1 = 1.000; APOC2*1 = 1.000. The findings confirm, whenever the comparison was possible, quite a good resemblance of the Cayapa with other Native American populations.

Survey of seven plasma protein polymorphisms in the Amhara and Oromo populations of Ethiopia

The Ethiopian population is very difficult to specify due to a very high degree of intermixing among different peoples. The two groups of the present study, the Amhara and Oromo, constitute 38% and 35% of the population, respectively. In order to investigate the genetic composition of the Amhara and Oromo, genetic polymorphisms of seven plasma proteins (F13A, F13B, ORM1, AHSG, C6, C7, and APOC2), already identified as useful anthropological markers, were studied. No statistically relevant differences were found between the two groups for all of the systems examined. ORM1 and F13A showed frequencies in the range observed in other populations of Caucasoid and Negroid origin. F13B, AHSG, and C6 displayed gene frequencies and a number of variant alleles that seem particular to these two groups. No variation was observed for C7 and APOC2. Correspondence and distance analyses were used to interpret and compare the gene frequencies of the Amhara and Oromo with those of other related populations. These methods locate Ethiopians in an intermediate position between African Blacks and a group of Caucasoid populations, confirming cultural and historical data. © 1994 Wiley-Liss, Inc.

Marriage distances among the Afroamericans of Bluefields, Nicaragua

In a sample of 311 couples from the Afroamerican community of Bluefields, Eastern Nicaragua, the distribution of matrimonial distance shows a deviation from the leptokurtic rule. This results from assortative mating among the population.

Investigations on the variability of four genetic serum protein markers (HP; TF, GC and PI subtypes) in Italy

14 population samples from various Italian regions with a total of 2.577 unrelated male and female individuals were typed for four polymorphic serum protein polymorphisms: HP, and TF, GC and PI subtypes. The regional distribution of the allele frequencies of these four polymorphisms shows a considerable heterogeneity, which is for the most part statistically significant, thus indicating an obvious genetic variability of the population of the Italian Peninsula.

Genetic structure of the population of Sicily

Genetic heterogeneity within Sicily was investigated on the basis of ACP1, ADA, ESD, GLO1, PGD, PGM1, PGM2, SODA, ABO, and MN gene frequencies, and compared to those of other regions of Italy for which these same loci have been examined. Correspondence analysis revealed no differences within the island, at least at the provincial level, but showed genetic differentiation among Italian regions, distinctly clustering northern, central, and southern populations, respectively. These data indicate a close relationship between Sicily and southern Italy. In addition, the contribution of Middle Eastern populations to the gene pool of Sicily was evident.

A survey of six genetic markers on the populations of Punjab and Rajasthan (India)

190 Punjabis (Hindus and Sikhs) of Chandigarh and 152 Hindus of Jodhpur (Rajasthan) were examined for six genetic markers, four of which (APO C-II, C6, C7 and FXIIIA) were not studied before in Asiatic Indians. For APO C-II and C7 only the common phenotype was found in a total of 229 and 99 subjects, respectively. For the remaining four markers the two samples were pooled since the gene frequency estimates were not significantly different: FXIIIA*2 = 0.205 +/- 0.016; C6*B = 0.366 +/- 0.037; PGM1*2 = 0.247 +/- 0.017; PGD*C = 0.041 +/- 0.008. These data may contribute to evaluate the extent of the Mongoloid genetic admixture into the Caucasoid gene pool of the Punjab and Rajasthan Hindu population.

ESD, GLO1, PGD, PGM1 and PGM2 gene frequencies in the Salerno Province (Italy)

Esterase D (ESD), glyoxalase 1 (GLO1), phosphogluconate dehydrogenase (PGD) and phosphoglucomutase 1 and 2 (PGM1 and PGM2) systems have been studied in the Salerno province (Campania, Southern Italy). The mean weighted frequencies for the Campania region were calculated. These frequencies show a general similarity to those reported for the other Italian regions.

Genetic polymorphisms in the Croatian ethno-linguistic minority of Italy

Phenotype and gene frequencies of twelve genetic markers (ABO, RH, MNS, ACP1, ESD, PGD, PGM1, PGM2, HB, ALB, CP and HP) of the three Croatian communities (Acquaviva Collecroce, Montemitro and S. Felice del Molise) living in Southern Italy are reported. From the comparison with the surrounding Italian population and with Balkan populations, some instances of still incomplete genetic admixture can be inferred (ABO*A and O, ESD, PGD and PGM1).

Red-cell enzyme polymorphisms in the Reggio Calabria province (Italy)

Acid phosphatase (ACP1), adenosine deaminase (ADA), esterase D (ESD), glyoxalase 1 (GLO1), phosphogluconate dehydrogenase (PGD) and phosphoglucomutase 1 and 2 (PGM1 and PGM2) polymorphisms have been studied in the Reggio Calabria province (Southern Italy). The ACP1*A allele and ADA, GLO1, PGD and PGM1 systems have frequencies similar to those reported for Sicily and Southern Italy.

Migration pattern and genetic marker distribution of the Afro-American population of Bluefields, Nicaragua

On a sample of the population of mixed African ancestry living in Bluefields, Nicaragua, the pattern of migration and the distribution of red cell and serum genetic markers have been studied. It is concluded that, in spite of a considerable level of internal and external migration, a distinctive genetic structure is maintained by the population. Moreover, a strongly negative assortative mating can be observed between people inhabiting the western and eastern areas of Nicaragua. It is estimated that most, if not all, of the genetic pool of the population is accounted for by a process of admixture between African and Indian peoples.

Red cell polymorphisms in Sardinia

Acid phosphatase (ACP1), esterase D (ESD) and phosphoglucomutase 1 (PGM1) polymorphisms have been studied in Sardinia and the following gene frequencies have been found: ACP1*A = 0.235, ACP1*B = 0.684 and ACP1*C = 0.081; ESD*2 = 0.118 and PGM1*2 = 0.233. These findings confirm the genetic uniqueness of Sardinians compared to the other Italian and European populations.

Genetic study of the haptoglobin polymorphism in Italy: I. Bari and Genoa provinces

A random sample of 686 unrelated subjects from Bari (Southern Italy) and Genoa (Northern Italy) provinces was studied for HP polymorphism. The correlation between the HP*1 frequencies and geographical coordinates was studied for the populations of Italy, Europe, Middle East and Mediterranean basin. The results reveal the existence of a gradient of declining HP*1 frequencies from north-west to south-east across Europe and the Middle East.

On the variability of Gc subtypes in Italy

909 individuals from different places of Italy were analyzed for the distribution of Gc subtypes. The observed heterogeneity in the distribution of the allele frequencies was found to be statistically significant. Comparing our results with those reported by other authors it is seen that within Italy a considerable regional variation in the frequencies of the Gc subtype alleles is present. However, there are no indications for any particular distribution patterns or gradients. In one of our samples (Bari district), one case of Gc 1S-1C3 was found.

Some erythrocyte polymorphisms in Bari and its district (South Italy)

Seven erythrocyte polymorphisms, namely AcP, PGM1, PGM2, EsD, GLO I, G-6-PD and Hb, have been typed in 556 unrelated adult male subjects from Bari (South Italy) and its district. The gene frequencies obtained in this sample are compared with the hitherto reported corresponding data from other Italian population samples. The results are critically discussed.

Characterization of a rare allele of the phosphoglucomutase locus 1 (PGM81) in an Italian family by isoelectric focusing

A rare phenotype at the phosphoglucomutase locus 1 with an electrophoretic mobility similar to that of PGM1 8-1 was found in an Italian family. The study of this variant was performed by isoelectric focusing on polyacrylamide gel. Also the isoelectric point of the PGM81 gene product was determined.

An anthropobiological study in Basse Kotto (Central Africa). I. Erythrocyte and sero-genetic markers: an analysis of the genetic differentiation

Phenotype and allele frequencies for hemoglobin types (Hb beta), acid phosphatase (AcP), phosphoglucomutase (PGM1 and PGM2), esterase D (EsD), 6-phosphogluconate dehydrogenase (6-PGD), glyoxalase I (GLO), superoxide dismutase (SOD A), and adenylate kinase (AK) as well as for haptoglobins (Hp), group-specific component (Gc), transferrin (Tf), Gm, and Inv groups and albumin, are reported in the Mbugu, Sango, Yakpa, and Baya Mandja ethnic groups in the Basse Kotto district of the Central African Republic. The total sample size amounts to 133 males and 128 females aged from 16 to 60, unrelated and healthy. A new albumin variant (albumin Mbugu) is described and discussed. The average heterozygosity is high in each group because of a high degree of exogamy. the FST average standardized value among the four groups indicates that the genetic differentiation in Basse Kotto is at level of about 2%. This indicates that the four examined groups might be considered genetically homogeneous, in spite of their different ethnic origins. The genetic distances among the four groups show that only the Baya Mandja are less closely related to the other three groups because of their foreign origin.