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.

Methodology for Y Chromosome Capture: A complete genome sequence of Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads.

This study is a comparison of the efficiency of three technologies used for Y chromosome capture and the next-generation sequencing (NGS) technologies applied for determining its whole sequence. Our main findings disclose that streptavidin-biotin magnetic particle-based capture methodology offers better and a deeper sequence coverage for Y chromosome capture, compared to chromosome sorting and microdissection procedures. Moreover, this methodology is less time consuming and the most selective for capturing only Y chromosomal material, in contrast with other methodologies that result in considerable background material from other, non-targeted chromosomes. NGS results compared between two platforms, NextSeq 500 and SOLID 5500xl, produce the same coverage results. This is the first study to explore a methodological comparison of Y chromosome capture and genetic analysis. Our results indicate an improved strategy for Y chromosome research with applications in several scientific fields where this chromosome plays an important role, such as forensics, medical sciences, molecular anthropology and cancer sciences.

Characterisation of genetic structure of the Mayan population in Guatemala by autosomal STR analysis.

BACKGROUND: Currently, the Guatemalan population comprises genetically isolated groups due to geographic, linguistic and cultural factors. For example, Mayan groups within the Guatemala population have preserved their own language, culture and religion. These practices have limited genetic admixture and have maintained the genetic identity of Mayan populations. AIM: This study is designed to define the genetic structure of the Mayan-Guatemalan groups Kaqchiquel, K'iche', Mam and Q'eqchi' through autosomal short tandem repeat (STR) polymorphisms and to analyse the genetic relationships between them and with other Mayan groups. SUBJECTS AND METHODS: Fifteen STR polymorphisms were analysed in 200 unrelated donors belonging to the Kaqchiquel (n = 50), K'iche' (n = 50), Mam (n = 50) and Q'eqchi' (n = 50) groups living in Guatemala. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between population groups. RESULTS: Within the Mayan population, the STRs D18S51 and FGA were the most informative markers and TH01 was the least informative. AMOVA and genetic distance analyses showed that the Guatemalan-Native American populations are highly similar to Mayan populations living in Mexico. CONCLUSIONS: The Mayan populations from Guatemala and other Native American groups display high genetic homogeneity. Genetic relationships between these groups are more affected by cultural and linguistic factors than geographical and local flow. This study represents one of the first steps in understanding Mayan-Guatemalan populations, the associations between their sub-populations and differences in gene diversity with other populations. This article also demonstrates that the Mestizo population shares most of its ancestral genetic components with the Guatemala Mayan populations.

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.

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.

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.

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.

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.

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.

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.

Variability of six STR loci in populations from Central Spain.

Allele frequency distributions of six short tandem repeat (STR) loci, HUMTH01, HUMFES/FPS, HUMTPOX, HUMVWF/A31, HUMF13B, and HUMLPL, were determined in a population (101 individuals) of the Vera-Jerte region in West Central Spain. Amplified products were electrophoresed on denaturing polyacrylamide gels and silver-stained. The exact test demonstrated that none of the six loci deviated from Hardy-Weinberg equilibrium. R-matrix analysis in relation to other European samples agrees well with genetic distance results of Reynolds et al. (1983). Comparisons show that our population comes reasonably well within the range of variation of other European samples, and that the representation of these samples on the genetic map indicates a close relation between geographical location and distribution in the diagram.

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).

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.

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.

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.

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.