[Show abstract][Hide abstract] ABSTRACT: Abstract Background: Archaeological bones contain only small amounts of DNA due to post-mortem DNA degradation and the changes endogenous DNA is subjected to during diagenesis. An important step before undertaking such time-consuming and costly analyses as ancient DNA investigation is to predict the presence of DNA in ancient samples. To date, the leading screening method has been amino acid racemization; however, other analytical techniques can also be used to assess the degree of bone preservation. Aim: The aim of the present study was to relate the presence of DNA with bone preservation in order to select samples potentially suitable for ancient DNA analysis. Subjects and methods: Bones collected from several archaeological sites, different locations (cave, rockshelter or sub divo) and diachronic periods were selected for analytical and spectroscopic analysis in order to correlate bone tissue preservation with the presence of DNA. Different techniques were combined to assess the degree of preservation of organic and inorganic components. Results: As determined by different analytical methods, preservation of the inorganic component was best associated with the presence of DNA. Conclusion: Evaluation of the bone preservation state may be an efficient step to predict the presence of DNA in ancient samples prior to aDNA analysis.
Annals of Human Biology 09/2014; · 1.48 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The frequencies of HLA-A, HLA-B and HLA-DRB1 alleles in 118 unrelated Libyans from Benghazi (Cyrenaica) were analyzed using high resolution typing and compared with other populations. Their relatedness has been tested by correspondence analyses and principal component analysis. The most frequent HLA-A alleles were A∗02:01:01:01 (15.7%), A∗01:01:01:01 (11.4%) and A∗03:01:01:01 (9.3%). For the HLA-B locus, the commonest allele was HLA-B∗50:01:01 (14.4%) followed by B∗51:01:01 (9.8%) and B∗08:01:01 (6.4%). For the HLA-DRB1 locus, the commonest was HLA-DRB1∗07:01:01:01(16.9%) followed by DRB1∗03:01:01:01 (13.6%) and DRB1∗13:02:01 (9.3%). The most frequent two-locus haplotypes were HLA-A∗02:01:01:01-B∗07:02:01 (3.0%) and HLA-B∗50:01:01-DRB1∗07:01:01:01 (9.6%), and three-locus haplotypes were HLA-A∗02:01:01:01-B∗50:01:01-DRB1∗07:01:01:01 (4.2%) and HLA-A∗11:01:01-B∗52:01:01:01-DRB1∗15:02:01 (2.5%). This study is the first on the HLA status of a Libyan population. The results, when compared to similar HLA data obtained previously from African and Mediterranean populations, indicate genetic influences from several ethnic groups. Moreover, the differences in the HLA allele frequencies between the Libyan population and others reveals that significant admixture has occurred between the original Berber inhabitants and neighbouring and more distant populations, even though a strong genetic Berber substratum remains. These data will be of value to future anthropological and disease association studies involving the Libyan population.
[Show abstract][Hide abstract] ABSTRACT: We recently presented the case of a first century AD young woman, found in the archaeological site of Cosa, showing clinical signs of malnutrition, such as short height, osteoporosis, dental enamel hypoplasia and cribra orbitalia, indirect sign of anemia, all strongly suggestive for celiac disease (CD). However, whether these findings were actually associated to CD was not shown based on genetic parameters. To investigate her human leukocyte antigen (HLA) class II polymorphism, we extracted DNA from a bone sample and a tooth and genotyped HLA using three HLA-tagging single nucleotide polymorphisms for DQ8, DQ2.2 and DQ2.5, specifically associated to CD. She displayed HLA DQ 2.5, the haplotype associated to the highest risk of CD. This is the first report showing the presence of a HLA haplotype compatible for CD in archaeological specimens.
World Journal of Gastroenterology 10/2012; 18(37):5300-4. · 2.55 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: According to most historians, Christopher Columbus was born in Genoa, Italy. However, based on some key facts in the discoverer's biography, as well as in the linguistic analysis of his texts, some historians and linguists believe that Columbus could have been of Catalan origin. A Ligurian Columbus would have carried the Colombo surname, whereas he would have been called Colom if he were Catalan. In order to test whether it would be possible to discriminate between a Ligurian or a Catalan origin were Columbus' Y-chromosome haplotype to be retrieved, we genotyped 17 Y-chromosome STRs in 238 Spanish (from Catalonia, Valencia, and the Balearic Islands) and French Colom men, and 114 North Italian Colombo (from Liguria, Lombardy, and Piedmont). The Italian samples and, in particular, the Lombard Colombos were genetically as diverse as the general population, and we found little evidence of clusters of haplotypes that could indicate descent from a single founder. Colombo is actually the most frequent surname in Lombardy, where foundlings and orphans used to be given the surname Colombo. By contrast, Y-chromosome diversity was reduced in the Iberian Colom, where most of the men had Y chromosomes belonging to a few lineages. This implies that a positive identification would be more likely if Columbus were of Catalan descent. In this study, we have shown the diverse dynamics of two surnames linked by their etymology, in what is, to the best of our knowledge, the first genetic analysis of a surname in Southern Europe.
European journal of human genetics: EJHG 08/2011; 20(2):211-6. · 3.56 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In this study, a sample of 225 Guatemalan males, comprising 115 Mestizo-Guatemalan and 110 Mayan-Guatemalan, was typed for 17 Y-short tandem repeats (STRs) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385a/b). The haplotype diversity (H=1) and discrimination capacity (96.86%) were calculated. Analysis of molecular variance (AMOVA) demonstrated a low but significant interpopulation differentiation when compared with the results obtained when we confront the Mestizo and Mayan populations with the European populations. Furthermore, the genetic variability and differences among the American, African, Asian, and European populations were analyzed with the software Statistica 9.1. In addition, the genetic distances were also calculated using other published data. Reynolds and Slatkińs genetic distance was visualized using the multidimensional scaling (MDS) analysis. All the analysis performed locates the Mayan population next to the Native American population, while Guatemalan-Mestizo population was found to be between these populations and the European population, similar to other Mestizo one. The implementation of the estimation of individual ancestry proportions of the whole population sample showed the presence of two well-differentiated population groups.
[Show abstract][Hide abstract] ABSTRACT: Glutathione S-transferases (GSTs) are a superfamily of detoxificant enzymes. Pharmacogenomic studies have revealed interethnic differences in GST allelic frequencies. This study is focused on GSTT1 (gene deletion, rs17850155, rs2234953, and rs11550605) and GSTM1 (gene deletion) gene frequency distributions in two population samples of Europe origin (Italy, n = 120; Spain, n = 94) and two population samples of Africa origin (Cameroon, n = 126; Ethiopia, n = 153). Detection of GSTT1 and GSTM1 null genotypes was performed by multiplex PCR analysis, while the other GSTT1 gene polymorphisms were detected using allele specific PCR and sequencing. GSTT1 and GSTM1 null frequencies in the samples analyzed fit with the variability range observed in European and African populations, respectively. The SNP analysis in GSTT1 gene did not highlight any nucleotide substitution in 493 individuals analyzed. The comparisons among GSTM1 and GSTT1 null phenotype frequencies in worldwide populations show different patterns between Asians, Africans, and Europeans. Important insights into the effects of GSTM1 and GSTT1 gene deletions on the pathogenesis of human diseases have been hypothesized. Detailed studies on the geography of GST variants could therefore increase knowledge about the relationship between ethnicity and the prevalence of certain diseases.
[Show abstract][Hide abstract] ABSTRACT: Recent genetic studies of the Tuareg have begun to uncover the origin of this semi-nomadic northwest African people and their relationship with African populations. For centuries they were caravan traders plying the trade routes between the Mediterranean coast and south-Saharan Africa. Their origin most likely coincides with the fall of the Garamantes who inhabited the Fezzan (Libya) between the 1st millennium BC and the 5th century AD. In this study we report novel data on the Y-chromosome variation in the Libyan Tuareg from Al Awaynat and Tahala, two villages in Fezzan, whose maternal genetic pool was previously characterized. High-resolution investigation of 37 Y-chromosome STR loci and analysis of 35 bi-allelic markers in 47 individuals revealed a predominant northwest African component (E-M81, haplogroup E1b1b1b) which likely originated in the second half of the Holocene in the same ancestral population that contributed to the maternal pool of the Libyan Tuareg. A significant paternal contribution from south-Saharan Africa (E-U175, haplogroup E1b1a8) was also detected, which may likely be due to recent secondary introduction, possibly through slavery practices or fusion between different tribal groups. The difference in haplogroup composition between the villages of Al Awaynat and Tahala suggests that founder effects and drift played a significant role in shaping the genetic pool of the Libyan Tuareg.
American Journal of Physical Anthropology 02/2011; 145(1):118-24. · 2.48 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Stable isotope analysis of carbon (δ13C), nitrogen (δ15N) and sulphur (δ34S) were carried out on one of the largest assemblages of Late Upper Palaeolithic human remains in Southern Europe, at Grotta del Romito (Cosenza), Italy. The burials were stratigraphically dated from ca. 18,000 to 13,000 cal BP, which was confirmed by a series of new AMS dates made directly on the bone collagen. Dietary reconstruction from carbon and nitrogen stable isotopes revealed that eight of the nine individuals analysed, dating to the Final Epigravettian, had very consistent diets, rich in terrestrial animal protein, regardless of their age or sex. These included two individuals who were suffering from severe pathologies. A single individual, dating to the Evolved Epigravettian had a more variable diet, which was significantly enriched in protein from marine or freshwater fish compared to the later burials. Overall, the results are consistent with the very limited number of other studies which describe a change to more specialised and less variable subsistence strategies, in this case the hunting of large herbivores, towards the end of the Palaeolithic period. Sulphur isotope values of all of the nine burials and several faunal samples were notably consistent, showing no evidence of long-distance migration to the site from a different geological zone.
[Show abstract][Hide abstract] ABSTRACT: The Tuareg of the Fezzan region (Libya) are characterized by an extremely high frequency (61%) of haplogroup H1, a mitochondrial DNA (mtDNA) haplogroup that is common in all Western European populations. To define how and when H1 spread from Europe to North Africa up to the Central Sahara, in Fezzan, we investigated the complete mitochondrial genomes of eleven Libyan Tuareg belonging to H1. Coalescence time estimates suggest an arrival of the European H1 mtDNAs at about 8,000-9,000 years ago, while phylogenetic analyses reveal three novel H1 branches, termed H1v, H1w and H1x, which appear to be specific for North African populations, but whose frequencies can be extremely different even in relatively close Tuareg villages. Overall, these findings support the scenario of an arrival of haplogroup H1 in North Africa from Iberia at the beginning of the Holocene, as a consequence of the improvement in climate conditions after the Younger Dryas cold snap, followed by in situ formation of local H1 sub-haplogroups. This process of autochthonous differentiation continues in the Libyan Tuareg who, probably due to isolation and recent founder events, are characterized by village-specific maternal mtDNA lineages.
PLoS ONE 01/2010; 5(10):e13378. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Several studies have demonstrated a link between cardiovascular disease (CVD) susceptibility and the genetic background of populations. Endothelial activation and dysfunction induced by oxidized low-density lipoprotein (ox-LDL) is one of the key steps in the initiation of atherosclerosis. The oxidized low density lipoprotein (lectin-like) receptor 1 (OLR1) gene is the main receptor of ox-LDL. We have previously characterized two polymorphisms (rs3736235 and rs11053646) associated with the risk for coronary artery disease (CAD) and acute myocardial infarction (AMI).
Given their clinical significance, it is of interest to know the distribution of these variants in populations from different continents.
A total of 1229 individuals from 17 different African, Asian and European populations was genotyped for the two considered markers.
The high frequencies of ancestral alleles in South-Saharan populations is concordant with the African origin of our species. The results highlight that African populations are closer to Asians, and clearly separated from the Europeans.
The results confirm significant genetic structuring among populations and suggest a possible basis for varying susceptibility to CVD among groups correlated with the geographical location of populations linked with the migrations out of Africa, or with different lifestyle.
Annals of Human Biology 12/2009; 37(2):136-48. · 1.48 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Since prehistoric times Southern Italy has been a cultural crossroads of the Mediterranean basin. Genetic data on the peoples of Basilicata and Calabria are scarce and, particularly, no records on mtDNA variability have been published.
In this study mtDNA haplotypes of populations from Basilicata, Calabria and Sicily are compared with those of other Italian and Mediterranean populations, so as to investigate their genetic relationships.
A total of 341 individuals was analysed for mtDNA in order to provide their classification into haplogroups. Multivariate analysis was used to compare the studied populations with other Mediterranean samples; median-joining network analysis was applied to observe the relationship between the major lineages of the Southern Italians.
The haplogroup distribution in the Southern Italian samples falls within the typical pattern of mtDNA variability of Western Eurasia. The comparison with other Mediterranean countries showed a substantial homogeneity of the area, which is probably related to the historic contact through the Mediterranean Sea.
The mtDNA analysis demonstrated that Southern Italy displays a typical pattern of Mediterranean basin variability, even though it appears plausible that Southern Italy was less affected by the effects of the Late Glacial Maximum, which reduced genetic diversity in Europe.
Annals of Human Biology 10/2009; 36(6):785-811. · 1.48 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Tuaregs are a semi-nomadic pastoralist people of northwest Africa. Their origins are still a matter of debate due to the scarcity of genetic and historical data. Here we report the first data on the mitochondrial DNA (mtDNA) genetic characterization of a Tuareg sample from Fezzan (Libyan Sahara). A total of 129 individuals from two villages in the Acacus region were genetically analysed. Both the hypervariable regions and the coding region of mtDNA were investigated. Phylogeographic investigation was carried out in order to reconstruct human migratory shifts in central Sahara, and to shed light on the origin of the Libyan Tuaregs. Our results clearly show low genetic diversity in the sample, possibly due to genetic drift and founder effect associated with the separation of Libyan Tuaregs from an ancestral population. Furthermore, the maternal genetic pool of the Libyan Tuaregs is characterized by a major "European" component shared with the Berbers that could be traced to the Iberian Peninsula, as well as a minor 'south Saharan' contribution possibly linked to both Eastern African and Near Eastern populations.
Annals of Human Genetics 08/2009; 73(Pt 4):438-48. · 2.22 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Restriction fragment length polymorphisms (RFLPs) of the COL1A2 and CYP1A1 and short tandem repeats of HS1,2 Ig enhancer genes are proving to be useful markers for describing human populations and thus are of interest for anthropogenetic research. Moreover, they can provide useful information in identifying alleles and haplotypes associated with particular forms of common diseases or for pharmacogenomics studies.
The objective of this study was to define the genetic structure of Libyan Tuaregs and to establish the degree of genetic homogeneity amongst the El Awaynat and Tahala groups.
Tuareg individuals from El Awaynat (n = 99) and Tahala (n = 18), in Libyan Sahara, were analysed for the RFLPs of COL1A2 and CYP1A1 and short tandem repeats of HS1,2 Ig enhancer genes. In order to provide a clearer picture of COL1A2, CYP1A1 and HS1,2 Ig enhancer allele and haplotype frequency distributions in various human groups distributed over a wide geographic area, comparisons with other African, European and Asian populations were carried out by analysis of molecular variance (AMOVA) and genetic distance analysis.
No significant level of differentiation was evident between the two Libyan Tuareg groups according to AMOVA. For the CYP1A1 gene, a possible new haplotype was observed, even though at a very low frequency. Linkage disequilibrium was assessed only for COL1A2, since CYP1A1 turned out to be poorly polymorphic for m2 and m3.
Statistical analyses showed that Tuaregs from Libya are located in a intermediate position between south Saharan populations on one side and the Europeans and the Asians on the other.
Annals of Human Biology 07/2009; 34(4):425-36. · 1.48 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Here we report on a stable isotope palaeodietary study of a Imperial Roman population interred near the port of Velia in Southern Italy during the 1st and 2nd centuries AD. Carbon and nitrogen stable isotope analyses were performed on collagen extracted from 117 adult humans as well as a range of fauna to reconstruct individual dietary histories. For the majority of individuals, we found that stable isotope data were consistent with a diet high in cereals, with relatively modest contributions of meat and only minor contributions of marine fish. However, substantial isotopic variation was found within the population, indicating that diets were not uniform. We suggest that a number of individuals, mainly but not exclusively males, had greater access to marine resources, especially high trophic level fish. However, the observed dietary variation did not correlate with burial type, number of grave goods, nor age at death. Also, individuals buried at the necropolis at Velia ate much less fish overall compared with the contemporaneous population from the necropolis of Portus at Isola Sacra, located on the coast close to Rome. Marine and riverine transport and commerce dominated the economy of Portus, and its people were in a position to supplement their own stocks of fish with imported goods in transit to Rome, whereas at Velia marine exploitation existed side-by-side with land-based economic activities.
American Journal of Physical Anthropology 04/2009; 139(4):572-83. · 2.48 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Ancestry informative markers (AIMs) are human polymorphisms that exhibit substantially allele frequency differences among populations. These markers can be useful to provide information about ancestry of samples which may be useful in predicting a perpetrator's ethnic origin to aid criminal investigations. Variations in human pigmentation are the most obvious phenotypes to distinguish individuals. It has been recently shown that the variation of a G in an A allele of the coding single-nucleotide polymorphism (SNP) rs1426654 within SLC24A5 gene varies in frequency among several population samples according to skin pigmentation. Because of these observations, the SLC24A5 locus has been evaluated as Ancestry Informative Region (AIR) by typing rs1426654 together with two additional intragenic markers (rs2555364 and rs16960620) in 471 unrelated individuals originating from three different continents (Africa, Asia and Europe). This study further supports the role of human SLC24A5 gene in skin pigmentation suggesting that variations in SLC24A5 haplotypes can correlate with human migration and ancestry. Furthermore, our data do reveal the utility of haplotype and combined unphased genotype analysis of SLC24A5 in predicting ancestry and provide a good example of usefulness of genetic characterization of larger regions, in addition to single polymorphisms, as candidates for population-specific sweeps in the ancestral population.
Current Genomics 05/2008; 9(2):110-4. · 2.48 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: 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.
Molecular Human Reproduction 09/2007; 13(8):537-40. · 4.54 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Mitochondrial and Y-chromosome DNA were analyzed from 10,300-year-old human remains excavated from On Your Knees Cave on Prince of Wales Island, Alaska (Site 49-PET-408). This individual's mitochondrial DNA (mtDNA) represents the founder haplotype of an additional subhaplogroup of haplogroup D that was brought to the Americas, demonstrating that widely held assumptions about the genetic composition of the earliest Americans are incorrect. The amount of diversity that has accumulated in the subhaplogroup over the past 10,300 years suggests that previous calibrations of the mtDNA clock may have underestimated the rate of molecular evolution. If substantiated, the dates of events based on these previous estimates are too old, which may explain the discordance between inferences based on genetic and archaeological evidence regarding the timing of the settlement of the Americas. In addition, this individual's Y-chromosome belongs to haplogroup Q-M3*, placing a minimum date of 10,300 years ago for the emergence of this haplogroup.
American Journal of Physical Anthropology 05/2007; 132(4):605-21. · 2.48 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Native Americans derive from a small number of Asian founders who likely arrived to the Americas via Beringia. However, additional details about the initial colonization of the Americas remain unclear. To investigate the pioneering phase in the Americas we analyzed a total of 623 complete mtDNAs from the Americas and Asia, including 20 new complete mtDNAs from the Americas and seven from Asia. This sequence data was used to direct high-resolution genotyping from 20 American and 26 Asian populations. Here we describe more genetic diversity within the founder population than was previously reported. The newly resolved phylogenetic structure suggests that ancestors of Native Americans paused when they reached Beringia, during which time New World founder lineages differentiated from their Asian sister-clades. This pause in movement was followed by a swift migration southward that distributed the founder types all the way to South America. The data also suggest more recent bi-directional gene flow between Siberia and the North American Arctic.
[Show abstract][Hide abstract] ABSTRACT: 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.
Annals of Human Genetics 12/2006; 70(Pt 6):946-50. · 2.22 Impact Factor