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To reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method... more
To reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method based on syntactic data, here we focus on the non-straightforward relation of genes and languages among Finno-Ugric (FU) speakers, in comparison to their Indo-European (IE) and Altaic (AL) neighbors. Syntactic analysis, in agreement with the indications of more traditional linguistic levels, supports at least three distinct clusters, corresponding to these three Eurasian families; yet, the outliers of the FU group show linguistic convergence with their geographical neighbors. By analyzing genome-wide data in both ancient and contemporary populations, we uncovered remarkably matching patterns, with north-western FU speakers linguistically and genetically closer in parallel degrees to their IE-speaking neighbors, and eastern FU speakers to AL speakers. Th...
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Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies,... more
Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data are consistent with the proposed long-distance migration from Pannonia to Northern ...
Research Interests: Medieval History, Genomics, Medieval Archaeology, Migration Studies, Social Organisation (Archaeology), and 10 moreEthnicity, Multidisciplinary, Barbarians, Archeologia medievale, Paleogenetics, Lombards, Lombards burial rituals, Archaeology Of The Migration Period And The Early Middle Ages, Roman and Lombards, and Nature Communications
Flores Island, Indonesia, was inhabited by the small-bodied hominin species , which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale... more
Flores Island, Indonesia, was inhabited by the small-bodied hominin species , which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores.
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A correction to this article has been published and is linked from the HTML version of this paper. The error has not been fixed in the paper.
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Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of... more
Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Neolithic farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here we present the first and oldest complete mitochondrial sequences from Sardinia, dated back to 10,000 yBP. These two individuals, while confirming a Mesolithic occupation of the island, belong to rare mtDNA lineages, which have never been found before in Mesolithic samples and that are currently present at low frequencies not only in Sardinia, but in the whole Europe. Preliminary Approximate Bayesian Computations, restricted by biased reference samples for Mesolithic Sardinia (the two typed samples) and Neolithic Europe (limited to central and north European seq...
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In Stenico et al. (1996) we reported unusually high levels of mitochondrial diversity in the Alps. In particular, two communities of Ladin speakers appeared the most extreme European mitochondrial outliers at that time. Recently, it has... more
In Stenico et al. (1996) we reported unusually high levels of mitochondrial diversity in the Alps. In particular, two communities of Ladin speakers appeared the most extreme European mitochondrial outliers at that time. Recently, it has been observed that some rare nucleotide substitutions occur repeatedly among those sequences, raising the possibility of systematic sequencing errors. No biological material was left from the previous study, and hence we had to sample new individuals from the same communities. Here, we present the HVSI sequence variation, along with haplogroup assignment based on restriction fragment length polymorphism (RFLP), in 20 Ladin speakers of Colle Santa Lucia. None of the new sequences displays substitutions at the sites viewed as problematic. However, Ladins still show high levels of mtDNA diversity, both within their community and with respect to other Europeans, and they can still be considered one of the main European mitochondrial outliers.
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Regions of abrupt genetic change, which result from either rapid spatial change of selective pressures or limited admixture, were investigated in Europe and Asia on the basis of eight red cell markers typed in 960 samples. Two methods... more
Regions of abrupt genetic change, which result from either rapid spatial change of selective pressures or limited admixture, were investigated in Europe and Asia on the basis of eight red cell markers typed in 960 samples. Two methods were employed, one based on genetic distances and one on evaluation of the first derivative of the surfaces representing allele-frequency variation. Genetic divergence tends to be maximal between populations that are separated by physical factors (mountain ranges and seas) but also separated by cultural barriers (different language affiliation). This suggests that mating isolation, rather than adaptive response to environmental change, accounts for spatially abrupt genetic change at the loci studied and that cultural differences associated with language contribute to isolating populations. Although selection may have determined two wide allele-frequency gradients, the genetic structure of European and Asian populations seems primarily to reflect isolation by distance when investigated on a small scale and migration patterns (or absence of migration) when investigated on a larger scale.
Research Interests: Geography, Anthropology, Population Genetics, Comparative Study, Biological Sciences, and 15 moreHumans, Europe, Asia, Oxidoreductases, Genetic Population Structure, Clinical Sciences, Analysis of Variance, Genetic Polymorphism, Genetic variation, Erythrocytes, Case History, Genetic Markers, alleles, Gene frequency, and Medical and Health Sciences
We evaluated, by deterministic computer simulation, some effects of a screening programme for carriers of cystic fibrosis mutations. Two different selective regimes (heterozygote advantage and directional selection against recessive... more
We evaluated, by deterministic computer simulation, some effects of a screening programme for carriers of cystic fibrosis mutations. Two different selective regimes (heterozygote advantage and directional selection against recessive homozygotes) and three kinds of response to the screening were simulated. The curves describing the expected decline in the frequency of CF homozygotes allow one to predict some benefits of a screening campaign. In addition, it is shown that a strategy aimed at testing couples, rather than individuals, may become less expensive after only two generations of screening. The main source of uncertainty for a screening programme remains the selection mechanism, namely the existence of some sort of biological advantage for heterozygous carriers of CF mutations.
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Three approaches were employed to evaluate the relative importance of geographic and linguistic factors in maintaining genetic differentiation of Italian populations as shown by blood groups and erythrocyte and serum markers. Genetic... more
Three approaches were employed to evaluate the relative importance of geographic and linguistic factors in maintaining genetic differentiation of Italian populations as shown by blood groups and erythrocyte and serum markers. Genetic distances are closer to linguistic than to geographic distances. Gene-frequency change across 12 linguistic boundaries is significantly more rapid than at random locations. The zones of sharp genetic variation correspond to physical barriers to gene flow and to boundaries between dialect families, which overlap widely. However, two linguistically differentiated populations appear genetically differentiated despite the absence of physical obstacles to gene flow around them. The Po River is associated with abrupt genetic change only in the area where it corresponds to a dialect boundary. At most loci the genetic population structure seems affected by linguistic rather than geographic factors; exceptions are the systems that were subject to malarial selection in geographically close but linguistically heterogeneous localities. Gene flow appears to homogenize gene frequencies within regions corresponding to dialect families but not between them, leading to the patchy distributions of allele frequencies that were detected in an earlier study.
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Common variants in the UMOD gene encoding uromodulin, associated with risk of hypertension and CKD in the general population, increase UMOD expression and urinary excretion of uromodulin, causing salt-sensitive hypertension and renal... more
Common variants in the UMOD gene encoding uromodulin, associated with risk of hypertension and CKD in the general population, increase UMOD expression and urinary excretion of uromodulin, causing salt-sensitive hypertension and renal lesions. To determine the effect of selective pressure on variant frequency, we investigated the allelic frequency of the lead UMOD variant rs4293393 in 156 human populations, in eight ancient human genomes, and in primate genomes. The T allele of rs4293393, associated with CKD risk, has high frequency in most modern populations and was the one detected in primate genomes. In contrast, we identified only the derived, C allele in Denisovan and Neanderthal genomes. The distribution of the UMOD ancestral allele did not follow the ancestral susceptibility model observed for variants associated with salt-sensitive hypertension. Instead, the global frequencies of the UMOD alleles significantly correlated with pathogen diversity (bacteria, helminths) and preva...
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Analysis of geographic variation for eight red cell markers in Italy shows significant spatial structure for most alleles. Effective population sizes estimated from FST values at these loci are much smaller than those predicted from data... more
Analysis of geographic variation for eight red cell markers in Italy shows significant spatial structure for most alleles. Effective population sizes estimated from FST values at these loci are much smaller than those predicted from data on consanguineous marriage, suggesting the presence of factors (presumably barriers) that have reduced gene flow and enhanced the evolutionary weight of genetic drift. Most regions of sharp gene frequency change correspond to geographic and linguistic barriers. Two allele frequencies are significantly correlated with measures of linguistic differentiation but not with indexes describing broad religious and social attitudes. The similarity between patterns of genetic and linguistic variation in Italy, also observed in a previous study, suggests that in specific areas linguistic diversity has acted as a biological barrier constraining mating, dispersal, or both. There is no evidence for a similar role of other extent cultural barriers.
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... LR 12,000 0.961 0.019 0.021 LR 6,000 0.970 0.012 0.018 AR 500 0.760 0.120 0.120 AR 100 0.860 0.090 0.050 Page 3. www.isita-org.com 237 JASs forum: Interdisciplinary views on Molecular Anthropology in the Genomic Era from Anatolia less... more
... LR 12,000 0.961 0.019 0.021 LR 6,000 0.970 0.012 0.018 AR 500 0.760 0.120 0.120 AR 100 0.860 0.090 0.050 Page 3. www.isita-org.com 237 JASs forum: Interdisciplinary views on Molecular Anthropology in the Genomic Era from Anatolia less than 3000 years ago. ...
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Genetic variation at the phosphoglucomutase-1 (PGM) and acid phosphatase (ACP) loci, in 160 and 120 European and Asian populations, respectively, is described by spatial autocorrelation statistics and directional variograms.... more
Genetic variation at the phosphoglucomutase-1 (PGM) and acid phosphatase (ACP) loci, in 160 and 120 European and Asian populations, respectively, is described by spatial autocorrelation statistics and directional variograms. Short-distance patterns of gene frequencies correspond to those predicted by models of isolation by distance, but long-range differentiation of populations is observed as well. A possible role of climatic selection in maintaining the PGM polymorphism is supported by the north-south orientation of the gradient for that locus, but not by biochemical evidence. By and large, the observed patterns of gene frequencies seem to reflect a combination of demographic processes, subdivision and isolation of local populations among them.
Research Interests: Evolutionary Biology, Genetics, Geography, Archaeology, Anthropology, and 15 moreComparative Study, Biological Sciences, Enzymes, Europe, Asia, Genetic Population Structure, Clinical Sciences, Analysis of Variance, Genetic variation, Erythrocytes, Case History, Genetic Markers, Acid Phosphatase, alleles, and Gene frequency
Research Interests: Evolutionary Biology, Archaeology, Algorithms, Anthropology, Historical Anthropology, and 15 moreHuman Genetics, Languages and Linguistics, Historical Linguistics, Historical Syntax, Computational Linguistics, Formal syntax, Language, Biolinguistics, Generative linguistics, Humans, Europe, Genome, Biological evolution, Generative Syntax, and Genetic variation
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A previous investigation demonstrated the existence of extensive allele frequency diversity within an area of northern Italy crossed by a linguistic (dialect) boundary and by the Po River, either of them or both presumably constraining... more
A previous investigation demonstrated the existence of extensive allele frequency diversity within an area of northern Italy crossed by a linguistic (dialect) boundary and by the Po River, either of them or both presumably constraining gene flow. We obtained hair samples from 45 school pupils from 9 localities in that area and sequenced a 255-bp segment of the mtDNA D loop. Estimates of the minimum number of migration events from gene genealogies suggest that the linguistic barrier impaired gene flow more than the river did. However, an analysis of molecular variance (AMOVA) showed that most sequence diversity occurs within rather than between populations and that the differences between groups of populations, defined either by linguistic or geographic criteria, do not reach significance. Three areas of rapid genetic variation were identified; their locations suggest that populations of the western part of the study area evolved in relative isolation. Therefore mtDNA sequence variat...
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CYP2D6, a member of the cytochrome P450 superfamily, is responsible for the metabolism of about 25% of the commonly prescribed drugs. Its activity ranges from complete deficiency to excessive activity, potentially causing toxicity of... more
CYP2D6, a member of the cytochrome P450 superfamily, is responsible for the metabolism of about 25% of the commonly prescribed drugs. Its activity ranges from complete deficiency to excessive activity, potentially causing toxicity of medication or therapeutic failure with recommended drug dosages. This study aimed to describe the CYP2D6 diversity at the global level. A total of 1060 individuals belonging to 52 worldwide-distributed populations were genotyped at 12 highly informative variable sites, as well as for gene deletion and duplications. Phenotypes were predicted on the basis of haplotype combinations. Our study shows that (i) CYP2D6 diversity is far greater within than between populations and groups thereof, (ii) null or low-activity variants occur at high frequencies in various areas of the world, (iii) linkage disequilibrium is lowest in Africa and highest in the Americas. Patterns of variation, within and among populations, are similar to those observed for other autosoma...
Research Interests: Genetics, Geography, Polymorphism, Population Genetics, High Frequency, and 13 moreHumans, Haplotypes, Pharmacogenetics, Cluster Analysis, Frequency, Phenotype, Analysis of Variance, Genotyping, Linkage Disequilibrium, Genetic variation, Genetic Variability, Gene frequency, and Pharmacology and pharmaceutical sciences
Geographic patterns of genetic diversity allow us to make inferences about population histories and the evolution of inherited disease. The statistical methods describing genetic variation in space, such as estimation of genetic... more
Geographic patterns of genetic diversity allow us to make inferences about population histories and the evolution of inherited disease. The statistical methods describing genetic variation in space, such as estimation of genetic variances, mapping of allele frequencies, and principal components analysis, have opened up the possibility to reconstruct demographic processes whose effects have been tested by a variety of approaches, including spatial autocorrelation, cladistic analyses, and simulations. These studies have significantly contributed to our understanding of human genetic variation; however, the molecular data that have accumulated since the mid-1980s have also created new complications. Reasons include the generally limited sample sizes, but, more generally, it is the nature of molecular variation itself that makes it necessary to develop and apply specific models and methods for the treatment of DNA data. The foreseeable diffusion of laboratory techniques for the rapid ty...
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Genetic evidence is consistent with the view that the Indo-European languages were propagated in Europe by the diffusion of early farmers. The existence of phylogenetic relationships between European populations speaking other languages... more
Genetic evidence is consistent with the view that the Indo-European languages were propagated in Europe by the diffusion of early farmers. The existence of phylogenetic relationships between European populations speaking other languages has been proposed on linguistic and archaeological grounds, and is here tested by analyzing allele frequencies at ten polymorphic protein and blood group loci. Genetic distances between speakers of Basque and Caucasian languages are compared with those between controls, i.e. contiguous populations speaking Indo-European and Altaic. Although some statistical tests show an excess of genetic similarity between Basque and South Caucasian speakers, most results do not support their common origin. If the Basques and the Caucasian-speaking populations share common ancestors, recent evolutionary phenomena must have caused divergence between them, so that their gene frequencies do not appear more similar now than those of random pairs of populations separated...
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The threonine-glycine (Thr-Gly) repeat region of the period (per) gene of eight natural populations of Drosophila simulans from Europe and North Africa was analyzed by polymerase chain reaction, DNA sequencing and heteroduplex formation.... more
The threonine-glycine (Thr-Gly) repeat region of the period (per) gene of eight natural populations of Drosophila simulans from Europe and North Africa was analyzed by polymerase chain reaction, DNA sequencing and heteroduplex formation. Five different length alleles encoding 21, 23, 25 and two different kinds of 24 Thr-Gly pairs in the uninterrupted repeat were found. In the 3' region flanking the repeat 6 nucleotide substitutions (3 synonymous, 3 replacement) were observed in three different combinations that we called haplotypes I, II and III. The complete linkage disequilibrium observed between the haplotypes and these length variants allowed us to infer from the repeat length, the DNA sequence at the 3' polymorphic sites. The haplotypes were homogeneously distributed across Europe and North Africa. The data show statistically significant departures from neutral expectations according to the Tajima test. The results suggest that balancing selection might have played a ro...
Research Interests: Genetics, Polymorphism, Genetic Diversity, DNA, Drosophila, and 13 morePhylogeny, North Africa, Animals, Polymerase Chain Reaction, Statistical Significance, Balancing selection, Linkage Disequilibrium, Genetic Polymorphism, Amino Acid Sequence, Base Sequence, DNA sequence, Molecular Sequence Data, and Nucleotide substitution
Two statistics are proposed for summarizing spatial patterns of DNA diversity. These autocorrelation indices for DNA analysis, or AIDAs, can be applied to RFLP and sequence data; the resulting set of autocorrelation coefficients, or... more
Two statistics are proposed for summarizing spatial patterns of DNA diversity. These autocorrelation indices for DNA analysis, or AIDAs, can be applied to RFLP and sequence data; the resulting set of autocorrelation coefficients, or correlogram, measures whether, and to what extent, individual DNA sequences or haplotypes resemble the haplotypes sampled at arbitrarily chosen spatial distances. Analyses of computer-generated sets of data, and of RFLP data from two natural populations, show that AIDAs allow one to objectively and simply identify basic patterns in the spatial distribution of haplotypes. These statistics, therefore, seem to be a useful tool both to explore the genetic structure of a population and to suggest hypotheses on the evolutionary processes that shaped the observed patterns.
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Spatial autocorrelation statistics are used for description of geographic variation of gene frequencies, but the relationship of these indices with the parameters describing the genetic structure of populations is not established. A... more
Spatial autocorrelation statistics are used for description of geographic variation of gene frequencies, but the relationship of these indices with the parameters describing the genetic structure of populations is not established. A simple relation is derived here between kinship coefficient and a measure of spatial autocorrelation, Moran's I. The autocorrelation coefficient of gene frequencies at a given distance is a direct function of the kinship at that distance, and an inverse function of the standardized gene frequency variance, Fst. Under isolation by distance, the expected values of Moran's I for any allele may be calculated by means of Malécot-Morton function, which predicts an exponential decline of genetic similarity in space. This allows comparison of observed gene frequency patterns with the patterns that should be caused by interaction of short range migration and random genetic drift.
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... 2. Karel et al. say that we "assumed" incomplete penetrance and that this concept may be misleading. A gene is said to be incompletely penetrant when not all the individuals with a certain genotype show the... more
... 2. Karel et al. say that we "assumed" incomplete penetrance and that this concept may be misleading. A gene is said to be incompletely penetrant when not all the individuals with a certain genotype show the corresponding phenotype (see, eg, Cavalli-Sforza and Bodmer 1971 ...
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The diversity of spatial patterns of 61 allele frequencies for 20 genetic systems (15 loci) in Italy is presented. Blood antigens, enzymes, and proteins were analyzed. The total number of data points over all systems and localities was... more
The diversity of spatial patterns of 61 allele frequencies for 20 genetic systems (15 loci) in Italy is presented. Blood antigens, enzymes, and proteins were analyzed. The total number of data points over all systems and localities was 1119. We used homogeneity tests, one-dimensional and directional spatial correlograms, and SYMAP interpolated surfaces. The data matrices were reduced by clustering techniques to reveal the principal patterns. Only a few allele frequency surfaces are strongly correlated across loci. All systems but one (ADA) exhibit significant heterogeneity in allele frequencies among the localities. Significant spatial patterns are shown by 27 of the 61 surfaces. Only one pattern (cde; system 4.19) is clinal; another (PGM1) exhibits a pure isolation by distance pattern; the others show long-range differentiation in addition to the short-distance decline of autocorrelation expected under isolation by distance. There is a marked decline in overall genetic similarity w...
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ABSTRACT. In this paper, we shall review some important contributions of aDNA studies to the reconstruction of human evolutionary history. We shall argue that, despite non-negligible problems mainly related to difficult-to-detect DNA... more
ABSTRACT. In this paper, we shall review some important contributions of aDNA studies to the reconstruction of human evolutionary history. We shall argue that, despite non-negligible problems mainly related to difficult-to-detect DNA damage, contamination by exogenous ...
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... Molecular Biology and Evolution 9: 552569. ... CrossRef. Sokal RR, Oden NL, Walker J, Di Giovanni D and Thomson BA (1996) Historical population movements in Europe influence genetic relationships in modern samples. Human Biology 68:... more
... Molecular Biology and Evolution 9: 552569. ... CrossRef. Sokal RR, Oden NL, Walker J, Di Giovanni D and Thomson BA (1996) Historical population movements in Europe influence genetic relationships in modern samples. Human Biology 68: 873898. ... on human variation. ...
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Page 1. 31 Human Genetic Diversity and its History G. Barbujani Dipartimento di Biologia ed Evoluzione, Universit`a di Ferrara, Ferrara, Italia and L. Chikhi Laboratoire Evolution et Diversité Biobgique, Université Paul Sabatier,... more
Page 1. 31 Human Genetic Diversity and its History G. Barbujani Dipartimento di Biologia ed Evoluzione, Universit`a di Ferrara, Ferrara, Italia and L. Chikhi Laboratoire Evolution et Diversité Biobgique, Université Paul Sabatier, Toulouse, France ...