[Show abstract][Hide abstract] ABSTRACT: Despite broad consensus on Africa as the main place of origin for anatomically modern humans, their dispersal pattern out of the continent continues to be intensely debated. In extant human populations, the observation of decreasing genetic and phenotypic diversity at increasing distances from sub-Saharan Africa has been interpreted as evidence for a single dispersal, accompanied by a series of founder effects. In such a scenario, modern human genetic and phenotypic variation was primarily generated through successive population bottlenecks and drift during a rapid worldwide expansion out of Africa in the Late Pleistocene. However, recent genetic studies, as well as accumulating archaeological and paleoanthropological evidence, challenge this parsimonious model. They suggest instead a "southern route" dispersal into Asia as early as the late Middle Pleistocene, followed by a separate dispersal into northern Eurasia. Here we test these competing out-of-Africa scenarios by modeling hypothetical geographical migration routes and assessing their correlation with neutral population differentiation, as measured by genetic polymorphisms and cranial shape variables of modern human populations from Africa and Asia. We show that both lines of evidence support a multiple-dispersals model in which Australo-Melanesian populations are relatively isolated descendants of an early dispersal, whereas other Asian populations are descended from, or highly admixed with, members of a subsequent migration event.
Proceedings of the National Academy of Sciences 04/2014; · 9.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The greater Himalayan region demarcates two of the most prominent linguistic phyla in Asia: Tibeto-Burman and Indo-European. Previous genetic surveys, mainly using Y-chromosome polymorphisms and/or mitochondrial DNA polymorphisms suggested a substantially reduced geneflow between populations belonging to these two phyla. These studies, however, have mainly focussed on populations residing far to the north and/or south of this mountain range, and have not been able to study geneflow patterns within the greater Himalayan region itself. We now report a detailed, linguistically informed, genetic survey of Tibeto-Burman and Indo-European speakers from the Himalayan countries Nepal and Bhutan based on autosomal microsatellite markers and compare these populations with surrounding regions. The genetic differentiation between populations within the Himalayas seems to be much higher than between populations in the neighbouring countries. We also observe a remarkable genetic differentiation between the Tibeto-Burman speaking populations on the one hand and Indo-European speaking populations on the other, suggesting that language and geography have played an equally large role in defining the genetic composition of present-day populations within the Himalayas.
PLoS ONE 01/2014; 9(3):e91534. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Background: Atlantic Bluefin Tuna (ABFT) shows complex demography and ecological variation in the Mediterranean Sea. Genetic surveys have detected significant, although weak, signals of population structuring; catch series analyses and tagging programs identified complex ABFT spatial dynamics and migration patterns. Here, we tested the hypothesis that the genetic structure of the ABFT in the Mediterranean is correlated with mean surface temperature and salinity. Methodology: We used six samples collected from Western and Central Mediterranean integrated with a new sample collected from the recently identified easternmost reproductive area of Levantine Sea. To assess population structure in the Mediterranean we used a multidisciplinary framework combining classical population genetics, spatial and Bayesian clustering methods and a multivariate approach based on factor analysis. Conclusions: F ST analysis and Bayesian clustering methods detected several subpopulations in the Mediterranean, a result also supported by multivariate analyses. In addition, we identified significant correlations of genetic diversity with mean salinity and surface temperature values revealing that ABFT is genetically structured along two environmental gradients. These results suggest that a preference for some spawning habitat conditions could contribute to shape ABFT genetic structuring in the Mediterranean. However, further studies should be performed to assess to what extent ABFT spawning behaviour in the Mediterranean Sea can be affected by environmental variation. Copyright: ß 2013 Riccioni et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
[Show abstract][Hide abstract] ABSTRACT: Understanding how and why humans are biologically different is indispensable to get oriented in the ever-growing body of genomic data. Here we discuss the evidence based on which we can confidently state that humans are the least genetically variable primate, both when individuals and when populations are compared, and that each individual genome can be regarded as a mosaic of fragments of different origins. Each population is somewhat different from any other population, and there are geographical patterns in that variation. These patterns clearly indicate an African origin for our species, and keep a record of the main demographic changes accompanying the peopling of the whole planet. However, only a minimal fraction of alleles, and a small fraction of combinations of alleles along the chromosome, is restricted to a single geographical region (and even less so to a single population), and diversity between members of the same population is very large. The small genomic differences between populations and the extensive allele sharing across continents explain why historical attempts to identify, once and for good, major biological groups in humans have always failed. Nevertheless, racial categorization is all but gone, especially in clinical studies. We argue that racial labels may not only obscure important differences between patients but also that they have become positively useless now that cheap and reliable methods for genotyping are making it possible to pursue the development of truly personalized medicine.
[Show abstract][Hide abstract] ABSTRACT: In order to describe the isonymic structure of Albania, the distribution of 3,068,447 surnames was studied in the 12 prefectures and their administrative subdivisions: the 36 districts and 321 communes. The number of different surnames found was 37,184. Effective surname number for the entire country was 1327, the average for prefectures was 653.3 ± 84.3, for districts 365.9 ± 42.0 and for communes 122.6 ± 8.7. These values display a variation of inbreeding between administrative levels in the Albanian population, which can be attributed to the previously published "Prefecture effect". Matrices of isonymic distances between units within administrative levels were tested for correlation with geographic distances. The correlations were highest for prefectures (r = 0.71 ± 0.06 for Euclidean distance) and lowest for communes (r = 0.37 ± 0.011 for Nei's distance). The multivariate analyses (Principal component analysis and Multidimensional Scaling) of prefectures identify three main clusters, one toward the North, the second in Central Albania, and the third in the South. This pattern is consistent with important subclusters from districts and communes, which point out that the country may have been colonised by diffusion of groups in the North-South direction, and from Macedonia in the East, over a pre-existing Illiryan population.
Annals of Human Genetics 03/2013; · 2.22 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Etruscan culture is documented in Etruria, Central Italy, from the 8(th) to the 1(st) century BC. For more than 2,000 years there has been disagreement on the Etruscans' biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans' and modern populations in the same genealogy. We extracted and typed the hypervariable region of mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals from the Mediterranean basin. Comparing ancient (30 Etruscans, 27 Medieval individuals) and modern DNA sequences (370 Tuscans), with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the current inhabitants of Casentino and Volterra, but not to the general contemporary population of the former Etruscan homeland. By further considering two Anatolian samples (35 and 123 individuals) we could estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, and not as an immediate consequence of immigration from the Eastern Mediterranean shores.
PLoS ONE 01/2013; 8(2):e55519. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Atlantic Bluefin Tuna (ABFT) shows complex demography and ecological variation in the Mediterranean Sea. Genetic surveys have detected significant, although weak, signals of population structuring; catch series analyses and tagging programs identified complex ABFT spatial dynamics and migration patterns. Here, we tested the hypothesis that the genetic structure of the ABFT in the Mediterranean is correlated with mean surface temperature and salinity.
We used six samples collected from Western and Central Mediterranean integrated with a new sample collected from the recently identified easternmost reproductive area of Levantine Sea. To assess population structure in the Mediterranean we used a multidisciplinary framework combining classical population genetics, spatial and Bayesian clustering methods and a multivariate approach based on factor analysis.
FST analysis and Bayesian clustering methods detected several subpopulations in the Mediterranean, a result also supported by multivariate analyses. In addition, we identified significant correlations of genetic diversity with mean salinity and surface temperature values revealing that ABFT is genetically structured along two environmental gradients. These results suggest that a preference for some spawning habitat conditions could contribute to shape ABFT genetic structuring in the Mediterranean. However, further studies should be performed to assess to what extent ABFT spawning behaviour in the Mediterranean Sea can be affected by environmental variation.
PLoS ONE 01/2013; 8(11):e80105. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: It was many years ago. Robert Sokal and I were walking through the streets of Padua. It was spring, the sky was darkening, it was the time of day at which more intimate communication becomes sometimes possible. Without my asking, he started talking about his early years in Europe. On April 2, 1938, in front of an enthusiastic Viennese crowd, Adolf Hitler had proclaimed the annexation of Austria to Germany; Vienna was no longer a safe place for a Jewish family. The Sokals packed all they could carry with them in a few pieces of luggage and caught a train to Trieste. They were lucky enough to make it on time for the last ship that European Jews were allowed to board. Its name was Conte Rosso; its destination was Shanghai. At that crucial turning point of his life, Robert Sokal had little perception of how serious the moment was, he told me; everything onboard the big steamer was just exciting for a 13-year-old. The cook's speciality, he remembered, was risotto with chicken liver. Maybe he wanted to have one that night, fifty years later? I asked. Off we went, and Sokal was initially amused at the idea, less so when, after more than an hour of useless wandering, we had yet to find a restaurant listing that old-time delicacy on its menu. His back was aching; it was inevitable to surrender. I promised that next time I would do a careful search in advance to make sure he could enjoy a proper risotto with chicken liver. I did not keep my promise; that was his last trip to Italy.
When I joined Robert Sokal in Stony Brook, at the beginning of 1987, I was immediately exposed to myth. I am not speaking here of the reputation of the group and of its leader, although the term would not be totally inappropriate for them. I am speaking of the legends circulating in the broad assemblage of postdocs, graduate students, and generic scientists who at that time were variously associated with Sokal's lab. Two main myths, among several, were popular. The first one was that the discipline of numerical taxonomy was born out of a bet over six or twelve (sources disagreed) cans of beer; the second one was that one of Sokal's early papers was sent to 36 referees by the hostile editor of Systematic Zoology. Both turned out not to be myths at all, but it took me months before I had the chance to listen to Sokal's version. On that occasion, I also first heard the expression "from the horse's mouth," by which Sokal was referring to himself. I was struck by the realization that the last name of Sokal's main scientific adversary at the time, Cavalli, means "horses." Thus, in the horse, like in the symbol of Taiji philosophy, the two conflicting principles, yin and yang, Sokal and Cavalli-Sforza, could somehow meet and be one.
The two men could hardly be more different, personally and professionally. Cavalli is a polyedric artist/scientist, with outstanding entrepreneurial abilities; Sokal was a careful craftsman/scientist whose artifacts were made to last. As an Italian human geneticist, I had grown up reading Cavalli's books and papers; working now in Sokal's group was worryingly similar to being one of those ambiguous characters of spy stories, figures who act in the shade and generally die a horrible death shortly before the movie credits. It is understandable, then, that for months I avoided asking questions unrelated to my project. But eventually I did; both stories, Sokal guaranteed, were true, and the cans of beer were six. He also told me that in the fifties, when he stated it was time to develop quantitative methods for establishing taxonomic relationships, he had no idea how to do it. And then he added that he made sure that the editor of Systematic Zoology was fired for handling his manuscript that way.
Thus, Robert Sokal could also act impulsively, and he could occasionally take revenge. Everybody who has known him in person can testify that normally he had quite different attitudes. I suspect that these episodes...
Human Biology 10/2012; 84(5):481-488. · 1.52 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: DNA extracted from the remains of two Mesolithic individuals reveals that they had genetically little in common with modern Europeans. The ancestors of most modern Europeans thus most likely entered Europe only with the advent of farming.
Current biology: CB 08/2012; 22(16):R631-3. · 10.99 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Estimates of mutation rates for the noncoding hypervariable Region I (HVR-I) of mitochondrial DNA vary widely, depending on whether they are inferred from phylogenies (assuming that molecular evolution is clock-like) or directly from pedigrees. All pedigree-based studies so far were conducted on populations of European origin. In this article, we analyzed 19 deep-rooting pedigrees in a population of mixed origin in Costa Rica. We calculated two estimates of the HVR-I mutation rate, one considering all apparent mutations, and one disregarding changes at sites known to be mutational hot spots and eliminating genealogy branches which might be suspected to include errors, or unrecognized adoptions along the female lines. At the end of this procedure, we still observed a mutation rate equal to 1.24 × 10(-6) , per site per year, i.e., at least threefold as high as estimates derived from phylogenies. Our results confirm that mutation rates observed in pedigrees are much higher than estimated assuming a neutral model of long-term HVRI evolution. We argue that until the cause of these discrepancies will be fully understood, both lower estimates (i.e., those derived from phylogenetic comparisons) and higher, direct estimates such as those obtained in this study, should be considered when modeling evolutionary and demographic processes.
American Journal of Physical Anthropology 03/2012; 148(3):327-33. · 2.48 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Neandertals, the archaic human form documented in Eurasia until 29,000 years ago, share no mitochondrial haplotype with modern Europeans. Whether this means that the two groups were reproductively isolated is controversial, and indeed nuclear data have been interpreted as suggesting that they admixed. We explored the range of demographic parameters that may have generated the observed mitochondrial diversity, simulating 3.0 million genealogies under six models differing as for the relationships among contemporary Europeans, Neandertals, and Upper Palaeolithic European early modern humans (EEMH), who coexisted with Neandertals for millennia. We compared by Approximate Bayesian Computations the simulation results with mitochondrial diversity in 7 Neandertals, 3 EEMH, and 150 opportunely chosen modern Europeans. A model of genealogical continuity between EEMH and contemporary Europeans, with no Neandertal contribution, received overwhelming support from the analyses. The maximum degree of Neandertal admixture, under the model of gene flow supported by nuclear data, was estimated at 1.5%, but this model proved 20-32 times less likely than a model without any gene flow. Nuclear and mitochondrial evidence might be reconciled if smaller population sizes led to faster lineage sorting for mitochondrial DNA, and Neandertals shared a longer period of common ancestry with the non-African's than with the African's ancestors.
American Journal of Physical Anthropology 10/2011; 146(2):242-52. · 2.48 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: There is general agreement among scientists about a recent (less than 200,000 yrs ago) African origin of anatomically modern humans, whereas there is still uncertainty about whether, and to what extent, they admixed with archaic populations, which thus may have contributed to the modern populations' gene pools. Data on cranial morphology have been interpreted as suggesting that, before the main expansion from Africa through the Near East, anatomically modern humans may also have taken a Southern route from the Horn of Africa through the Arabian peninsula to India, Melanesia and Australia, about 100,000 yrs ago. This view was recently supported by archaeological findings demonstrating human presence in Eastern Arabia >90,000 yrs ago. In this study we analyzed genetic variation at 111,197 nuclear SNPs in nine populations (Kurumba, Chenchu, Kamsali, Madiga, Mala, Irula, Dalit, Chinese, Japanese), chosen because their genealogical relationships are expected to differ under the alternative models of expansion (single vs. multiple dispersals). We calculated correlations between genomic distances, and geographic distances estimated under the alternative assumptions of a single dispersal, or multiple dispersals, and found a significantly stronger association for the multiple dispersal model. If confirmed, this result would cast doubts on the possibility that some non-African populations (i.e., those whose ancestors expanded through the Southern route) may have had any contacts with Neandertals.
Human Biology 08/2011; 83(4):477-89. · 1.52 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Cholinesterase inhibitors are commonly prescribed to patients with Alzheimer's disease (AD) to enhance cholinergic neurotransmission. Differential response to these treatments has been observed, and claims have been made that individual genetic variants may influence the pharmacokinetic and pharmacodynamic properties of these drugs. Here we assess the effects of genetic variation at two loci involved in the activity of cholinesterase inhibitors on longitudinal clinical change in AD patients being treated with donepezil, galantamine, and rivastigmine.
This was an open study in which 171 Italian AD patients treated with donepezil (n = 92), galantamine (n = 33), or rivastigmine (n = 46) were enrolled. Response to treatment was quantified by grading the patient's cognitive state (Mini-Mental State Examination) and the patient's ability to perform normal daily activities (Activities of Daily Living, Instrumental Activities of Daily Living) at baseline and after 6 and 12 months of treatment. Genetic variation was comprehensively characterized and analyzed at two loci: CYP2D6, which is involved in donepezil and galantamine metabolism, and BCHE, which codes for an enzyme (butyrylcholinesterase) which is both target and metabolizer of rivastigmine. APOE (coding for apolipoprotein E), which is associated with the risk of AD and inefficacy of specific AD treatments, was genotyped to control for patient stratification. The influence of the CYP2D6 and BCHE genotype on clinical changes after 12 months was evaluated by several tests of association.
After 1 year of treatment, 29, 12, and 12 of the patients receiving donepezil, galantamine, and rivastigmine, respectively, showed a cognitive decrement, while eight patients interrupted the therapy before 12 months of treatment. No significant differences between the three treatments were observed in terms of response and tolerability. Non-responders show a higher proportion of BCHE and CYP2D6 mutated alleles, but genetic variation at the two loci was not a reliable predictor of clinical changes in AD patients treated with cholinesterase inhibitors.
Individualized therapy based on CYP2D6 and BCHE genotypes is unlikely to be beneficial for treating Alzheimer's disease patients in routine clinical practice.
European Journal of Clinical Pharmacology 06/2011; 67(11):1147-57. · 2.74 Impact Factor