Publications by authors named "Paolo Francalacci"

30 Publications

  • Page 1 of 1

Worldwide variation of the COL14A1 gene is shaped by genetic drift rather than selective pressure.

Mol Genet Genomic Med 2021 Mar 2:e1629. Epub 2021 Mar 2.

Department of Life and Environment Sciences, University of Cagliari, Cagliari, Italy.

Background: The aim of this study is to analyze the worldwide distribution of SNP rs4870723 in COL14A1 gene to check if there are significant genetic differences among different populations and to test if the gene is a trait under selection.

Methods: Genomic DNA was extracted from 69 unrelated individuals from Sardinia and genotyped for SNP rs4870723. Data were compared with 26 different populations, clustered in 5 super-populations, from the public 1000 genomes database. Allele frequency and heterozygosity were calculated with Genepop. The Hardy-Weinberg equilibrium and pairwise population differentiation through analysis of molecular variance (AMOVA FST) were determined with Arlequin.

Results: Allele frequencies of COL14A1 rs4870723 were compared in 27 populations clustered in 5 super-populations. All populations were in the Hardy-Weinberg equilibrium. In almost all populations, allele C was the most frequent allele, reaching the highest values in East Asia. The 27 populations showed an appreciable structure, with significant differences observed between European, African, and Asian populations.

Conclusion: Significant differences were observed in the rs4870723 SNP distribution among the populations studied. However, we found no evidence for a selective pressure. Rather, the differentiation among the populations is likely the result of founder effect, genetic drift, and cultural factors, all events known to establish and maintain genetic diversity between populations.
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http://dx.doi.org/10.1002/mgg3.1629DOI Listing
March 2021

Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case.

Int J Mol Sci 2019 Nov 16;20(22). Epub 2019 Nov 16.

Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, 27100 Pavia, Italy.

Many anthropological, linguistic, genetic and genomic analyses have been carried out to evaluate the potential impact that evolutionary forces had in shaping the present-day Sardinian gene pool, the main outlier in the genetic landscape of Europe. However, due to the homogenizing effect of internal movements, which have intensified over the past fifty years, only partial information has been obtained about the main demographic events. To overcome this limitation, we analyzed the male-specific region of the Y chromosome in three population samples obtained by reallocating a large number of Sardinian subjects to the place of origin of their monophyletic surnames, which are paternally transmitted through generations in most of the populations, much like the Y chromosome. Three Y-chromosome founding lineages, G2-L91, I2-M26 and R1b-V88, were identified as strongly contributing to the definition of the outlying position of Sardinians in the European genetic context and marking a significant differentiation within the island. The present distribution of these lineages does not always mirror that detected in ancient DNAs. Our results show that the analysis of the Y-chromosome gene pool coupled with a sampling method based on the origin of the family name, is an efficient approach to unravelling past heterogeneity, often hidden by recent movements, in the gene pool of modern populations. Furthermore, the reconstruction and comparison of past genetic isolates represent a starting point to better assess the genetic information deriving from the increasing number of available ancient DNA samples.
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http://dx.doi.org/10.3390/ijms20225763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6888588PMC
November 2019

Inter-individual genomic heterogeneity within European population isolates.

PLoS One 2019 9;14(10):e0214564. Epub 2019 Oct 9.

Dipartimento di Biologia Ambientale, Università di Roma "La Sapienza", Rome, Italy.

A number of studies carried out since the early '70s has investigated the effects of isolation on genetic variation within and among human populations in diverse geographical contexts. However, no extensive analysis has been carried out on the heterogeneity among genomes within isolated populations. This issue is worth exploring since events of recent admixture and/or subdivision could potentially disrupt the genetic homogeneity which is to be expected when isolation is prolonged and constant over time. Here, we analyze literature data relative to 87,815 autosomal single-nucleotide polymorphisms, which were obtained from a total of 28 European populations. Our results challenge the traditional paradigm of population isolates as structured as genetically (and genomically) uniform entities. In fact, focusing on the distribution of variance of intra-population diversity measures across individuals, we show that the inter-individual heterogeneity of isolated populations is at least comparable to the open ones. More in particular, three small and highly inbred isolates (Sappada, Sauris and Timau in Northeastern Italy) were found to be characterized by levels of inter-individual heterogeneity largely exceeding that of all other populations, possibly due to relatively recent events of genetic introgression. Finally, we propose a way to monitor the effects of inter-individual heterogeneity in disease-gene association studies.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0214564PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6785074PMC
March 2020

Understanding 6th-century barbarian social organization and migration through paleogenomics.

Nat Commun 2018 09 11;9(1):3547. Epub 2018 Sep 11.

Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11790, USA.

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 Italy.
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http://dx.doi.org/10.1038/s41467-018-06024-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6134036PMC
September 2018

Overcoming the dichotomy between open and isolated populations using genomic data from a large European dataset.

Sci Rep 2017 02 1;7:41614. Epub 2017 Feb 1.

Dipartimento di Biologia, Università di Pisa, Via Ghini 13, Pisa, 56126, Italy.

Human populations are often dichotomized into "isolated" and "open" categories using cultural and/or geographical barriers to gene flow as differential criteria. Although widespread, the use of these alternative categories could obscure further heterogeneity due to inter-population differences in effective size, growth rate, and timing or amount of gene flow. We compared intra and inter-population variation measures combining novel and literature data relative to 87,818 autosomal SNPs in 14 open populations and 10 geographic and/or linguistic European isolates. Patterns of intra-population diversity were found to vary considerably more among isolates, probably due to differential levels of drift and inbreeding. The relatively large effective size estimated for some population isolates challenges the generalized view that they originate from small founding groups. Principal component scores based on measures of intra-population variation of isolated and open populations were found to be distributed along a continuum, with an area of intersection between the two groups. Patterns of inter-population diversity were even closer, as we were able to detect some differences between population groups only for a few multidimensional scaling dimensions. Therefore, different lines of evidence suggest that dichotomizing human populations into open and isolated groups fails to capture the actual relations among their genomic features.
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http://dx.doi.org/10.1038/srep41614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5286425PMC
February 2017

Dissecting mitochondrial dna variability of balearic populations from the bronze age to the current era.

Am J Hum Biol 2017 Jan 13;29(1). Epub 2016 Jun 13.

Unitat d'Antropologia Biològica, Departament BABVE, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.

Objectives: To determine ancient population influences on ancient and current Balearic populations and to reconstruct their mitochondrial DNA (mtDNA) gene pool evolution.

Methods: We analyzed 239 individuals belonging to five archaeological populations from Majorca and Minorca, four dating to the transition between the Bronze Age and the Iron Age, and one Late Roman Majorcan population. Six additional individuals from Santa Teresa di Gallura from the Nuragic period were characterized and added to the existing samples from that culture to make comparisons with Talaiotic populations.

Results: We characterized the haplogroups of 138 individuals and obtained 69 sequences from mtDNA hypervariable region I. In the intra-island study, the apparent differences in social and funerary rites between two contiguous Majorcan necropolises were correlated with genetic characteristics. Also, the likely occurrence of consanguinity in a population with a very particular burial pattern was supported by genetic data. Despite the uniqueness of each necropolis, the global comparison of the five necropolises revealed no significant differences between them, or between ancient and modern populations from the islands. Ancient Balearics showed a similar mtDNA gene pool to Ancient Catalans, had a Near Eastern component, and showed continuity with European populations since at least the Bronze Age.

Conclusion: We characterized five Balearic necropolises in the context of their geographic and cultural characteristics. The similarity between ancient Balearic and ancient Catalan gene pools reinforces their known historic interactions, while the lack of a consistent genetic continuity with Ancient Sardinians suggests that Talaiotic and Nuragic cultures arose in differentiated populations. Am. J. Hum. Biol. 29:e22883, 2017. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/ajhb.22883DOI Listing
January 2017

The First Mitogenome of the Cyprus Mouflon (Ovis gmelini ophion): New Insights into the Phylogeny of the Genus Ovis.

PLoS One 2015 4;10(12):e0144257. Epub 2015 Dec 4.

Department of Biomedical Sciences, University of Sassari, Sassari, Italy.

Sheep are thought to have been one of the first livestock to be domesticated in the Near East, thus playing an important role in human history. The current whole mitochondrial genome phylogeny for the genus Ovis is based on: the five main domestic haplogroups occurring among sheep (O. aries), along with molecular data from two wild European mouflons, three urials, and one argali. With the aim to shed some further light on the phylogenetic relationship within this genus, the first complete mitochondrial genome sequence of a Cypriot mouflon (O. gmelini ophion) is here reported. Phylogenetic analyses were performed using a dataset of whole Ovis mitogenomes as well as D-loop sequences. The concatenated sequence of 28 mitochondrial genes of one Cypriot mouflon, and the D-loop sequence of three Cypriot mouflons were compared to sequences obtained from samples representatives of the five domestic sheep haplogroups along with samples of the extant wild and feral sheep. The sample included also individuals from the Mediterranean islands of Sardinia and Corsica hosting remnants of the first wave of domestication that likely went then back to feral life. The divergence time between branches in the phylogenetic tree has been calculated using seven different calibration points by means of Bayesian and Maximum Likelihood inferences. Results suggest that urial (O. vignei) and argali (O. ammon) diverged from domestic sheep about 0.89 and 1.11 million years ago (MYA), respectively; and dates the earliest radiation of domestic sheep common ancestor at around 0.3 MYA. Additionally, our data suggest that the rise of the modern sheep haplogroups happened in the span of time between six and 32 thousand years ago (KYA). A close phylogenetic relationship between the Cypriot and the Anatolian mouflon carrying the X haplotype was detected. The genetic distance between this group and the other ovine haplogroups supports the hypothesis that it may be a new haplogroup never described before. Furthermore, the updated phylogenetic tree presented in this study determines a finer classification of ovine species and may help to classify more accurately new mitogenomes within the established haplogroups so far identified.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144257PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670089PMC
June 2016

First insights on the mitochondrial genetic variability of Lightiella magdalenina (Crustacea), the sole Mediterranean cephalocarid species.

J Biol Res (Thessalon) 2014 Dec 13;21(1). Epub 2014 May 13.

Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica - Università di Sassari, Via Francesco Muroni 25, 07100 Sassari, Italy.

Background: Here we report the first insight into the mitochondrial (Cytochrome c Oxidase subunit I - COI and Cytochrome b - Cyt b) genetic variation of the only Mediterranean cephalocarid Lightiella magdalenina.

Findings: COI sequences provide a scenario of low intraspecific variability, while significant genetic divergence occurs between L. magdalenina and L. incisa. Interestingly, Cyt b sequences reveal a higher degree of intraspecific variability, with no shared haplotypes between the sites considered.

Conclusions: In the future, COI and Cyt b molecular markers could be used as valuable tools to shed new light into the extant species within the genus Lightiella thus providing molecular support to the taxonomical identifications carried out on a morphological basis.
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http://dx.doi.org/10.1186/2241-5793-21-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376088PMC
December 2014

Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample.

BMC Res Notes 2015 Apr 30;8:174. Epub 2015 Apr 30.

Istituto di Ricerca Genetica e Biomedica CNR, Cagliari, Italy.

Background: Next-Generation Sequencing methods have led to a great increase in phylogenetically useful markers within the male specific portion of the Y chromosome, but previous studies have limited themselves to the study of the X-degenerate regions.

Methods: DNA was extracted from peripheral blood samples of adult males whose paternal grandfathers were born in Sardinia. The DNA samples were sequenced, genotyped and subsequently analysed for variant calling for approximately 23.1 Mbp of the Y chromosome. A phylogenetic tree was built using Network 4.6 software.

Results: From low coverage whole genome sequencing of 1,194 Sardinian males, we extracted 20,155 phylogenetically informative single nucleotide polymorphisms from the whole euchromatic region, including the X-degenerate, X-transposed, and Ampliconic regions, along with variants in other unclassified chromosome intervals and in the readable sequences of the heterochromatic region.

Conclusions: The non X-degenerate classes contain a significant portion of the phylogenetic variation of the whole chromosome and their inclusion in the analysis, almost doubling the number of informative polymorphisms, refining the known molecular phylogeny of the human Y chromosome.
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http://dx.doi.org/10.1186/s13104-015-1130-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423141PMC
April 2015

Mitochondrial and Y chromosome haplotype motifs as diagnostic markers of Jewish ancestry: a reconsideration.

Front Genet 2014 10;5:384. Epub 2014 Nov 10.

Division of Biological Anthropology, University of Cambridge Cambridge, UK ; Department of Biological, Geological and Environmental Sciences, University of Bologna Bologna, Italy.

Several authors have proposed haplotype motifs based on site variants at the mitochondrial genome (mtDNA) and the non-recombining portion of the Y chromosome (NRY) to trace the genealogies of Jewish people. Here, we analyzed their main approaches and test the feasibility of adopting motifs as ancestry markers through construction of a large database of mtDNA and NRY haplotypes from public genetic genealogical repositories. We verified the reliability of Jewish ancestry prediction based on the Cohen and Levite Modal Haplotypes in their "classical" 6 STR marker format or in the "extended" 12 STR format, as well as four founder mtDNA lineages (HVS-I segments) accounting for about 40% of the current population of Ashkenazi Jews. For this purpose we compared haplotype composition in individuals of self-reported Jewish ancestry with the rest of European, African or Middle Eastern samples, to test for non-random association of ethno-geographic groups and haplotypes. Overall, NRY and mtDNA based motifs, previously reported to differentiate between groups, were found to be more represented in Jewish compared to non-Jewish groups. However, this seems to stem from common ancestors of Jewish lineages being rather recent respect to ancestors of non-Jewish lineages with the same "haplotype signatures." Moreover, the polyphyly of haplotypes which contain the proposed motifs and the misuse of constant mutation rates heavily affected previous attempts to correctly dating the origin of common ancestries. Accordingly, our results stress the limitations of using the above haplotype motifs as reliable Jewish ancestry predictors and show its inadequacy for forensic or genealogical purposes.
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http://dx.doi.org/10.3389/fgene.2014.00384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4229899PMC
November 2014

Geographic population structure analysis of worldwide human populations infers their biogeographical origins.

Nat Commun 2014 Apr 29;5:3513. Epub 2014 Apr 29.

Department of ecology and evolutionary biology, University of Arizona, Tucson, Arizona 85721, USA.

The search for a method that utilizes biological information to predict humans' place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700 km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000-130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50 km of their villages. GPS's accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing.
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http://dx.doi.org/10.1038/ncomms4513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4007635PMC
April 2014

Linguistic, geographic and genetic isolation: a collaborative study of Italian populations.

J Anthropol Sci 2014 3;92:201-31. Epub 2014 Mar 3.

Istituto di Scienze Neurologiche, CNR, Mangone, Cosenza, Italy.

The animal and plant biodiversity of the Italian territory is known to be one of the richest in the Mediterranean basin and Europe as a whole, but does the genetic diversity of extant human populations show a comparable pattern? According to a number of studies, the genetic structure of Italian populations retains the signatures of complex peopling processes which took place from the Paleolithic to modern era. Although the observed patterns highlight a remarkable degree of genetic heterogeneity, they do not, however, take into account an important source of variation. In fact, Italy is home to numerous ethnolinguistic minorities which have yet to be studied systematically. Due to their difference in geographical origin and demographic history, such groups not only signal the cultural and social diversity of our country, but they are also potential contributors to its bio-anthropological heterogeneity. To fill this gap, research groups from four Italian Universities (Bologna, Cagliari, Pisa and Roma Sapienza) started a collaborative study in 2007, which was funded by the Italian Ministry of Education, University and Research and received partial support by the Istituto Italiano di Antropologia. In this paper, we present an account of the results obtained in the course of this initiative. Four case-studies relative to linguistic minorities from the Eastern Alps, Sardinia, Apennines and Southern Italy are first described and discussed, focusing on their micro-evolutionary and anthropological implications. Thereafter, we present the results of a systematic analysis of the relations between linguistic, geographic and genetic isolation. Integrating the data obtained in the course of the long-term study with literature and unpublished results on Italian populations, we show that a combination of linguistic and geographic factors is probably responsible for the presence of the most robust signatures of genetic isolation. Finally, we evaluate the magnitude of the diversity of Italian populations in the European context. The human genetic diversity of our country was found to be greater than observed throughout the continent at short (0-200 km) and intermediate (700-800km) distances, and accounted for most of the highest values of genetic distances observed at all geographic ranges. Interestingly, an important contribution to this pattern comes from the "linguistic islands"( e.g. German speaking groups of Sappada and Luserna from the Eastern Italian Alps), further proof of the importance of considering social and cultural factors when studying human genetic variation.
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http://dx.doi.org/10.4436/JASS.92001DOI Listing
February 2015

Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny.

Science 2013 Aug;341(6145):565-9

Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy.

Genetic variation within the male-specific portion of the Y chromosome (MSY) can clarify the origins of contemporary populations, but previous studies were hampered by partial genetic information. Population sequencing of 1204 Sardinian males identified 11,763 MSY single-nucleotide polymorphisms, 6751 of which have not previously been observed. We constructed a MSY phylogenetic tree containing all main haplogroups found in Europe, along with many Sardinian-specific lineage clusters within each haplogroup. The tree was calibrated with archaeological data from the initial expansion of the Sardinian population ~7700 years ago. The ages of nodes highlight different genetic strata in Sardinia and reveal the presumptive timing of coalescence with other human populations. We calculate a putative age for coalescence of ~180,000 to 200,000 years ago, which is consistent with previous mitochondrial DNA-based estimates.
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http://dx.doi.org/10.1126/science.1237947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500864PMC
August 2013

Mitochondrial DNA reveals genetic structuring of Pinna nobilis across the Mediterranean Sea.

PLoS One 2013 28;8(6):e67372. Epub 2013 Jun 28.

Dipartimento di Scienze della Natura e del Territorio-Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy.

Pinna nobilis is the largest endemic Mediterranean marine bivalve. During past centuries, various human activities have promoted the regression of its populations. As a consequence of stringent standards of protection, demographic expansions are currently reported in many sites. The aim of this study was to provide the first large broad-scale insight into the genetic variability of P. nobilis in the area that encompasses the western Mediterranean, Ionian Sea, and Adriatic Sea marine ecoregions. To accomplish this objective twenty-five populations from this area were surveyed using two mitochondrial DNA markers (COI and 16S). Our dataset was then merged with those obtained in other studies for the Aegean and Tunisian populations (eastern Mediterranean), and statistical analyses (Bayesian model-based clustering, median-joining network, AMOVA, mismatch distribution, Tajima's and Fu's neutrality tests and Bayesian skyline plots) were performed. The results revealed genetic divergence among three distinguishable areas: (1) western Mediterranean and Ionian Sea; (2) Adriatic Sea; and (3) Aegean Sea and Tunisian coastal areas. From a conservational point of view, populations from the three genetically divergent groups found may be considered as different management units.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067372PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696058PMC
January 2014

The GenoChip: a new tool for genetic anthropology.

Genome Biol Evol 2013 ;5(5):1021-31

Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, USA.

The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and nonmedical, and, through its Legacy Fund, supports locally led efforts to preserve indigenous and traditional cultures. Although the first phase of the project was focused on uniparentally inherited markers on the Y-chromosome and mitochondrial DNA (mtDNA), the current phase focuses on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism (SNP) genotyping, they were designed for medical genetic studies and contain medically related markers that are inappropriate for global population genetic studies. GenoChip, the Genographic Project's new genotyping array, was designed to resolve these issues and enable higher resolution research into outstanding questions in genetic anthropology. The GenoChip includes ancestry informative markers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was designed to identify all known Y-chromosome and mtDNA haplogroups. The chip was carefully vetted to avoid inclusion of medically relevant markers. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. The chip performances are illustrated in a principal component analysis for 14 worldwide populations. In summary, the GenoChip is a dedicated genotyping platform for genetic anthropology. With an unprecedented number of approximately 12,000 Y-chromosomal and approximately 3,300 mtDNA SNPs and over 130,000 autosomal and X-chromosomal SNPs without any known health, medical, or phenotypic relevance, the GenoChip is a useful tool for genetic anthropology and population genetics.
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http://dx.doi.org/10.1093/gbe/evt066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3673633PMC
December 2013

Mendelian breeding units versus standard sampling strategies: Mitochondrial DNA variation in southwest Sardinia.

Genet Mol Biol 2011 Apr 1;34(2):187-94. Epub 2011 Apr 1.

Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari, Italy.

We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region) in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3115307PMC
http://dx.doi.org/10.1590/s1415-47572011000200003DOI Listing
April 2011

Genetic affinities within a large global collection of pathogenic Leptospira: implications for strain identification and molecular epidemiology.

PLoS One 2010 Aug 27;5(8):e12637. Epub 2010 Aug 27.

Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, India.

Leptospirosis is an important zoonosis with widespread human health implications. The non-availability of accurate identification methods for the individualization of different Leptospira for outbreak investigations poses bountiful problems in the disease control arena. We harnessed fluorescent amplified fragment length polymorphism analysis (FAFLP) for Leptospira and investigated its utility in establishing genetic relationships among 271 isolates in the context of species level assignments of our global collection of isolates and strains obtained from a diverse array of hosts. In addition, this method was compared to an in-house multilocus sequence typing (MLST) method based on polymorphisms in three housekeeping genes, the rrs locus and two envelope proteins. Phylogenetic relationships were deduced based on bifurcating Neighbor-joining trees as well as median joining network analyses integrating both the FAFLP data and MLST based haplotypes. The phylogenetic relationships were also reproduced through Bayesian analysis of the multilocus sequence polymorphisms. We found FAFLP to be an important method for outbreak investigation and for clustering of isolates based on their geographical descent rather than by genome species types. The FAFLP method was, however, not able to convey much taxonomical utility sufficient to replace the highly tedious serotyping procedures in vogue. MLST, on the other hand, was found to be highly robust and efficient in identifying ancestral relationships and segregating the outbreak associated strains or otherwise according to their genome species status and, therefore, could unambiguously be applied for investigating phylogenetics of Leptospira in the context of taxonomy as well as gene flow. For instance, MLST was more efficient, as compared to FAFLP method, in clustering strains from the Andaman island of India, with their counterparts from mainland India and Sri Lanka, implying that such strains share genetic relationships and that leptospiral strains might be frequently circulating between the islands and the mainland.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012637PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929200PMC
August 2010

A comparison of Y-chromosome variation in Sardinia and Anatolia is more consistent with cultural rather than demic diffusion of agriculture.

PLoS One 2010 Apr 29;5(4):e10419. Epub 2010 Apr 29.

Dipartimento di Zoologia e Genetica evoluzionistica, Università di Sassari, Sassari, Italy.

Two alternative models have been proposed to explain the spread of agriculture in Europe during the Neolithic period. The demic diffusion model postulates the spreading of farmers from the Middle East along a Southeast to Northeast axis. Conversely, the cultural diffusion model assumes transmission of agricultural techniques without substantial movements of people. Support for the demic model derives largely from the observation of frequency gradients among some genetic variants, in particular haplogroups defined by single nucleotide polymorphisms (SNPs) in the Y-chromosome. A recent network analysis of the R-M269 Y chromosome lineage has purportedly corroborated Neolithic expansion from Anatolia, the site of diffusion of agriculture. However, the data are still controversial and the analyses so far performed are prone to a number of biases. In the present study we show that the addition of a single marker, DYSA7.2, dramatically changes the shape of the R-M269 network into a topology showing a clear Western-Eastern dichotomy not consistent with a radial diffusion of people from the Middle East. We have also assessed other Y-chromosome haplogroups proposed to be markers of the Neolithic diffusion of farmers and compared their intra-lineage variation--defined by short tandem repeats (STRs)--in Anatolia and in Sardinia, the only Western population where these lineages are present at appreciable frequencies and where there is substantial archaeological and genetic evidence of pre-Neolithic human occupation. The data indicate that Sardinia does not contain a subset of the variability present in Anatolia and that the shared variability between these populations is best explained by an earlier, pre-Neolithic dispersal of haplogroups from a common ancestral gene pool. Overall, these results are consistent with the cultural diffusion and do not support the demic model of agriculture diffusion.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010419PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2861676PMC
April 2010

Mitochondrial DNA patterns in the Iberian Northern plateau: population dynamics and substructure of the Zamora province.

Am J Phys Anthropol 2010 Aug;142(4):531-9

Unitat Antropologia Biològica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.

Several studies have shown the importance of recent events in the configuration of the genetic landscape of a specific territory. In this context, due to the phenomena of repopulation and demographic fluctuations that took place in recent centuries, the Iberian Northern plateau is a very interesting case study. The main aim of this work is to check if recent population movements together with existing boundaries (geographical and administrative) have influenced the current genetic composition of the area. To accomplish this general purpose, mitochondrial DNA variations of 214 individuals from a population located in the Western region of the Iberian Northern plateau (the province of Zamora) were analyzed. Results showed a typical Western European mitochondrial DNA haplogroup composition. However, unexpected high frequencies of U5, HV0, and L haplogroups were found in some regions. The analyses of microdifferentiation showed that there are differences between regions, but no geographic substructure organization can be noticed. It can be stated that the differences observed in the genetic pool of the sampled area at regional level results from the mixture of different populations carrying new lineages into this area at different points in history.
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http://dx.doi.org/10.1002/ajpa.21252DOI Listing
August 2010

Population structure of the Monocelis lineata (Proseriata, Monocelididae) species complex assessed by phylogenetic analysis of the mitochondrial Cytochrome c Oxidase subunit I (COI) gene.

Genet Mol Biol 2009 Oct 1;32(4):864-7. Epub 2009 Dec 1.

Dipartimento di Zoologia e Genetica Evoluzionistica, University of Sassari, Sassari Italy.

Monocelis lineata consists of a complex of sibling species, widespread in the Mediterranean and Atlantic Ocean. Previous genetic analysis placed in evidence at least four sibling species. Nevertheless, this research was not conclusive enough to fully resolve the complex or to infer the phylogeny/phylogeography of the group. We designed specific primers aiming at obtaining partial sequences of the mtDNA gene Cytochrome c Oxidase subunit I (COI) of M. lineata, and have identified 25 different haplotypes in 32 analyzed individuals. The dendrogram generated by Neighbor-Joining analysis confirmed the differentiation between Atlantic and Mediterranean siblings, as well as the occurrence of at least two Mediterranean sibling species. Thus validated, the method here presented appears as a valuable tool in population genetics and biodiversity surveys on the Monocelis lineata complex.
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http://dx.doi.org/10.1590/S1415-47572009005000076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3036892PMC
October 2009

Mitochondrial haplogroup U5b3: a distant echo of the epipaleolithic in Italy and the legacy of the early Sardinians.

Am J Hum Genet 2009 Jun 4;84(6):814-21. Epub 2009 Jun 4.

Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy.

There are extensive data indicating that some glacial refuge zones of southern Europe (Franco-Cantabria, Balkans, and Ukraine) were major genetic sources for the human recolonization of the continent at the beginning of the Holocene. Intriguingly, there is no genetic evidence that the refuge area located in the Italian Peninsula contributed to this process. Here we show, through phylogeographic analyses of mitochondrial DNA (mtDNA) variation performed at the highest level of molecular resolution (52 entire mitochondrial genomes), that the most likely homeland for U5b3-a haplogroup present at a very low frequency across Europe-was the Italian Peninsula. In contrast to mtDNA haplogroups that expanded from other refugia, the Holocene expansion of haplogroup U5b3 toward the North was restricted by the Alps and occurred only along the Mediterranean coasts, mainly toward nearby Provence (southern France). From there, approximately 7,000-9,000 years ago, a subclade of this haplogroup moved to Sardinia, possibly as a result of the obsidian trade that linked the two regions, leaving a distinctive signature in the modern people of the island. This scenario strikingly matches the age, distribution, and postulated geographic source of a Sardinian Y chromosome haplogroup (I2a2-M26), a paradigmatic case in the European context of a founder event marking both female and male lineages.
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http://dx.doi.org/10.1016/j.ajhg.2009.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694970PMC
June 2009

Y-chromosome based evidence for pre-neolithic origin of the genetically homogeneous but diverse Sardinian population: inference for association scans.

PLoS One 2008 Jan 9;3(1):e1430. Epub 2008 Jan 9.

Laboratorio di Immunogenetica, Ospedale Microcitemico, Cagliari, Italy.

The island of Sardinia shows a unique high incidence of several autoimmune diseases with multifactorial inheritance, particularly type 1 diabetes and multiple sclerosis. The prior knowledge of the genetic structure of this population is fundamental to establish the optimal design for association studies in these diseases. Previous work suggested that the Sardinians are a relatively homogenous population, but some reports were contradictory and data were largely based on variants subject to selection. For an unbiased assessment of genetic structure, we studied a combination of neutral Y-chromosome variants, 21 biallelic and 8 short tandem repeats (STRs) in 930 Sardinian males. We found a high degree of interindividual variation but a homogenous distribution of the detected variability in samples from three separate regions of the island. One haplogroup, I-M26, is rare or absent outside Sardinia and is very common (0.37 frequency) throughout the island, consistent with a founder effect. A Bayesian full likelihood analysis (BATWING) indicated that the time from the most recent common ancestor (TMRCA) of I-M26, was 21.0 (16.0-25.5) thousand years ago (KYA) and that the population began to expand 14.0 (7.8-22.0) KYA. These results suggest a largely pre-Neolithic settlement of the island with little subsequent gene flow from outside populations. Consequently, Sardinia is an especially attractive venue for case-control genome wide association scans in common multifactorial diseases. Concomitantly, the high degree of interindividual variation in the current population facilitates fine mapping efforts to pinpoint the aetiologic polymorphisms.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001430PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174525PMC
January 2008

History and geography of human Y-chromosome in Europe: a SNP perspective.

J Anthropol Sci 2008 ;86:59-89

Dipartimento di Zoologia e Genetica Evoluzionistica, Universitá di Sassari, via Muroni 25, 07100 Sassari, Italy.

The genetic variation observed in the modern European populations can be used to reconstruct the history of the human peopling of the continent. In recent times, a great importance has been given to uniparental markers such as the Y-chromosome. This chromosome, which is passed from father to son, does not have a counterpart subject to recombination and the only possible source of variation is mutation. The nucleotide changes accumulate over time in the molecule, with no rearrangement among lineages. Lately, the D-HPLC technique, which allows the effective detection of single nucleotide polymorphisms (SNPs), was used to boost the number of available polymorphisms on the Y-chromosome. Since the year 2000, a number of studies were aimed both at the reconstruction of Y-chromosome phylogeny and the geographic distribution of Y-chromosome variation in Europe. The distribution of distinctive Y-chromosome lineages can also display a correspondence with geography, thus providing patterns of affinity and clues concerning past human movements. It is therefore possible to recognize the effect of the colonization of Europe following the Last Glacial Maximum, both from the western Iberian and the eastern Balkan refuges. Other lineages show a migratory wave from the Near East, consistent with the demic diffusion model of agriculture. A minor east-west genetic cline was proposed as a signal of an expansion from north of the Black Sea, related with the diffusion of people speaking languages of the Indo-European family.
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September 2010

Genetic variation in prehistoric Sardinia.

Hum Genet 2007 Nov 13;122(3-4):327-36. Epub 2007 Jul 13.

Dipartimento di Biologia Animale e Genetica, Laboratorio di Antropologia, Università di Firenze, Firenze, Italy.

We sampled teeth from 53 ancient Sardinian (Nuragic) individuals who lived in the Late Bronze Age and Iron Age, between 3,430 and 2,700 years ago. After eliminating the samples that, in preliminary biochemical tests, did not show a high probability to yield reproducible results, we obtained 23 sequences of the mitochondrial DNA control region, which were associated to haplogroups by comparison with a dataset of modern sequences. The Nuragic samples show a remarkably low genetic diversity, comparable to that observed in ancient Iberians, but much lower than among the Etruscans. Most of these sequences have exact matches in two modern Sardinian populations, supporting a clear genealogical continuity from the Late Bronze Age up to current times. The Nuragic populations appear to be part of a large and geographically unstructured cluster of modern European populations, thus making it difficult to infer their evolutionary relationships. However, the low levels of genetic diversity, both within and among ancient samples, as opposed to the sharp differences among modern Sardinian samples, support the hypothesis of the expansion of a small group of maternally related individuals, and of comparatively recent differentiation of the Sardinian gene pools.
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http://dx.doi.org/10.1007/s00439-007-0403-6DOI Listing
November 2007

Ancestral European roots of Helicobacter pylori in India.

BMC Genomics 2007 Jun 20;8:184. Epub 2007 Jun 20.

Pathogen Evolution Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.

Background: The human gastric pathogen Helicobacter pylori is co-evolved with its host and therefore, origins and expansion of multiple populations and sub populations of H. pylori mirror ancient human migrations. Ancestral origins of H. pylori in the vast Indian subcontinent are debatable. It is not clear how different waves of human migrations in South Asia shaped the population structure of H. pylori. We tried to address these issues through mapping genetic origins of present day H. pylori in India and their genomic comparison with hundreds of isolates from different geographic regions.

Results: We attempted to dissect genetic identity of strains by multilocus sequence typing (MLST) of the 7 housekeeping genes (atpA, efp, ureI, ppa, mutY, trpC, yphC) and phylogeographic analysis of haplotypes using MEGA and NETWORK software while incorporating DNA sequences and genotyping data of whole cag pathogenicity-islands (cagPAI). The distribution of cagPAI genes within these strains was analyzed by using PCR and the geographic type of cagA phosphorylation motif EPIYA was determined by gene sequencing. All the isolates analyzed revealed European ancestry and belonged to H. pylori sub-population, hpEurope. The cagPAI harbored by Indian strains revealed European features upon PCR based analysis and whole PAI sequencing.

Conclusion: These observations suggest that H. pylori strains in India share ancestral origins with their European counterparts. Further, non-existence of other sub-populations such as hpAfrica and hpEastAsia, at least in our collection of isolates, suggest that the hpEurope strains enjoyed a special fitness advantage in Indian stomachs to out-compete any endogenous strains. These results also might support hypotheses related to gene flow in India through Indo-Aryans and arrival of Neolithic practices and languages from the Fertile Crescent.
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http://dx.doi.org/10.1186/1471-2164-8-184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1925095PMC
June 2007

Determination of human caucasian mitochondrial DNA haplogroups by means of a hierarchical approach.

Hum Biol 2004 Jun;76(3):431-53

Anthropology Unit, Department BABVE, Faculty of Sciences, Autonomous University of Barcelona, 08193 Bellaterra (Barcelona), Spain.

In this paper we propose a hierarchical approach that allows the screening of mitochondrial DNA (mtDNA) haplogroups in populations that have essentially West Eurasian mtDNA backgrounds but that could have some non-West Eurasian contributions. To develop and validate this scheme, we used data on 18 coding region polymorphisms (17 analyzed by RFLP analysis and 1 by sequencing) and sequences of hypervariable segment I (HVSI) of the mtDNA control region from the Azores Islands (Portugal) population. The proposed scheme allows the characterization of almost all West Eurasian and African major clusters by means of RFLPs. Furthermore, the scheme includes information on situations in which sequencing is pertinent to defining a particular haplogroup. The validity of the scheme is ensured by (1) using relatively stable polymorphic positions, (2) screening more than one position to define a specific haplogroup, and (3) typing confirmatory positions. Dubious samples can be resolved by sequencing. The robustness of this approach was assessed by sequencing all samples for HVSI, taking advantage of the previously established relationships between RFLPs and control region sequence polymorphisms. The use of this hierarchical approach avoids the screening of unnecessary control region polymorphisms and therefore results in a more rapid and cost-efficient screening than one in which all polymorphic positions are analyzed. Even if this approach leads to a lower level of phylogeographic resolution than the sequencing of all samples, it allows us to define population movements on a continental level and can be applied, unlike sequencing all samples, with a low cost in any laboratory.
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http://dx.doi.org/10.1353/hub.2004.0049DOI Listing
June 2004

Sex-related bias and exclusion mapping of the nonrecombinant portion of chromosome Y in human type 1 diabetes in the isolated founder population of Sardinia.

Diabetes 2002 Dec;51(12):3573-6

Dipartimento di Scienze Biomediche e Biotecnologie, Università di Cagliari, Ospedale Microcitemico, Via Jenner, Cagliari 09121, Italy.

A male excess in Sardinian type 1 diabetic cases has previously been reported and was largely restricted to those patients carrying the HLA-DR3/nonDR4 genotype. In the present study, we have measured the male- to-female (M:F) ratio in a sample set of 542 newly collected, early-onset type 1 diabetic Sardinian patients. This data not only confirm the excess of male type 1 diabetic patients overall (M:F ratio = 1.3, P = 3.9 x 10(-3)) but also that the bias in male incidence is largely confined to patients with the DR3/nonDR4 genotype (M:F ratio = 1.6, P = 2.0 x 10(-4)). These sex effects could be due to a role for allelic variation of the Y chromosome in the susceptibility to type 1 diabetes, but to date this chromosome has not been evaluated in type 1 diabetes. We, therefore, established the frequencies of the various chromosome Y lineages and haplotypes in 325 Sardinian male patients, which included 180 cases with the DR3/nonDR4 genotype, and 366 Sardinian male control subjects. Our results do not support a significant involvement of the Y chromosome in DR3/nonDR4 type 1 diabetic cases nor in early-onset type 1 diabetes as a whole. Other explanations, such as X chromosome-linked inheritance, are thus required for the male bias in incidence in type 1 diabetes in Sardinia.
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http://dx.doi.org/10.2337/diabetes.51.12.3573DOI Listing
December 2002

Surname analysis of the Corsican population reveals an agreement with geographical and linguistic structure.

J Biosoc Sci 2002 Jul;34(3):289-301

Dipartimento di Zoologia e Antropologia Biologica, Università di Sassari, Italy.

The surname is a cultural trait that is extremely useful for historical and linguistic studies and can effectively be used as a genetic marker. In many human populations the surname is inherited in the paternal lineage, and can therefore be considered a marker for the Y chromosome. In this study, surnames were recorded from the white pages of telephone directories in current use in Corsica in 1993. All surnames present in thirteen villages scattered over the whole island and covering the main historical regions were transcribed. Surname variability was found to be higher in coastal villages, and lower in more isolated communities. The isonymy detected among the thirteen villages allowed the calculation of kinship values, visualized in a tree showing two main clusters, one referring to the northern villages and one encompassing the villages of the south. The pattern reflects the administrative division of the island, with the exception of Vico, which belongs to the southern administrative region but is geographically close to the northern villages, and Ghisoni, which belongs to the northern district but is more similar to the village of Bastelica in the southern district. The data presented here show a structure in the surname distribution that is in substantial agreement with the geographical patterns. The kinship values are consistent with a moderated gene flow among villages producing a surname structure according to the geographic features of the territory.
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http://dx.doi.org/10.1017/s0021932002002894DOI Listing
July 2002