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4. Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise

Author

Robino, C., Ralf, A., Pasino, S., De Marchi, M.R., Ballantyne, K.N., Barbaro, A., Bini, C., Carnevali, E., Casarino, L., Di Gaetano, C., Fabbri, M., Ferri, G., Giardina, E., Gonzalez, A., Matullo, G., Nutini, A.L., Onofri, V., Piccinini, A., Piglionica, M., Ponzano, E., Previderè, C., Resta, N., Scarnicci, F., Seidita, G., Sorçaburu-Cigliero, S., Turrina, S., Verzeletti, A., and Kayser, M.

Published
2015
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8. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

Author

Raveane, A, Aneli, S, Montinaro, F, Athanasiadis, G, Barlera, S, Birolo, G, Boncoraglio, G, Di Blasio, A, Di Gaetano, C, Pagani, L, Parolo, S, Paschou, P, Piazza, A, Stamatoyannopoulos, G, Angius, A, Brucato, N, Cucca, F, Hellenthal, G, Mulas, A, Peyret-Guzzon, M, Zoledziewska, M, Baali, A, Bycroft, C, Cherkaoui, M, Chiaroni, J, Di Cristofaro, J, Dina, C, Dugoujon, J, Galan, P, Giemza, J, Kivisild, T, Mazieres, S, Melhaoui, M, Metspalu, M, Myers, S, Pereira, L, Ricaut, F, Brisighelli, F, Cardinali, I, Grugni, V, Lancioni, H, Pascali, V, Torroni, A, Semino, O, Matullo, G, Achilli, A, Olivieri, A, Capelli, C, Raveane A., Aneli S., Montinaro F., Athanasiadis G., Barlera S., Birolo G., Boncoraglio G., Di Blasio A. M., Di Gaetano C., Pagani L., Parolo S., Paschou P., Piazza A., Stamatoyannopoulos G., Angius A., Brucato N., Cucca F., Hellenthal G., Mulas A., Peyret-Guzzon M., Zoledziewska M., Baali A., Bycroft C., Cherkaoui M., Chiaroni J., Di Cristofaro J., Dina C., Dugoujon J. M., Galan P., Giemza J., Kivisild T., Mazieres S., Melhaoui M., Metspalu M., Myers S., Pereira L., Ricaut F. X., Brisighelli F., Cardinali I., Grugni V., Lancioni H., Pascali V. L., Torroni A., Semino O., Matullo G., Achilli A., Olivieri A., Capelli C., Raveane, A, Aneli, S, Montinaro, F, Athanasiadis, G, Barlera, S, Birolo, G, Boncoraglio, G, Di Blasio, A, Di Gaetano, C, Pagani, L, Parolo, S, Paschou, P, Piazza, A, Stamatoyannopoulos, G, Angius, A, Brucato, N, Cucca, F, Hellenthal, G, Mulas, A, Peyret-Guzzon, M, Zoledziewska, M, Baali, A, Bycroft, C, Cherkaoui, M, Chiaroni, J, Di Cristofaro, J, Dina, C, Dugoujon, J, Galan, P, Giemza, J, Kivisild, T, Mazieres, S, Melhaoui, M, Metspalu, M, Myers, S, Pereira, L, Ricaut, F, Brisighelli, F, Cardinali, I, Grugni, V, Lancioni, H, Pascali, V, Torroni, A, Semino, O, Matullo, G, Achilli, A, Olivieri, A, Capelli, C, Raveane A., Aneli S., Montinaro F., Athanasiadis G., Barlera S., Birolo G., Boncoraglio G., Di Blasio A. M., Di Gaetano C., Pagani L., Parolo S., Paschou P., Piazza A., Stamatoyannopoulos G., Angius A., Brucato N., Cucca F., Hellenthal G., Mulas A., Peyret-Guzzon M., Zoledziewska M., Baali A., Bycroft C., Cherkaoui M., Chiaroni J., Di Cristofaro J., Dina C., Dugoujon J. M., Galan P., Giemza J., Kivisild T., Mazieres S., Melhaoui M., Metspalu M., Myers S., Pereira L., Ricaut F. X., Brisighelli F., Cardinali I., Grugni V., Lancioni H., Pascali V. L., Torroni A., Semino O., Matullo G., Achilli A., Olivieri A., and Capelli C.

Abstract

European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.

Published
2019

13. Y-chromosomal STR haplotypes in Sicily.

Author

Robino, Carlo, Inturri, S., Gino, S., Torre, C., Di Gaetano, C., Crobu, F., Romano, V., Matullo, G., and Piazza, A.

Subjects
Sicilians -- Genetic aspects -- Analysis -- Research, Haplotypes -- Analysis -- Genetic aspects -- Research, Human population genetics -- Research -- Genetic aspects -- Analysis, Y chromosome -- Analysis -- Research -- Genetic aspects
Abstract

Abstract Eight Y-chromosomal short tandem repeats (STRs)--DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393 and DYS385--were typed in a population sample (n = 255) of unrelated Sicilian males from nine different [...]

Published
2006

14. Population data for Y-chromosome STR haplotypes from Piedmont (Italy).

Author

Cerutti, N., Marin, A., Di Gaetano, C., Pappi, R., Crobu, F., Riccardino, F., Matullo, G., and Piazza, A.

Subjects
Haplotypes -- Research -- Genetic aspects -- Analysis, Italians -- Genetic aspects -- Analysis -- Research, Human population genetics -- Research -- Genetic aspects -- Analysis, Y chromosome -- Analysis -- Research -- Genetic aspects
Abstract

Abstract Eight Y-chromosome STR loci (DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393 and DYS385) were analysed in a sample of 236 unrelated males from four towns of Piedmont (Trino, Biella, [...]

Published
2006

15. Y-chromosomal STR haplotypes in a population sample from continental Greece, and the islands of Crete and Chios.

Author

Robino, C., Varacalli, S., Gino, S., Chatzikyriakidou, A., Kouvatsi, A., Triantaphyllidis, C., Di Gaetano, C., Crobu, F., Matullo, G., Piazza, A., and Torre, C.

Subjects
Haplotypes -- Research, Population genetics -- Research, Y chromosome -- Research
Abstract

Abstract Eight Y-chromosomal short tandem repeats (STRs)--DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, and DYS385--were typed in a population sample (n = 113) of unrelated males from seven different regions [...]

Published
2004

18. WITHDRAWN: Corrigendum to ‘Development of an Italian RM Y-STR haplotype database: results of the 2013 GEFI collaborative exercise’ [Forensic. Sci. Int. Genet. 15 (2015) 56-63]

Author

Robino, C, Ralf, A, Pasino, S, De Marchi, MR, Ballantyne, KN, Barbaro, A, Bini, C, Carnevali, E, Casarino, L, Di Gaetano, C, Fabbri, M, Ferri, G, Giardina, E, Gonzalez, A, Matullo, G, Nutini, AL, Onofri, V, Piccinini, A, Piglionica, M, Ponzano, E, Previderè, C, Resta, N, Scarnicci, F, Seidita, G, Sorçaburu-Cigliero, S, Turrina, S, Verzeletti, A, and Kayser, M

Published
2018
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19. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

Author

Raveane, A., primary, Aneli, S., additional, Montinaro, F., additional, Athanasiadis, G., additional, Barlera, S., additional, Birolo, G., additional, Boncoraglio, G., additional, Di Blasio, A. M., additional, Di Gaetano, C., additional, Pagani, L., additional, Parolo, S., additional, Paschou, P., additional, Piazza, A., additional, Stamatoyannopoulos, G., additional, Angius, A., additional, Brucato, N., additional, Cucca, F., additional, Hellenthal, G., additional, Mulas, A., additional, Peyret-Guzzon, M., additional, Zoledziewska, M., additional, Baali, A., additional, Bycroft, C., additional, Cherkaoui, M., additional, Chiaroni, J., additional, Di Cristofaro, J., additional, Dina, C., additional, Dugoujon, J. M., additional, Galan, P., additional, Giemza, J., additional, Kivisild, T., additional, Mazieres, S., additional, Melhaoui, M., additional, Metspalu, M., additional, Myers, S., additional, Pereira, L., additional, Ricaut, F. X., additional, Brisighelli, F., additional, Cardinali, I., additional, Grugni, V., additional, Lancioni, H., additional, Pascali, V. L., additional, Torroni, A., additional, Semino, O., additional, Matullo, G., additional, Achilli, A., additional, Olivieri, A., additional, and Capelli, C., additional

Published
2019
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21. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

Author

Raveane, A., Aneli, S., Montinaro, F., Athanasiadis, G., Barlera, S., Birolo, G., Boncoraglio, G., Di Blasio, A. M., Di Gaetano, C., Pagani, L., Parolo, S., Paschou, P., Piazza, A., Stamatoyannopoulos, G., Angius, A., Brucato, N., Cucca, F., Hellenthal, G., Mulas, A., Peyret-Guzzon, M., Zoledziewska, M., Baali, A., Bycroft, C., Cherkaoui, M., Chiaroni, J., Di Cristofaro, J., Dina, C., Dugoujon, J. M., Galan, P., Giemza, J., Kivisild, T., Mazieres, S., Melhaoui, M., Metspalu, M., Myers, S., Pereira, L., Ricaut, F. X., Brisighelli, Francesca, Cardinali, I., Grugni, V., Lancioni, H., Pascali, Vincenzo Lorenzo, Torroni, A., Semino, O., Matullo, G., Achilli, A., Olivieri, A., Capelli, C., Brisighelli F. (ORCID:0000-0001-5469-4413), Pascali V. L. (ORCID:0000-0001-6520-5224), Raveane, A., Aneli, S., Montinaro, F., Athanasiadis, G., Barlera, S., Birolo, G., Boncoraglio, G., Di Blasio, A. M., Di Gaetano, C., Pagani, L., Parolo, S., Paschou, P., Piazza, A., Stamatoyannopoulos, G., Angius, A., Brucato, N., Cucca, F., Hellenthal, G., Mulas, A., Peyret-Guzzon, M., Zoledziewska, M., Baali, A., Bycroft, C., Cherkaoui, M., Chiaroni, J., Di Cristofaro, J., Dina, C., Dugoujon, J. M., Galan, P., Giemza, J., Kivisild, T., Mazieres, S., Melhaoui, M., Metspalu, M., Myers, S., Pereira, L., Ricaut, F. X., Brisighelli, Francesca, Cardinali, I., Grugni, V., Lancioni, H., Pascali, Vincenzo Lorenzo, Torroni, A., Semino, O., Matullo, G., Achilli, A., Olivieri, A., Capelli, C., Brisighelli F. (ORCID:0000-0001-5469-4413), and Pascali V. L. (ORCID:0000-0001-6520-5224)

Abstract

European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.

Published
2019

22. Corrigendum to 'Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise' [Forensic. Sci. Int. Genet. 15 (2015) 56–63] (S1872497314002245) (10.1016/j.fsigen.2014.10.008))

Author

Robino, C., Ralf, A., Pasino, S., De Marchi, M. R., Ballantyne, K. N., Barbaro, A., Bini, C., Carnevali, E., Casarino, L., Di Gaetano, C., Fabbri, M., Ferri, G., Giardina, E., Gonzalez, A., Matullo, G., Nutini, A. L., Onofri, V., Piccinini, A., Piglionica, M., Ponzano, E., Previderè, C., Resta, N., Scarnicci, F., Seidita, G., Sorçaburu-Cigliero, S., Turrina, S., Verzeletti, A., and Kayser, M.

Subjects
Socio-culturale, LS2_6
Published
2018

24. Corrigendum to “Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise” [Forensic. Sci. Int. Genet. 15 (2015) 56–63]

Author

Robino, C., primary, Ralf, A., additional, Pasino, S., additional, De Marchi, M.R., additional, Ballantyne, K.N., additional, Barbaro, A., additional, Bini, C., additional, Carnevali, E., additional, Casarino, L., additional, Di Gaetano, C., additional, Fabbri, M., additional, Ferri, G., additional, Giardina, E., additional, Gonzalez, A., additional, Matullo, G., additional, Nutini, A.L., additional, Onofri, V., additional, Piccinini, A., additional, Piglionica, M., additional, Ponzano, E., additional, Previderè, C., additional, Resta, N., additional, Scarnicci, F., additional, Seidita, G., additional, Sorçaburu-Cigliero, S., additional, Turrina, S., additional, Verzeletti, A., additional, and Kayser, M., additional

Published
2018
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27. Molecular characterization and population genetics of the DYS458.2 variant

Author

Ferri G., Robino C., Alù M., LUISELLI, DONATA, Tofanelli S., Caciagli L., Onofri V., Di Gaetano C., Crobu F., Beduschi G., Capelli C., PELOTTI, SUSI, Ferri G., Robino C., Alù M., Luiselli D., Tofanelli S., Caciagli L., Onofri V., pelotti S., Di Gaetano C., Crobu F., Beduschi G., and Capelli C.

Published
2008

28. A.Y-chromosomal STR haplotypes in Sicily

Author

ROBINO C, INTURRI S, GINO S, TORRE C, DI GAETANO C, CROBU F, MATULLO G, PIAZZA, ROMANO, Valentino, ROBINO C, INTURRI S, GINO S, TORRE C, DI GAETANO C, CROBU F, ROMANO VALENTINO, MATULLO G, and PIAZZA

Published
2005

29. Y chromosome diversity in Piedmont

Author

Caratti, Stefano, Di Gaetano, C, Matullo, G, Gino, S, Inturri, S, and Robino, C.

Subjects
Y-chromosome, STR, piedmont
Published
2012

30. The population genetic structure of Y chromosomes in 1338 italians

Author

Onofri, V., Buscemi, L., Caenazzo, L., Capelli, C., Carnevali, E., Cerri, N., Di Gaetano, C., Domenici, R., Ferri, G., Nutini, L., Pelotti, S., Previderè, C., Robino, C., Scarnicci, F., Fabbri, Matteo, Seidita, G., Roewer, L., Tagliabracci, A., and the GeFi Group

Published
2010

34. On the use of principal components in contemporany population genetics: a case study

Author

Gasparini, Mauro, Di Gaetano, C., Thió i Fernández de Henestrosa, Santiago, Martín Fernández, Josep Antoni, Universitat de Girona. Departament d'Informàtica i Matemàtica Aplicada, and Universitat de Girona. Departament d’Informàtica i Matemàtica Aplicada

Subjects
Genètica de poblacions -- Mètodes estadístics
Abstract

In human Population Genetics, routine applications of principal component techniques are often required. Population biologists make widespread use of certain discrete classifications of human samples into haplotypes, the monophyletic units of phylogenetic trees constructed from several single nucleotide bimorphisms hierarchically ordered. Compositional frequencies of the haplotypes are recorded within the different samples. Principal component techniques are then required as a dimension-reducing strategy to bring the dimension of the problem to a manageable level, say two, to allow for graphical analysis. Population biologists at large are not aware of the special features of compositional data and normally make use of the crude covariance of compositional relative frequencies to construct principal components. In this short note we present our experience with using traditional linear principal components or compositional principal components based on logratios, with reference to a specific dataset Geologische Vereinigung; Universitat de Barcelona, Equip de Recerca Arqueomètrica; Institut d’Estadística de Catalunya; International Association for Mathematical Geology; Patronat de l’Escola Politècnica Superior de la Universitat de Girona; Fundació privada: Girona, Universitat i Futur.

Published
2003

45. Autosomal Microsatellite and mtDNA Genetic Analysis in Sicily (Italy)

Author

Romano, V., primary, Cali, F., additional, Ragalmuto, A., additional, D'Anna, R. P., additional, Flugy, A., additional, De Leo, G., additional, Giambalvo, O., additional, Lisa, A., additional, Fiorani, O., additional, Di Gaetano, C., additional, Salerno, A., additional, Tamouza, R., additional, Charron, D., additional, Zei, G., additional, Matullo, G., additional, and Piazza, A., additional

Published
2003
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47. Aberrant function of the C-terminal tail of HIST1H1E Aacelerates cellular senescence and causes premature aging

Author

Giuseppe Matullo, Brett H. Graham, Elisa Coluzzi, Karit Reinson, Antonella Sgura, Monica H. Wojcik, Luca Pannone, Melissa P. Wasserstein, Lucia Pedace, Seema R. Lalani, Elena Carcarino, Daniela Q.C.M. Barge-Schaapveld, Anke Van Dijck, Austin Larson, Giovanna Carpentieri, Alessandro Bruselles, Simona Petrucci, Simone Pizzi, Elisabetta Flex, Cornelia Di Gaetano, Francesca Clementina Radio, Bruno Dallapiccola, Serena Cecchetti, Clara Viberti, Enrico Bertini, Chieko Chijiwa, Emilia K. Bijlsma, Elisabetta Ferretti, William J. Craigen, Cristina Andreoli, Brian G. Skotko, Daan J. Kamphuis, Alessandro De Luca, J. Louw Roos, Giuseppina Catanzaro, Sandra Kenis, Mariëtte J.V. Hoffer, Katrin Õunap, Maria Karayiorgou, Gijs W. E. Santen, Annette P.M. van den Elzen, Kathleen Brown, Haley Streff, M. E. Suzanne Lewis, Claudia A. L. Ruivenkamp, Xiaoyan Ge, Andrea Ciolfi, Nathalie Van der Aa, Marco Tartaglia, Rossella Rota, Amber Begtrup, Richard E. Person, Simone Martinelli, Koen L.I. van Gassen, R. Frank Kooy, Marije Meuwissen, Magdalena Walkiewicz, Evelina Miele, Marije Koopmans, Sander Pajusalu, Flex, E., Martinelli, S., Van Dijck, A., Ciolfi, A., Cecchetti, S., Coluzzi, E., Pannone, L., Andreoli, C., Radio, F. C., Pizzi, S., Carpentieri, G., Bruselles, A., Catanzaro, G., Pedace, L., Miele, E., Carcarino, E., Ge, X., Chijiwa, C., Lewis, M. E. S., Meuwissen, M., Kenis, S., Van der Aa, N., Larson, A., Brown, K., Wasserstein, M. P., Skotko, B. G., Begtrup, A., Person, R., Karayiorgou, M., Roos, J. L., Van Gassen, K. L., Koopmans, M., Bijlsma, E. K., Santen, G. W. E., Barge-Schaapveld, D. Q. C. M., Ruivenkamp, C. A. L., Hoffer, M. J. V., Lalani, S. R., Streff, H., Craigen, W. J., Graham, B. H., van den Elzen, A. P. M., Kamphuis, D. J., Ounap, K., Reinson, K., Pajusalu, S., Wojcik, M. H., Viberti, C., Di Gaetano, C., Bertini, E., Petrucci, S., De Luca, A., Rota, R., Ferretti, E., Matullo, G., Dallapiccola, B., Sgura, A., Walkiewicz, M., Kooy, R. F., and Tartaglia, M.

Subjects
0301 basic medicine, Premature aging, Senescence, Male, Cell division, methylation profiling, Article, Chromatin remodeling, chromatin remodeling, Histones, 03 medical and health sciences, chemistry.chemical_compound, replicative senescence, 0302 clinical medicine, HIST1H1E, chromatin dynamic, Genetics, accelerated aging, cellular senescence, Humans, Genetics(clinical), Child, Biology, Genetics (clinical), chromatin compaction, chromatin dynamics, linker histone, linker histone H1.4, Aneuploidy, Cell Nucleolus, Cellular Senescence, Chromatin, DNA Methylation, Female, Infant, Middle Aged, biology, DNA replication, Cell biology, 030104 developmental biology, Histone, chemistry, biology.protein, Human medicine, 030217 neurology & neurosurgery, DNA
Abstract

Histones mediate dynamic packaging of nuclear DNA in chromatin, a process that is precisely controlled to guarantee efficient compaction of the genome and proper chromosomal segregation during cell division and to accomplish DNA replication, transcription, and repair. Due to the important structural and regulatory roles played by histones, it is not surprising that histone functional dysregulation or aberrant levels of histones can have severe consequences for multiple cellular processes and ultimately might affect development or contribute to cell transformation. Recently, germline frameshift mutations involving the C-terminal tail of HIST1H1E, which is a widely expressed member of the linker histone family and facilitates higher-order chromatin folding, have been causally linked to an as-yet poorly defined syndrome that includes intellectual disability. We report that these mutations result in stable proteins that reside in the nucleus, bind to chromatin, disrupt proper compaction of DNA, and are associated with a specific methylation pattern. Cells expressing these mutant proteins have a dramatically reduced proliferation rate and competence, hardly enter into the S phase, and undergo accelerated senescence. Remarkably, clinical assessment of a relatively large cohort of subjects sharing these mutations revealed a premature aging phenotype as a previously unrecognized feature of the disorder. Our findings identify a direct link between aberrant chromatin remodeling, cellular senescence, and accelerated aging.

Published
2019

48. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

Author

Simona Barlera, Giovanni Birolo, Simon Myers, Viola Grugni, Vincenzo Lorenzo Pascali, Andrea Angius, Mait Metspalu, Francesca Brisighelli, Antonio Torroni, Francesco Montinaro, Hovirag Lancioni, Luísa Pereira, Antonella Mulas, Mohammed Melhaoui, Alessandro Achilli, Serena Aneli, Mohammed Cherkaoui, Peristera Paschou, M. Peyret-Guzzon, Pilar Galan, Giorgio B. Boncoraglio, A. M. Di Blasio, Stéphane Mazières, C. Di Gaetano, Garrett Hellenthal, Giuseppe Matullo, George Stamatoyannopoulos, Joanna Giemza, J. Di Cristofaro, Magdalena Zoledziewska, Irene Cardinali, Georgios Athanasiadis, Cristian Capelli, François-Xavier Ricaut, Jacques Chiaroni, Anna Olivieri, Alessandro Raveane, Luca Pagani, Toomas Kivisild, Abdellatif Baali, Nicolas Brucato, Christian Dina, Jean-Michel Dugoujon, Clare Bycroft, Alberto Piazza, Silvia Parolo, Francesco Cucca, Ornella Semino, Dipartimento di Biologia e Biotecnologie ‘Lazzaro Spallanzani’, University of Pavia, University of Pavia, University of Oxford [Oxford], Aarhus University [Aarhus], Istituto di Ricerche Farmacologiche Mario Negri, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione 'Istituto Neurologico Nazionale C. Mondino'-Fondazione 'Istituto Neurologico Nazionale C. Mondino', University of Turin, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Dipartimento di Genetica, Biologica e Biochimica, Università degli studi di Torino (UNITO), Laboratoire d'Etude du Rayonnement et de la Matière en Astrophysique (LERMA), École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Centre National de la Recherche Scientifique (CNRS), Georgia Tech - CNRS [Metz] (UMI2958), Ecole Nationale Supérieure des Arts et Metiers Metz-SUPELEC-Georgia Institute of Technology [Atlanta]-Georgia Institute of Technology [Lorraine, France]-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Génétique des maladies multifactorielles (GMM), Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche en Epidémiologie Nutritionnelle (UREN), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Sorbonne Paris Cité (USPC)-Université Paris 13 (UP13)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut National de la Recherche Agronomique (INRA), Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC), Centre National de la Recherche Scientifique (CNRS), Dipartimento di Genetica e Microbiologica, Università di Pavia, Dipartimento di Genetica e Microbiologia, Instituto de Investigação e Inovação em Saúde, Raveane, A, Aneli, S, Montinaro, F, Athanasiadis, G, Barlera, S, Birolo, G, Boncoraglio, G, Di Blasio, A, Di Gaetano, C, Pagani, L, Parolo, S, Paschou, P, Piazza, A, Stamatoyannopoulos, G, Angius, A, Brucato, N, Cucca, F, Hellenthal, G, Mulas, A, Peyret-Guzzon, M, Zoledziewska, M, Baali, A, Bycroft, C, Cherkaoui, M, Chiaroni, J, Di Cristofaro, J, Dina, C, Dugoujon, J, Galan, P, Giemza, J, Kivisild, T, Mazieres, S, Melhaoui, M, Metspalu, M, Myers, S, Pereira, L, Ricaut, F, Brisighelli, F, Cardinali, I, Grugni, V, Lancioni, H, Pascali, V, Torroni, A, Semino, O, Matullo, G, Achilli, A, Olivieri, A, Capelli, C, Mazières, Stéphane, Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani' = Department of Biology and Biotechnology [Univ di Pavia] (DBB UNIPV), Università degli Studi di Pavia = University of Pavia (UNIPV), University of Oxford, Università degli studi di Torino = University of Turin (UNITO), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université de Cergy Pontoise (UCP), Georgia Tech Lorraine [Metz], Ecole Nationale Supérieure des Arts et Metiers Metz-Georgia Institute of Technology [Atlanta]-Ecole Supérieure d'Electricité - SUPELEC (FRANCE)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), École normale supérieure - Paris (ENS Paris), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Sorbonne Paris Cité (USPC)-Université Paris 13 (UP13)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut National de la Recherche Agronomique (INRA), HESAM Université (HESAM)-HESAM Université (HESAM)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA), Università degli Studi di Pavia, Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Paris 13 (UP13)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), and Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
SELECTION, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Distribution (economics), Population genetics, Neanderthal genome project, 0302 clinical medicine, Peninsula, HISTORY, Databases, Genetic, ADAPTATION, Research Articles, History, Ancient, media_common, Neanderthals, MODERN HUMANS, 0303 health sciences, Multidisciplinary, geography.geographical_feature_category, POPULATION GENETICS, GENOMICS, EUROPE, Population Genetic, SciAdv r-articles, ASSOCIATION, [SHS.ANTHRO-BIO] Humanities and Social Sciences/Biological anthropology, Multidisciplinary Sciences, ADMIXTURE, Geography, Italy, Ethnology, Science & Technology - Other Topics, Neanderthals / genetics, Research Article, EUROPE, MIGRATION, media_common.quotation_subject, Pastoralism, Human Genetic, Settore BIO/08 - ANTROPOLOGIA, GENETIC-STRUCTURE, SEQUENCE, White People, 03 medical and health sciences, Bronze Age, POPULATION GENETICS, Genetic variation, Animals, Humans, DNA, Ancient, European Continental Ancestry Group / genetics, 030304 developmental biology, Science & Technology, business.industry, Genome, Human, Genetic Drift, Human Genetics, Anthropology, GENOME-WIDE PATTERNS, business, GENOMICS, 030217 neurology & neurosurgery, Diversity (politics), Genome-Wide Association Study
Abstract

A population in a natural crossroad within Europe reveals multiple ancient contributions and substantial population structure., European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non–steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.

Published
2019
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49. Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise

Author

Andrea Piccinini, Solange Sorçaburu-Cigliero, Gregorio Seidita, A. Gonzalez, Andrea Verzeletti, Emiliano Giardina, E. Ponzano, Marilidia Piglionica, Carlo Robino, Giuseppe Matullo, Arwin Ralf, Manfred Kayser, Francesca Scarnicci, Carla Bini, A.L. Nutini, Valerio Onofri, C. Di Gaetano, Gianmarco Ferri, Stefania Turrina, Nicoletta Resta, M. De Marchi, Matteo Fabbri, Kaye N. Ballantyne, L. Casarino, A. Barbaro, Eugenia Carnevali, S Pasino, Carlo Previderè, Robino, C., Ralf, A., Pasino, S., De Marchi, M., Ballantyne, K., Barbaro, A., Bini, C., Carnevali, E., Casarino, L., Di Gaetano, C., Fabbri, M., Ferri, G., Giardina, E., Gonzalez, A., Matullo, G., Nutini, A., Onofri, V., Piccinini, A., Piglionica, M., Ponzano, E., Previderè, C., Resta, N., Scarnicci, F., Seidita, G., Sorçaburu-Cigliero, S., Turrina, S., Verzeletti, A., Kayser, M., and Genetic Identification

Subjects
Quality Control, Mutation rate, Regional Italian, Lineage differentiation, DNA Primer, Y-chromosome, Rapidly mutating Y-STRs (RM Y-STRs), Haplotype, Relative differentiation, Italy, Biology, computer.software_genre, Pathology and Forensic Medicine, Genetic, Databases, Genetic, Genetics, Haplotype, Italy, Lineage differentiation, Rapidly mutating Y-STRs (RM Y-STRs), Relative differentiation, Y-chromosome, Humans, Y-STR, Cooperative Behavior, DNA Primers, Chromosomes, Human, Y, Database, Base Sequence, Medicine (all), humanities, Forensic science, Haplotypes, Microsatellite, Haplotype estimation, computer, Human
Abstract

Recently introduced rapidly mutating Y-chromosomal short tandem repeat (RM Y-STR) loci, displaying a multiple-fold higher mutation rate relative to any other Y-STRs, including those conventionally used in forensic casework, have been demonstrated to improve the resolution of male lineage differentiation and to allow male relative separation usually impossible with standard Y-STRs. However, large and geographically-detailed frequency haplotype databases are required to estimate the statistical weight of RM Y-STR haplotype matches if observed in forensic casework. With this in mind, the Italian Working Group (GEFI) of the International Society for Forensic Genetics launched a collaborative exercise aimed at generating an Italian quality controlled forensic RM Y-STR haplotype database. Overall 1509 male individuals from 13 regional populations covering northern, central and southern areas of the Italian peninsula plus Sicily were collected, including both "rural'' and "urban'' samples classified according to population density in the sampling area. A subset of individuals was additionally genotyped for Y-STR loci included in the Yfiler and PowerPlex Y23 (PPY23) systems (75% and 62%, respectively), allowing the comparison of RM and conventional Y-STRs. Considering the whole set of 13 RM Y-STRs, 1501 unique haplotypes were observed among the 1509 sampled Italian men with a haplotype diversity of 0.999996, largely superior to Yfiler and PPY23 with 0.999914 and 0.999950, respectively. AMOVA indicated that 99.996% of the haplotype variation was within populations, confirming that genetic-geographic structure is almost undetected by RM Y-STRs. Haplotype sharing among regional Italian populations was not observed at all with the complete set of 13 RM Y-STRs. Haplotype sharing within Italian populations was very rare (0.27% non-unique haplotypes), and lower in urban (0.22%) than rural (0.29%) areas. Additionally, 422 father-son pairs were investigated, and 20.1% of them could be discriminated by the whole set of 13 RM Y-STRs, which was very close to the theoretically expected estimate of 19.5% given the mutation rates of the markers used. Results obtained from a high-coverage Italian haplotype dataset confirm on the regional scale the exceptional ability of RM Y-STRs to resolve male lineages previously observed globally, and attest the unsurpassed value of RM Y-STRs for male-relative differentiation purposes. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

Published
2014

50. A molecular approach to the taxonomy and biogeography of African parrots

Author

Matteo Piazza, Margherita Randazzo, Renato Massa, Maurizio Sarà, Goffredo Cognetti, Cornelia Di Gaetano, Massa R., Sara' M., Piazza M., Di Gaetano C., Randazzo M., and Cognetti G.

Subjects
Poicephalus, Speciation, Biogeography, Dendrogram, Settore BIO/05 - Zoologia, Zoology, Genetic relationship, DNA, Biology, biology.organism_classification, Animal Science and Zoology, Taxonomy (biology), Genus Poicephalus
Abstract

Random amplified polymorphic DNA analysis of blood samples from eight African parrot species was performed to study the genetic relationship within the genus Poicephalus and among Poi-cephalus and the two other main African parrot genuses, Agapornis and Psittacus. To this end, DNA from six Poicephalus species, one species, of the Agapornis group and the single Psittacus species was analysed. The amplification pattern was then converted into a binary matrix and scored by the unweighted pair-group method algorithm. The resulting dendrogram showed a neat separation of all the Poicephalus on one side, from Psittacus-Agapornis on the other side. Among the six analysed species of Poicephalus, two larger clusters occurred, one containing four species belonging to the P. meyeri superspecies and the other one containing the two species pertaining to the P. robustus superspecies. The larger one of these is further subdivided in two smaller clusters, each one containing two species, that is P. meyeri-P. cryptoxanthus and P. senegalus-P. rufiventris, respectively. These results are consistent with the hypothesis that the genus Poicephalus is a natural assemblage that, after undergoing a very early separation from Psittacus and Agapornis, was subsequently affected by a number of discrete speciation events, especially during episodes of aridity resulting in fragmentation of forest habitats. © 2000 Taylor & Francis Group, LLC.

Published
2000
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