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531 results on '"Pagani, Luca"'

4. Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Author

Posth, Cosimo, Yu, He, Ghalichi, Ayshin, Rougier, Hélène, Crevecoeur, Isabelle, Huang, Yilei, Ringbauer, Harald, Rohrlach, Adam B., Nägele, Kathrin, Villalba-Mouco, Vanessa, Radzeviciute, Rita, Ferraz, Tiago, Stoessel, Alexander, Tukhbatova, Rezeda, Drucker, Dorothée G., Lari, Martina, Modi, Alessandra, Vai, Stefania, Saupe, Tina, Scheib, Christiana L., Catalano, Giulio, Pagani, Luca, Talamo, Sahra, Fewlass, Helen, Klaric, Laurent, Morala, André, Rué, Mathieu, Madelaine, Stéphane, Crépin, Laurent, Caverne, Jean-Baptiste, Bocaege, Emmy, Ricci, Stefano, Boschin, Francesco, Bayle, Priscilla, Maureille, Bruno, Le Brun-Ricalens, Foni, Bordes, Jean-Guillaume, Oxilia, Gregorio, Bortolini, Eugenio, Bignon-Lau, Olivier, Debout, Grégory, Orliac, Michel, Zazzo, Antoine, Sparacello, Vitale, Starnini, Elisabetta, Sineo, Luca, van der Plicht, Johannes, Pecqueur, Laure, Merceron, Gildas, Garcia, Géraldine, Leuvrey, Jean-Michel, Garcia, Coralie Bay, Gómez-Olivencia, Asier, Połtowicz-Bobak, Marta, Bobak, Dariusz, Le Luyer, Mona, Storm, Paul, Hoffmann, Claudia, Kabaciński, Jacek, Filimonova, Tatiana, Shnaider, Svetlana, Berezina, Natalia, González-Rabanal, Borja, González Morales, Manuel R., Marín-Arroyo, Ana B., López, Belén, Alonso-Llamazares, Carmen, Ronchitelli, Annamaria, Polet, Caroline, Jadin, Ivan, Cauwe, Nicolas, Soler, Joaquim, Coromina, Neus, Rufí, Isaac, Cottiaux, Richard, Clark, Geoffrey, Straus, Lawrence G., Julien, Marie-Anne, Renhart, Silvia, Talaa, Dorothea, Benazzi, Stefano, Romandini, Matteo, Amkreutz, Luc, Bocherens, Hervé, Wißing, Christoph, Villotte, Sébastien, de Pablo, Javier Fernández-López, Gómez-Puche, Magdalena, Esquembre-Bebia, Marco Aurelio, Bodu, Pierre, Smits, Liesbeth, Souffi, Bénédicte, Jankauskas, Rimantas, Kozakaitė, Justina, Cupillard, Christophe, Benthien, Hartmut, Wehrberger, Kurt, Schmitz, Ralf W., Feine, Susanne C., Schüler, Tim, Thevenet, Corinne, Grigorescu, Dan, Lüth, Friedrich, Kotula, Andreas, Piezonka, Henny, Schopper, Franz, Svoboda, Jiří, Sázelová, Sandra, Chizhevsky, Andrey, Khokhlov, Aleksandr, Conard, Nicholas J., Valentin, Frédérique, Harvati, Katerina, Semal, Patrick, Jungklaus, Bettina, Suvorov, Alexander, Schulting, Rick, Moiseyev, Vyacheslav, Mannermaa, Kristiina, Buzhilova, Alexandra, Terberger, Thomas, Caramelli, David, Altena, Eveline, Haak, Wolfgang, and Krause, Johannes

Published
2023
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5. Light and Darkness: consistently coupling dark matter to photons via effective operators

Author

Arina, Chiara, Cheek, Andrew, Mimasu, Ken, and Pagani, Luca

Subjects
High Energy Physics - Phenomenology, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We revise the treatment of fermionic dark matter interacting with photons via dimension-5 and -6 effective operators. We show how the application of the effective operators beyond their validity introduces unphysical, gauge violating effects that are relevant for current experimental searches. Restoring gauge invariance by coupling dark matter to the hypercharge gauge field has implications for the parameter space above and below the electroweak scale. We review the phenomenology of these hypercharge form factors at the LHC as well as for direct and indirect detection experiments. We highlight where the electromagnetic and hypercharge descriptions lead to wildly different conclusions about the viable parameter space and the relative sensitivity of various probes. These include a drastic weakening of vector bosons fusion versus mono-jet searches at the LHC, and the incorrect impression that indirect searches could lead to better constraints than direct detection for larger dark matter masses. We find that the dimension-5 operators are strongly constrained by direct detection bounds, while for dimension-6 operators LHC mono-jet searches are competitive or performing better than the other probes we consider., Comment: 24 pages, 14 figures, 2 tables. Matches published version, additional information in figure 1

Published
2020
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6. DNA energy constraints shape biological evolutionary trajectories

Author

Fariselli, Piero, Taccioli, Cristian, Pagani, Luca, and Maritan, Amos

Subjects
Quantitative Biology - Biomolecules, Quantitative Biology - Genomics
Abstract

Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and patterns in the dsDNA sequence can emerge from the physical peculiarities of the dsDNA molecule itself and the maximum entropy principle alone, rather than from biological or environmental evolutionary pressure. The randomness justifies the human codon biases and context-dependent mutation patterns in human populations. Thus, the DNA "exceptional symmetries", emerged from the randomness, have to be taken into account when looking for the DNA encoded information. Our results suggest that the double helix energy constraints and, more generally, the physical properties of the dsDNA are the hard drivers of the overall DNA sequence architecture, whereas the biological selective processes act as soft drivers, which only under extraordinary circumstances overtake the overall entropy content of the genome., Comment: 21 pages, 8 figures

Published
2019

8. Fast and reliable ancestral reconstruction on ancient genotype data with non-negative Least square and Principal Component Analysis

Author

de Gennaro, Luciana, primary, Molinaro, Ludovica, additional, Raveane, Alessandro, additional, Santonastaso, Federica, additional, Saponetti, Sandro Sublimi, additional, Massi, Michela Carlotta, additional, Pagani, Luca, additional, Metspalu, Mait, additional, Hellenthal, Garrett, additional, Kivisild, Toomas, additional, Ventura, Mario, additional, and Montinaro, Francesco, additional

Published
2024
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10. Genomic variation in baboons from central Mozambique unveils complex evolutionary relationships with other Papio species

Author

Santander, Cindy, Molinaro, Ludovica, Mutti, Giacomo, Martínez, Felipe I., Mathe, Jacinto, Ferreira da Silva, Maria Joana, Caldon, Matteo, Oteo-Garcia, Gonzalo, Aldeias, Vera, Archer, Will, Bamford, Marion, Biro, Dora, Bobe, René, Braun, David R., Hammond, Philippa, Lüdecke, Tina, Pinto, Maria José, Meira Paulo, Luis, Stalmans, Marc, Regala, Frederico Tátá, Bertolini, Francesco, Moltke, Ida, Raveane, Alessandro, Pagani, Luca, Carvalho, Susana, and Capelli, Cristian

Published
2022
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11. Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans

Author

Jagoda, Evelyn, Lawson, Daniel J, Wall, Jeffrey D, Lambert, David, Muller, Craig, Westaway, Michael, Leavesley, Matthew, Capellini, Terence D, Mirazón Lahr, Marta, Gerbault, Pascale, Thomas, Mark G, Migliano, Andrea Bamberg, Willerslev, Eske, Metspalu, Mait, and Pagani, Luca

Subjects
Generic health relevance, adaptive introgression, Neanderthal, positive selection, archaic genomes, interferon, toll-like receptor, Biochemistry and Cell Biology, Evolutionary Biology, Genetics
Abstract

Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the postintrogression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI) in which archaic haplotypes rose to high frequencies in humans as a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse data set, we report novel cases of selection on introgressed variation in living humans and shortlist among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans.

Published
2018

13. The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal

Author

Vallini, Leonardo, primary, Zampieri, Carlo, additional, Shoaee, Mohamed Javad, additional, Bortolini, Eugenio, additional, Marciani, Giulia, additional, Aneli, Serena, additional, Pievani, Telmo, additional, Benazzi, Stefano, additional, Barausse, Alberto, additional, Mezzavilla, Massimo, additional, Petraglia, Michael D., additional, and Pagani, Luca, additional

Published
2024
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17. Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula

Author

Saupe, Tina, Montinaro, Francesco, Scaggion, Cinzia, Carrara, Nicola, Kivisild, Toomas, D’Atanasio, Eugenia, Hui, Ruoyun, Solnik, Anu, Lebrasseur, Ophélie, Larson, Greger, Alessandri, Luca, Arienzo, Ilenia, De Angelis, Flavio, Rolfo, Mario Federico, Skeates, Robin, Silvestri, Letizia, Beckett, Jessica, Talamo, Sahra, Dolfini, Andrea, Miari, Monica, Metspalu, Mait, Benazzi, Stefano, Capelli, Cristian, Pagani, Luca, and Scheib, Christiana L.

Published
2021
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18. Author Correction: Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Author

Posth, Cosimo, Yu, He, Ghalichi, Ayshin, Rougier, Hélène, Crevecoeur, Isabelle, Huang, Yilei, Ringbauer, Harald, Rohrlach, Adam B., Nägele, Kathrin, Villalba-Mouco, Vanessa, Radzeviciute, Rita, Ferraz, Tiago, Stoessel, Alexander, Tukhbatova, Rezeda, Drucker, Dorothée G., Lari, Martina, Modi, Alessandra, Vai, Stefania, Saupe, Tina, Scheib, Christiana L., Catalano, Giulio, Pagani, Luca, Talamo, Sahra, Fewlass, Helen, Klaric, Laurent, Morala, André, Rué, Mathieu, Madelaine, Stéphane, Crépin, Laurent, Caverne, Jean-Baptiste, Bocaege, Emmy, Ricci, Stefano, Boschin, Francesco, Bayle, Priscilla, Maureille, Bruno, Le Brun-Ricalens, Foni, Bordes, Jean-Guillaume, Oxilia, Gregorio, Bortolini, Eugenio, Bignon-Lau, Olivier, Debout, Grégory, Orliac, Michel, Zazzo, Antoine, Sparacello, Vitale, Starnini, Elisabetta, Sineo, Luca, van der Plicht, Johannes, Pecqueur, Laure, Merceron, Gildas, Garcia, Géraldine, Leuvrey, Jean-Michel, Garcia, Coralie Bay, Gómez-Olivencia, Asier, Połtowicz-Bobak, Marta, Bobak, Dariusz, Le Luyer, Mona, Storm, Paul, Hoffmann, Claudia, Kabaciński, Jacek, Filimonova, Tatiana, Shnaider, Svetlana, Berezina, Natalia, González-Rabanal, Borja, González Morales, Manuel R., Marín-Arroyo, Ana B., López, Belén, Alonso-Llamazares, Carmen, Ronchitelli, Annamaria, Polet, Caroline, Jadin, Ivan, Cauwe, Nicolas, Soler, Joaquim, Coromina, Neus, Rufí, Isaac, Cottiaux, Richard, Clark, Geoffrey, Straus, Lawrence G., Julien, Marie-Anne, Renhart, Silvia, Talaa, Dorothea, Benazzi, Stefano, Romandini, Matteo, Amkreutz, Luc, Bocherens, Hervé, Wißing, Christoph, Villotte, Sébastien, de Pablo, Javier Fernández-López, Gómez-Puche, Magdalena, Esquembre-Bebia, Marco Aurelio, Bodu, Pierre, Smits, Liesbeth, Souffi, Bénédicte, Jankauskas, Rimantas, Kozakaitė, Justina, Cupillard, Christophe, Benthien, Hartmut, Wehrberger, Kurt, Schmitz, Ralf W., Feine, Susanne C., Schüler, Tim, Thevenet, Corinne, Grigorescu, Dan, Lüth, Friedrich, Kotula, Andreas, Piezonka, Henny, Schopper, Franz, Svoboda, Jiří, Sázelová, Sandra, Chizhevsky, Andrey, Khokhlov, Aleksandr, Conard, Nicholas J., Valentin, Frédérique, Harvati, Katerina, Semal, Patrick, Jungklaus, Bettina, Suvorov, Alexander, Schulting, Rick, Moiseyev, Vyacheslav, Mannermaa, Kristiina, Buzhilova, Alexandra, Terberger, Thomas, Caramelli, David, Altena, Eveline, Haak, Wolfgang, and Krause, Johannes

Published
2023
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23. Genomic analyses inform on migration events during the peopling of Eurasia

Author

Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mörseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D, Cardona, Alexia, Mägi, Reedik, Sayres, Melissa A Wilson, Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L, Järve, Mari, Karmin, Monika, Jacobs, Guy S, Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C, Lambert, David M, Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D, Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, François-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P, Barashkov, Nikolay A, Škaro, Vedrana, Mulahasanovic´, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A, Lichman, Daria V, Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph TS, Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanović, Damir, Yepiskoposyan, Levon, Behar, Doron M, Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A, Osipova, Ludmila P, Lahr, Marta Mirazón, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K, Metspalu, Ene, Thomas, Mark G, Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, and Metspalu, Mait

Subjects
Human Genome, Biotechnology, Genetics, Generic health relevance, Africa, Animals, Asia, Datasets as Topic, Estonia, Europe, Fossils, Gene Flow, Genetics, Population, Genome, Human, Genomics, Heterozygote, History, Ancient, Human Migration, Humans, Native Hawaiian or Other Pacific Islander, Neanderthals, New Guinea, Population Dynamics, Racial Groups, General Science & Technology
Abstract

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

Published
2016

24. Global diversity in the TAS2R38 bitter taste receptor: revisiting a classic evolutionary PROPosal

Author

Risso, Davide S, Mezzavilla, Massimo, Pagani, Luca, Robino, Antonietta, Morini, Gabriella, Tofanelli, Sergio, Carrai, Maura, Campa, Daniele, Barale, Roberto, Caradonna, Fabio, Gasparini, Paolo, Luiselli, Donata, Wooding, Stephen, and Drayna, Dennis

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Nutrition, Databases, Genetic, Evolution, Molecular, Genetic Variation, Haplotypes, Humans, Linkage Disequilibrium, Phenylthiourea, Propylthiouracil, Receptors, G-Protein-Coupled, Selection, Genetic, Taste
Abstract

The ability to taste phenylthiocarbamide (PTC) and 6-n-propylthiouracil (PROP) is a polymorphic trait mediated by the TAS2R38 bitter taste receptor gene. It has long been hypothesized that global genetic diversity at this locus evolved under pervasive pressures from balancing natural selection. However, recent high-resolution population genetic studies of TAS2Rs suggest that demographic events have played a critical role in the evolution of these genes. We here utilized the largest TAS2R38 database yet analyzed, consisting of 5,589 individuals from 105 populations, to examine natural selection, haplotype frequencies and linkage disequilibrium to estimate the effects of both selection and demography on contemporary patterns of variation at this locus. We found signs of an ancient balancing selection acting on this gene but no post Out-Of-Africa departures from neutrality, implying that the current observed patterns of variation can be predominantly explained by demographic, rather than selective events. In addition, we found signatures of ancient selective forces acting on different African TAS2R38 haplotypes. Collectively our results provide evidence for a relaxation of recent selective forces acting on this gene and a revised hypothesis for the origins of the present-day worldwide distribution of TAS2R38 haplotypes.

Published
2016

29. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

Author

Xue, Yali, Prado-Martinez, Javier, Sudmant, Peter H, Narasimhan, Vagheesh, Ayub, Qasim, Szpak, Michal, Frandsen, Peter, Chen, Yuan, Yngvadottir, Bryndis, Cooper, David N, de Manuel, Marc, Hernandez-Rodriguez, Jessica, Lobon, Irene, Siegismund, Hans R, Pagani, Luca, Quail, Michael A, Hvilsom, Christina, Mudakikwa, Antoine, Eichler, Evan E, Cranfield, Michael R, Marques-Bonet, Tomas, Tyler-Smith, Chris, and Scally, Aylwyn

Subjects
Human Genome, Genetics, Biotechnology, Generic health relevance, Life on Land, Adaptation, Physiological, Animals, Biological Evolution, DNA Copy Number Variations, Democratic Republic of the Congo, Endangered Species, Female, Genetic Variation, Genome, Gorilla gorilla, Homozygote, Inbreeding, Linkage Disequilibrium, Male, Mutation, Population Dynamics, Rwanda, Selection, Genetic, Sequence Analysis, DNA, Species Specificity, Time Factors, General Science & Technology
Abstract

Mountain gorillas are an endangered great ape subspecies and a prominent focus for conservation, yet we know little about their genomic diversity and evolutionary past. We sequenced whole genomes from multiple wild individuals and compared the genomes of all four Gorilla subspecies. We found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation. A further recent decline in the mountain gorilla population has led to extensive inbreeding, such that individuals are typically homozygous at 34% of their sequence, leading to the purging of severely deleterious recessive mutations from the population. We discuss the causes of their decline and the consequences for their future survival.

Published
2015

30. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin, Monika, Saag, Lauri, Vicente, Mário, Sayres, Melissa A Wilson, Järve, Mari, Talas, Ulvi Gerst, Rootsi, Siiri, Ilumäe, Anne-Mai, Mägi, Reedik, Mitt, Mario, Pagani, Luca, Puurand, Tarmo, Faltyskova, Zuzana, Clemente, Florian, Cardona, Alexia, Metspalu, Ene, Sahakyan, Hovhannes, Yunusbayev, Bayazit, Hudjashov, Georgi, DeGiorgio, Michael, Loogväli, Eva-Liis, Eichstaedt, Christina, Eelmets, Mikk, Chaubey, Gyaneshwer, Tambets, Kristiina, Litvinov, Sergei, Mormina, Maru, Xue, Yali, Ayub, Qasim, Zoraqi, Grigor, Korneliussen, Thorfinn Sand, Akhatova, Farida, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Ricaut, François-Xavier, Kusuma, Pradiptajati, Razafindrazaka, Harilanto, Pierron, Denis, Cox, Murray P, Sultana, Gazi Nurun Nahar, Willerslev, Rane, Muller, Craig, Westaway, Michael, Lambert, David, Skaro, Vedrana, Kovačevic´, Lejla, Turdikulova, Shahlo, Dalimova, Dilbar, Khusainova, Rita, Trofimova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Lichman, Daria V, Isakova, Jainagul, Pocheshkhova, Elvira, Sabitov, Zhaxylyk, Barashkov, Nikolay A, Nymadawa, Pagbajabyn, Mihailov, Evelin, Seng, Joseph Wee Tien, Evseeva, Irina, Migliano, Andrea Bamberg, Abdullah, Syafiq, Andriadze, George, Primorac, Dragan, Atramentova, Lubov, Utevska, Olga, Yepiskoposyan, Levon, Marjanovic´, Damir, Kushniarevich, Alena, Behar, Doron M, Gilissen, Christian, Vissers, Lisenka, Veltman, Joris A, Balanovska, Elena, Derenko, Miroslava, Malyarchuk, Boris, Metspalu, Andres, Fedorova, Sardana, Eriksson, Anders, Manica, Andrea, Mendez, Fernando L, Karafet, Tatiana M, Veeramah, Krishna R, Bradman, Neil, Hammer, Michael F, Osipova, Ludmila P, Balanovsky, Oleg, Khusnutdinova, Elza K, Johnsen, Knut, Remm, Maido, Thomas, Mark G, Tyler-Smith, Chris, Underhill, Peter A, Willerslev, Eske, Nielsen, Rasmus, Metspalu, Mait, Villems, Richard, and Kivisild, Toomas

Subjects
Biological Sciences, Genetics, Human Genome, Base Sequence, Chromosomes, Human, Y, DNA, Mitochondrial, Evolution, Molecular, Genetic Variation, Genetics, Population, Haplotypes, Humans, Male, Models, Genetic, Phylogeny, Racial Groups, Sequence Analysis, DNA, Medical and Health Sciences, Bioinformatics
Abstract

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Published
2015

31. A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations

Author

Clemente, Florian J, Cardona, Alexia, Inchley, Charlotte E, Peter, Benjamin M, Jacobs, Guy, Pagani, Luca, Lawson, Daniel J, Antão, Tiago, Vicente, Mário, Mitt, Mario, DeGiorgio, Michael, Faltyskova, Zuzana, Xue, Yali, Ayub, Qasim, Szpak, Michal, Mägi, Reedik, Eriksson, Anders, Manica, Andrea, Raghavan, Maanasa, Rasmussen, Morten, Rasmussen, Simon, Willerslev, Eske, Vidal-Puig, Antonio, Tyler-Smith, Chris, Villems, Richard, Nielsen, Rasmus, Metspalu, Mait, Malyarchuk, Boris, Derenko, Miroslava, and Kivisild, Toomas

Subjects
Biological Sciences, Genetics, Human Genome, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6-23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment.

Published
2014

35. Female biased adult sex ratio in the Bronze Age cemetery of Shahr‐i Sokhta (Iran) as an indicator of long distance trade and matrilocality.

Author

Vincenti, Giorgia, Molinaro, Ludovica, Sajjadi, Seyed Mansur Seyed, Moradi, Hossein, Pagani, Luca, and Fabbri, Pier Francesco

Subjects
BRONZE Age, SEX ratio, X chromosome, ADULTS, SOCIAL status, SEX determination, WOMEN'S roles
Abstract

Objectives: This paper starts from the unusual observation of the overrepresentation of females among adults in the cemetery of Bronze Age Shahr‐i Sokhta (Seistan, Iran) and explores the post marital residence pattern. By integrating taphonomical (skeletal preservation), anthropological (sex ratio [SR], sexual dimorphism, stress indicators, age at death), archeological (long distance trade indicators, habitation floor area, social role of women), and ancient DNA (heterozygosity levels in X chromosomes) data we test the hypothesis of post marital matrilocality in the site. Methods: We computed the SR (pelvis‐based sex determination) in a random unpublished adult sample from the cemetery of Shahr‐i Sokhta and in two samples previously published by other authors. We used comparative data on SR from: a large Supra Regional multi‐chronological sample of sites, n = 47, with 8808 adult sexed individuals, from Southern Europe, Egypt, Middle East, Southern Russia; a Regional Bronze Age sample of sites (n = 10) from Bactria Margiana and Indus Valley with 1324 adult sexed individuals. We estimated the heterozygosity levels in X chromosomes compared with the rest of the autosomes on the assumption that in a matrilocal society females should show lower variability than men. Results: Adult SR in a sample (n = 549) from Shahr‐i Sokhta is 70.5, the overrepresentation of females is shared with Regional Bronze Age sites from Bactria Margiana (SR = 72.09) and Indus Valley (SR = 67.54). On the contrary, in a larger Supra Regional multi‐chronological sample of sites, mean SR ranges between 112.7 (Bronze Age) and 163.1 (Middle Ages). Taphonomical and anthropological indicators do not explain the overrepresentation of female skeletons. Archeological indicators suggest a high social status of women and that the society was devoted to long range trade activities. heterozygosity levels in X chromosomes are in agreement with a matrilocal society. Conclusions: Indicators suggest that Bronze Age Shahr‐ì Sokhta was a matrilocal society and that long distance trade was an important economic factor producing an overrepresentation of adult female skeletons in the cemetery. [ABSTRACT FROM AUTHOR]

Published
2024
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36. Ancient human parallel lineages within North America contributed to a coastal expansion

Author

Scheib, C. L., Li, Hongjie, Desai, Tariq, Link, Vivian, Kendall, Christopher, Dewar, Genevieve, Griffith, Peter William, Mörseburg, Alexander, Johnson, John R., Potter, Amiee, Kerr, Susan L., Endicott, Phillip, Lindo, John, Haber, Marc, Xue, Yali, Tyler-Smith, Chris, Sandhu, Manjinder S., Lorenz, Joseph G., Randall, Tori D., Faltyskova, Zuzana, Pagani, Luca, Danecek, Petr, O’Connell, Tamsin C., Martz, Patricia, Boraas, Alan S., Byrd, Brian F., Leventhal, Alan, Cambra, Rosemary, Williamson, Ronald, Lesage, Louis, Holguin, Brian, Soto, Ernestine Ygnacio-De, Rosas, JohnTommy, Metspalu, Mait, Stock, Jay T., Manica, Andrea, Scally, Aylwyn, Wegmann, Daniel, Malhi, Ripan S., and Kivisild, Toomas

Published
2018

45. Inferring patterns of folktale diffusion using genomic data

Author

Bortolini, Eugenio, Pagani, Luca, Crema, Enrico R., Sarno, Stefania, Barbieri, Chiara, Boattini, Alessio, Sazzini, Marco, da Silva, Sara Graca, Martini, Gessica, Metspalu, Mait, Pettener, Davide, Luiselli, Donata, and Tehrani, Jamshid J.

Published
2017

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