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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. 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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9. 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

12. 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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13. 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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15. 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

16. 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

19. 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

20. 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

21. 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

22. The GenoChip: A New Tool for Genetic Anthropology

Author

Elhaik, Eran, Greenspan, Elliott, Staats, Sean, Krahn, Thomas, Tyler-Smith, Chris, Xue, Yali, Tofanelli, Sergio, Francalacci, Paolo, Cucca, Francesco, Pagani, Luca, Jin, Li, Li, Hui, Schurr, Theodore G., Greenspan, Bennett, Wells, R. Spencer, and Consortium, the Genographic

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics
Abstract

The Genographic Project is an international effort using genetic data to chart human migratory history. The project is non-profit and non-medical, and through its Legacy Fund supports locally led efforts to preserve indigenous and traditional cultures. In its second phase, the project is focusing 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 SNP genotyping, they were designed for medical genetic studies and contain medically related markers that are not appropriate 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. We developed novel methods to identify AIMs and genomic regions that may be enriched with alleles shared with ancestral hominins. Overall, we collected and ascertained AIMs from over 450 populations. Containing an unprecedented number of Y-chromosomal and mtDNA SNPs and over 130,000 SNPs from the autosomes and X-chromosome, the chip was carefully vetted to avoid inclusion of medically relevant markers. The GenoChip results were successfully validated. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays for three continental populations. While 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 GenoChip is a dedicated genotyping platform for genetic anthropology and promises to be the most powerful tool available for assessing population structure and migration history., Comment: 11 pages, 5 Figures, 2 supplementary notes

Published
2012

25. Through the layers of the Ethiopian genome : a survey of human genetic variation based on genome-wide genotyping and re-sequencing data

Author

Pagani, Luca

Subjects
611, Ethiopia Genome Project, Biological Anthropology, Evolutionary Genetics
Abstract

Understanding our evolutionary history as a species has since long been one of the most attracting and controversial themes of the scientific investigation. From its geographical position, outstanding fossil record and richness of human diversity, the Horn of Africa and, particularly, the Ethiopian region offers an unmatched opportunity to investigate our origins from a genetic perspective. To carry out a genome-wide survey of this region, 13 out of the estimated 80 extant Ethiopian populations were typed on an Illumina Omni 1M SNP array. The results showed a good concordance between genetic and linguistic stratification and, overall, a complex population structure placing the Ethiopians in between North and Sub Saharan Africans, due to the recent non African gene flow which was dated at around 3000 years ago. Furthermore the SNP array data unveiled putative traces of the out of Africa migrations as well as, in two of the typed populations, signatures of genetic adaptation to high altitude. To obtain an unbiased, high resolution representation of the Ethiopian genetic landscape, 25 individuals from each of five populations were newly collected and sequenced on an Illumina HiSeq platform. These populations were chosen, from among the ones typed on the SNP array, to represent the main components of Ethiopian genetic diversity. Of the 25 samples per population, 24 were sequenced at low depth to generate a broad list of genetic variants, while one sample from each was sequenced at high depth to provide a higher resolution list of variants peculiar to each analysed population. The 125 Ethiopian genomes thus sequenced, while overall consistent with the genotyping results, described the Ethiopian populations in a less biased way than the SNP array data. Furthermore estimation of past effective population size fluctuations from the individual genomes unveiled a unique pattern in the ancestry of the Ethiopian populations in the early stages of human evolution. These results provide a data resource which can be used in future analyses.

Published
2013
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30. Genetic Signatures Reveal High-Altitude Adaptation in a Set of Ethiopian Populations

Author

Huerta-Sánchez, Emilia, DeGiorgio, Michael, Pagani, Luca, Tarekegn, Ayele, Ekong, Rosemary, Antao, Tiago, Cardona, Alexia, Montgomery, Hugh E, Cavalleri, Gianpiero L, Robbins, Peter A, Weale, Michael E, Bradman, Neil, Bekele, Endashaw, Kivisild, Toomas, Tyler-Smith, Chris, and Nielsen, Rasmus

Subjects
Biological Sciences, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Acclimatization, Altitude, Biological Evolution, Ethiopia, Gene Regulatory Networks, Genetics, Population, Genome-Wide Association Study, Humans, Hypoxia, Polymorphism, Single Nucleotide, Selection, Genetic, Transcriptome, adaptation to high altitude, natural selection, Biochemistry and Cell Biology, Evolutionary Biology, Biochemistry and cell biology, Evolutionary biology
Abstract

The Tibetan and Andean Plateaus and Ethiopian highlands are the largest regions to have long-term high-altitude residents. Such populations are exposed to lower barometric pressures and hence atmospheric partial pressures of oxygen. Such "hypobaric hypoxia" may limit physical functional capacity, reproductive health, and even survival. As such, selection of genetic variants advantageous to hypoxic adaptation is likely to have occurred. Identifying signatures of such selection is likely to help understanding of hypoxic adaptive processes. Here, we seek evidence of such positive selection using five Ethiopian populations, three of which are from high-altitude areas in Ethiopia. As these populations may have been recipients of Eurasian gene flow, we correct for this admixture. Using single-nucleotide polymorphism genotype data from multiple populations, we find the strongest signal of selection in BHLHE41 (also known as DEC2 or SHARP1). Remarkably, a major role of this gene is regulation of the same hypoxia response pathway on which selection has most strikingly been observed in both Tibetan and Andean populations. Because it is also an important player in the circadian rhythm pathway, BHLHE41 might also provide insights into the mechanisms underlying the recognized impacts of hypoxia on the circadian clock. These results support the view that Ethiopian, Andean, and Tibetan populations living at high altitude have adapted to hypoxia differently, with convergent evolution affecting different genes from the same pathway.

Published
2013

32. 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

35. Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals

Author

Jagoda, Evelyn, primary, Marnetto, Davide, primary, Senevirathne, Gayani, additional, Gonzalez, Victoria, additional, Baid, Kaushal, additional, Montinaro, Francesco, additional, Richard, Daniel, additional, Falzarano, Darryl, additional, LeBlanc, Emmanuelle V, additional, Colpitts, Che C, additional, Banerjee, Arinjay, additional, Pagani, Luca, additional, and Capellini, Terence D, additional

Published
2023
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36. Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Author

Universidad de Alicante. Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, 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, Fernández‐López de Pablo, Javier, 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, Krause, Johannes, Universidad de Alicante. Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, 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, Fernández‐López de Pablo, Javier, 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

Abstract

Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.

Published
2023

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

Author

Max Planck Society, European Research Council, 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 I., 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, Emy, Ricci, Stefano, Boschin, Francesco, 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, Baye, Priscilla, Gómez-Olivencia, Asier, González-Rabanal, Borja, González Morales, Manuel R., Marín-Arroyo, Ana B., López, Belén, Alonso-Llamazares, Carmen, Soler, Joaquim, Coromina, Neus, Rufí, Isaac, Straus, Lawrence G., Fernández-López de Pablo, Javier, Gómez-Puche, Magdalena, Esquembre-Bebia, Marco Aurelio, Max Planck Society, European Research Council, 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 I., 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, Emy, Ricci, Stefano, Boschin, Francesco, 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, Baye, Priscilla, Gómez-Olivencia, Asier, González-Rabanal, Borja, González Morales, Manuel R., Marín-Arroyo, Ana B., López, Belén, Alonso-Llamazares, Carmen, Soler, Joaquim, Coromina, Neus, Rufí, Isaac, Straus, Lawrence G., Fernández-López de Pablo, Javier, Gómez-Puche, Magdalena, and Esquembre-Bebia, Marco Aurelio

Abstract

Modern humans have populated Europe for more than 45,000 years. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.

Published
2023

48. The final results from the ARTIE experiment

Author

Pagani, Luca

Abstract

A measurement of the transmission coefficient for neutrons through a thick (∼3 atoms/b) liquid natural argon target in the energy range30−70keV was performed by the Argon Resonance Transmission Interaction Experiment (ARTIE) using a time of flight neutron beam at Los Alamos National Laboratory. In this energy range, theory predicts an anti-resonance in the40Ar cross section near57keV, but the existing data (Winters. et al.) does not support this. This discrepancy gives rise to significant uncertainty in the penetration depth of neutrons through liquid argon, an essential parameter for next-generation neutrino and dark matter experiments. In this talk, the ARTIE experiment's final results will be presented, which will improve the knowledge of neutron transport in argon. The ARTIE measurement of the total cross section as a function of energy is consistent with the existence of the anti-resonance near57keV, but not as deep as the theory predicts. A possible follow-on run with reduced systematic uncertainties is under discussion.

Published
2022
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49. Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy

Author

Raveane, Alessandro, primary, Molinaro, Ludovica, additional, Aneli, Serena, additional, Capodiferro, Marco Rosario, additional, de Gennaro, Luciana, additional, Ongaro, Linda, additional, Rambaldi Migliore, Nicola, additional, Soffiati, Sara, additional, Scarano, Teodoro, additional, Torroni, Antonio, additional, Achilli, Alessandro, additional, Ventura, Mario, additional, Pagani, Luca, additional, Capelli, Cristian, additional, Olivieri, Anna, additional, Bertolini, Francesco, additional, Semino, Ornella, additional, and Montinaro, Francesco, additional

Published
2022
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