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101. A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

Author

Fu, Qiaomei, primary, Mittnik, Alissa, additional, Johnson, Philip L.F., additional, Bos, Kirsten, additional, Lari, Martina, additional, Bollongino, Ruth, additional, Sun, Chengkai, additional, Giemsch, Liane, additional, Schmitz, Ralf, additional, Burger, Joachim, additional, Ronchitelli, Anna Maria, additional, Martini, Fabio, additional, Cremonesi, Renata G., additional, Svoboda, Jiří, additional, Bauer, Peter, additional, Caramelli, David, additional, Castellano, Sergi, additional, Reich, David, additional, Pääbo, Svante, additional, and Krause, Johannes, additional

Published
2013
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104. Origins and Evolution of the Etruscans’ mtDNA

Author

Ghirotto, Silvia, primary, Tassi, Francesca, additional, Fumagalli, Erica, additional, Colonna, Vincenza, additional, Sandionigi, Anna, additional, Lari, Martina, additional, Vai, Stefania, additional, Petiti, Emmanuele, additional, Corti, Giorgio, additional, Rizzi, Ermanno, additional, De Bellis, Gianluca, additional, Caramelli, David, additional, and Barbujani, Guido, additional

Published
2013
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107. The Mountain Meadows Massacre and “poisoned springs”: scientific testing of the more recent, anthrax theory

Author

Perego, Ugo A., primary, Achilli, Alessandro, additional, Ekins, Jayne E., additional, Milani, Lucio, additional, Lari, Martina, additional, Pilli, Elena, additional, Brown, Alexis, additional, Price, Erin P., additional, Wolken, Spenser R., additional, Matthews, Molly, additional, Allen, Christina A., additional, Pearson, Talima R., additional, Angerhofer, Norman, additional, Caramelli, David, additional, Kupferschmid, Tim, additional, Keim, Paul S., additional, and Woodward, Scott R., additional

Published
2012
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108. The Complete Mitochondrial Genome of an 11,450-year-old Aurochsen (Bos primigenius) from Central Italy

Author

Lari, Martina, primary, Rizzi, Ermanno, additional, Mona, Stefano, additional, Corti, Giorgio, additional, Catalano, Giulio, additional, Chen, Kefei, additional, Vernesi, Cristiano, additional, Larson, Greger, additional, Boscato, Paolo, additional, De Bellis, Gianluca, additional, Cooper, Alan, additional, Caramelli, David, additional, and Bertorelle, Giorgio, additional

Published
2011
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109. The Microcephalin Ancestral Allele in a Neanderthal Individual

Author

Lari, Martina, primary, Rizzi, Ermanno, additional, Milani, Lucio, additional, Corti, Giorgio, additional, Balsamo, Carlotta, additional, Vai, Stefania, additional, Catalano, Giulio, additional, Pilli, Elena, additional, Longo, Laura, additional, Condemi, Silvana, additional, Giunti, Paolo, additional, Hänni, Catherine, additional, De Bellis, Gianluca, additional, Orlando, Ludovic, additional, Barbujani, Guido, additional, and Caramelli, David, additional

Published
2010
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110. Population dynamic of the extinct European aurochs: genetic evidence of a north-south differentiation pattern and no evidence of post-glacial expansion

Author

Mona, Stefano, primary, Catalano, Giulio, additional, Lari, Martina, additional, Larson, Greger, additional, Boscato, Paolo, additional, Casoli, Antonella, additional, Sineo, Luca, additional, Di Patti, Carolina, additional, Pecchioli, Elena, additional, Caramelli, David, additional, and Bertorelle, Giorgio, additional

Published
2010
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111. A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences

Author

Caramelli, David, primary, Milani, Lucio, additional, Vai, Stefania, additional, Modi, Alessandra, additional, Pecchioli, Elena, additional, Girardi, Matteo, additional, Pilli, Elena, additional, Lari, Martina, additional, Lippi, Barbara, additional, Ronchitelli, Annamaria, additional, Mallegni, Francesco, additional, Casoli, Antonella, additional, Bertorelle, Giorgio, additional, and Barbujani, Guido, additional

Published
2008
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112. The Origin of Native Americans from a Mitochondrial DNA Viewpoint

Author

PEREGO, Ugo A, primary, Achilli, Alessandro, additional, Milani, Lucio, additional, Lari, Martina, additional, Pala, Maria, additional, Olivieri, Anna, additional, Kashani, Baharak, additional, Gomez-Palmieri, J. Edgar, additional, Angerhofer, Norman, additional, Hughes, Robert, additional, Ritchie, Katie H, additional, Myres, Natalie M, additional, Woodward, Scott R, additional, Caramelli, David, additional, and Torroni, Antonio, additional

Published
2008
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114. A highly divergent mtDNA sequence in a Neandertal individual from Italy

Author

Caramelli, David, primary, Lalueza-Fox, Carles, additional, Condemi, Silvana, additional, Longo, Laura, additional, Milani, Lucio, additional, Manfredini, Alessandro, additional, de Saint Pierre, Michelle, additional, Adoni, Francesca, additional, Lari, Martina, additional, Giunti, Paolo, additional, Ricci, Stefano, additional, Casoli, Antonella, additional, Calafell, Francesc, additional, Mallegni, Francesco, additional, Bertranpetit, Jaume, additional, Stanyon, Roscoe, additional, Bertorelle, Giorgio, additional, and Barbujani, Guido, additional

Published
2006
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115. Specific inactivation of two immunomodulatory SIGLEC genes during human evolution.

Author

Xiaoxia Wang, Mitra, Nivedita, Secundino, Ismael, Banda, Kalyan, Cruz, Pedro, Padler-Karavani, Vered, Verhagen, Andrea, Reid, Chris, Lari, Martina, Rizzi, Ermanno, Balsamo, Carlotta, Corti, Giorgio, De Bellis, Gianluca, Longo, Laura, Beggs, William, Caramelli, David, Tishkoff, Sarah A., Hayakawa, Toshiyuki, Green, Eric D., and Mullikin, James C.

Subjects
IMMUNOREGULATION, HUMAN evolution, SIALIC acids, LECTINS, CHIMPANZEES, MESSENGER RNA, CELLULAR immunity, NATURAL immunity
Abstract

Sialic acid-recognizing lg-like lectins (Siglecs) are signaling receptors that modulate immune responses, and are targeted for interactions by certain pathogens. We describe two primate Siglecs that were rendered nonfunctional by single genetic events during hominin evolution after our common ancestor with the chimpanzee. SIGLEC13 was deleted by an A/u-mediated recombination event, and a single base pair deletion disrupted the ORF of SIGLEC17. Siglec-13 is expressed on chimpanzee monocytes, innate immune cells that react to bacteria. The human SIGLEC17P pseudogene mRNA is still expressed at high levels in human natural killer cells, which bridge innate and adaptive immune responses. As both resulting pseudogenes are homozygous in all human populations, we resurrected the originally encoded proteins and examined their functions. Chimpanzee Siglec-13 and the resurrected human Siglec-17 recruit a signaling adapter and bind sialic acids. Expression of either Siglec in innate immune cells alters inflammatory cytokine secretion in response to Toll-like receptor-4 stimulation. Both Siglecs can also be engaged by two potentially lethal sialylated bacterial pathogens of newborns and infants, agents with a potential impact on reproductive fitness. Neanderthal and Denisovan genomes show human-like sequences at both loci, corroborating estimates that the initial pseudogenization events occurred in the common ancestral population of these hominins. Both loci also show limited polymorphic diversity, suggesting selection forces predating the origin of modern humans. Taken together, these data suggest that genetic elimination of Siglec-13 and/or Siglec-17 represents signatures of infectious and/or other inflammatory selective processes contributing to population restrictions during hominin origins. [ABSTRACT FROM AUTHOR]

Published
2012
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116. Population dynamic of the extinct Europeanaurochs: genetic evidence of a north-southdifferentiation pattern and no evidence ofpost-glacial expansion.

Author

Mona, Stefano, Catalano, Giulio, Lari, Martina, Larson, Greger, Boscato, Paolo, Casoli, Antonella, Sineo, Luca, Patti, Carolina Di, Pecchioli, Elena, Caramelli, David, and Bertorelle, Giorgio

Subjects
URUS, DNA, PHYSIOLOGY, GENETIC research, GLACIAL climates
Abstract

Background: The aurochs (Bos primigenius) was a large bovine that ranged over almost the entirety of the Eurasian continent and North Africa. It is the wild ancestor of the modern cattle (Bos taurus), and went extinct in 1627 probably as a consequence of human hunting and the progressive reduction of its habitat. To investigate in detail the genetic history of this species and to compare the population dynamics in different European areas, we analysed Bos primigenius remains from various sites across Italy. Results: Fourteen samples provided ancient DNA fragments from the mitochondrial hypervariable region. Our data, jointly analysed with previously published sequences, support the view that Italian aurochsen were genetically similar to modern bovine breeds, but very different from northern/central European aurochsen. Bayesian analyses and coalescent simulations indicate that the genetic variation pattern in both Italian and northern/central European aurochsen is compatible with demographic stability after the last glaciation. We provide evidence that signatures of population expansion can erroneously arise in stable aurochsen populations when the different ages of the samples are not taken into account. Conclusions: Distinct groups of aurochsen probably inhabited Italy and northern/central Europe after the last glaciation, respectively. On the contrary, Italian and Fertile Crescent aurochsen likely shared several mtDNA sequences, now common in modern breeds. We argue that a certain level of genetic homogeneity characterized aurochs populations in Southern Europe and the Middle East, and also that post-glacial recolonization of northern and central Europe advanced, without major demographic expansions, from eastern, and not southern, refugia. [ABSTRACT FROM AUTHOR]

Published
2010
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117. Understanding 6th-century barbarian social organization and migration through paleogenomics

Author

Amorim, Carlos Eduardo G, Vai, Stefania, Posth, Cosimo, Modi, Alessandra, Koncz, István, Hakenbeck, Susanne, La Rocca, Maria Cristina, Mende, Balazs, Bobo, Dean, Pohl, Walter, Baricco, Luisella Pejrani, Bedini, Elena, Francalacci, Paolo, Giostra, Caterina, Vida, Tivadar, Winger, Daniel, Von Freeden, Uta, Ghirotto, Silvia, Lari, Martina, Barbujani, Guido, Krause, Johannes, Caramelli, David, Geary, Patrick J, and Veeramah, Krishna R

Subjects
Principal Component Analysis, Strontium Isotopes, Archaeology, Geography, Human Migration, Humans, Paleontology, Cemeteries, Genomics, 10. No inequality, Social Behavior, History, Medieval, Phylogeny
Abstract

Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data are consistent with the proposed long-distance migration from Pannonia to Northern Italy.

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

Author

Cosimo Posth, He Yu, Ayshin Ghalichi, Hélène Rougier, Isabelle Crevecoeur, Yilei Huang, Harald Ringbauer, Adam B. Rohrlach, Kathrin Nägele, Vanessa Villalba-Mouco, Rita Radzeviciute, Tiago Ferraz, Alexander Stoessel, Rezeda Tukhbatova, Dorothée G. Drucker, Martina Lari, Alessandra Modi, Stefania Vai, Tina Saupe, Christiana L. Scheib, Giulio Catalano, Luca Pagani, Sahra Talamo, Helen Fewlass, Laurent Klaric, André Morala, Mathieu Rué, Stéphane Madelaine, Laurent Crépin, Jean-Baptiste Caverne, Emmy Bocaege, Stefano Ricci, Francesco Boschin, Priscilla Bayle, Bruno Maureille, Foni Le Brun-Ricalens, Jean-Guillaume Bordes, Gregorio Oxilia, Eugenio Bortolini, Olivier Bignon-Lau, Grégory Debout, Michel Orliac, Antoine Zazzo, Vitale Sparacello, Elisabetta Starnini, Luca Sineo, Johannes van der Plicht, Laure Pecqueur, Gildas Merceron, Géraldine Garcia, Jean-Michel Leuvrey, Coralie Bay Garcia, Asier Gómez-Olivencia, Marta Połtowicz-Bobak, Dariusz Bobak, Mona Le Luyer, Paul Storm, Claudia Hoffmann, Jacek Kabaciński, Tatiana Filimonova, Svetlana Shnaider, Natalia Berezina, Borja González-Rabanal, Manuel R. González Morales, Ana B. Marín-Arroyo, Belén López, Carmen Alonso-Llamazares, Annamaria Ronchitelli, Caroline Polet, Ivan Jadin, Nicolas Cauwe, Joaquim Soler, Neus Coromina, Isaac Rufí, Richard Cottiaux, Geoffrey Clark, Lawrence G. Straus, Marie-Anne Julien, Silvia Renhart, Dorothea Talaa, Stefano Benazzi, Matteo Romandini, Luc Amkreutz, Hervé Bocherens, Christoph Wißing, Sébastien Villotte, Javier Fernández-López de Pablo, Magdalena Gómez-Puche, Marco Aurelio Esquembre-Bebia, Pierre Bodu, Liesbeth Smits, Bénédicte Souffi, Rimantas Jankauskas, Justina Kozakaitė, Christophe Cupillard, Hartmut Benthien, Kurt Wehrberger, Ralf W. Schmitz, Susanne C. Feine, Tim Schüler, Corinne Thevenet, Dan Grigorescu, Friedrich Lüth, Andreas Kotula, Henny Piezonka, Franz Schopper, Jiří Svoboda, Sandra Sázelová, Andrey Chizhevsky, Aleksandr Khokhlov, Nicholas J. Conard, Frédérique Valentin, Katerina Harvati, Patrick Semal, Bettina Jungklaus, Alexander Suvorov, Rick Schulting, Vyacheslav Moiseyev, Kristiina Mannermaa, Alexandra Buzhilova, Thomas Terberger, David Caramelli, Eveline Altena, Wolfgang Haak, Johannes Krause, Helsinki Institute of Sustainability Science (HELSUS), Department of Cultures, Faculty Common Matters (Faculty of Arts), Universidad de Cantabria, Posth, Cosimo [0000-0002-8206-3907], Yu, He [0000-0003-1323-4730], Rougier, Hélène [0000-0003-0358-0285], Ringbauer, Harald [0000-0002-4884-9682], Rohrlach, Adam B [0000-0002-4204-5018], Nägele, Kathrin [0000-0003-3861-8677], Villalba-Mouco, Vanessa [0000-0002-9357-5238], Radzeviciute, Rita [0000-0002-5800-3787], Stoessel, Alexander [0000-0003-2434-2542], Drucker, Dorothée G [0000-0003-0854-4371], Lari, Martina [0000-0002-7832-8212], Modi, Alessandra [0000-0001-9514-9868], Vai, Stefania [0000-0003-3844-5147], Scheib, Christiana L [0000-0003-4158-8296], Rué, Mathieu [0000-0001-7948-9459], Boschin, Francesco [0000-0001-5795-9050], Maureille, Bruno [0000-0002-7616-0073], Bortolini, Eugenio [0000-0001-6751-5680], Starnini, Elisabetta [0000-0002-3933-0854], Sineo, Luca [0000-0001-8634-2295], Garcia, Géraldine [0000-0001-5777-7126], Połtowicz-Bobak, Marta [0000-0003-1973-4971], Bobak, Dariusz [0000-0002-5216-6630], Le Luyer, Mona [0000-0001-7999-0294], Kabaciński, Jacek [0000-0002-2118-2005], Berezina, Natalia [0000-0001-5704-9153], González-Rabanal, Borja [0000-0002-1802-994X], Amkreutz, Luc [0000-0003-4664-5552], Bocherens, Hervé [0000-0002-0494-0126], Jankauskas, Rimantas [0000-0001-7611-2576], Conard, Nicholas J [0000-0002-4633-0385], Valentin, Frédérique [0000-0002-0575-7681], Harvati, Katerina [0000-0001-5998-4794], Schulting, Rick [0000-0002-4444-766X], Mannermaa, Kristiina [0000-0002-8510-1120], Buzhilova, Alexandra [0000-0001-6398-2177], Caramelli, David [0000-0001-6468-1675], Altena, Eveline [0000-0001-8911-7771], Haak, Wolfgang [0000-0003-2475-2007], Krause, Johannes [0000-0001-9144-3920], Apollo - University of Cambridge Repository, Rohrlach, Adam B. [0000-0002-4204-5018], Drucker, Dorothée G. [0000-0003-0854-4371], Scheib, Christiana L. [0000-0003-4158-8296], Conard, Nicholas J. [0000-0002-4633-0385], 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, Johanne, Pecqueur, Laure, Merceron, Gilda, 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, Nicola, Soler, Joaquim, Coromina, Neu, 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, Rimanta, Kozakaitė, Justina, Cupillard, Christophe, Benthien, Hartmut, Wehrberger, Kurt, Schmitz, Ralf W, Feine, Susanne C, Schüler, Tim, Thevenet, Corinne, Grigorescu, Dan, Lüth, Friedrich, Kotula, Andrea, 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, Thoma, Caramelli, David, Altena, Eveline, Haak, Wolfgang, Krause, Johannes, Universidad de Alicante. Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Prehistoria y Protohistoria, Pagani, Luca [0000-0002-6639-524X], and Alonso-Llamazares, Carmen [0000-0002-1053-1388]

Subjects
History, Ancient dna, Interactions, Cave, 45/23, Admixture, Settore BIO/08 - Antropologia, 631/208/457, 631/181/27, 6160 Other humanities, Contamination, Humans, Hunting, Palaeogenomics, Population-structure, Archaeology, Biological anthropology, Evolutionary genetics, Population genetics, History, Ancient, Human evolution, Diversity, Occupation, Multidisciplinary, 45, Genome, Human, article, Paleontology, Last glacial maximum, Human Genetics, Gene Pool, Genomics, 631/181/19/2471, Pleistocene, Europe, Genomic transformations, 631/181/2474, Anthropology, Hunter-gatherers, Genome sequence
Abstract

Acknowledgements: The authors thank G. Marciani and O. Jöris for comments on archaeology; C. Jeong, M. Spyrou and K. Prüfer for comments on genetics; M. O’Reilly for graphical support for Fig. 5 and Extended Data Fig. 9; the entire IT and laboratory teams at the Department of Archaeogenetics of MPI-SHH for technical assistance; M. Meyer and S. Nagel for support with single-stranded library preparation; K. Post, P. van Es, J. Glimmerveen, M. Medendorp, M. Sier, S. Dikstra, M. Dikstra, R. van Eerden, D. Duineveld and A. Hoekman for providing access to human specimens from the North Sea (The Netherlands); M. D. Garralda and A. Estalrrich for providing access to human specimens from La Riera (Spain); J. Górski and M. Zając for providing access to human specimens from Maszycka cave; C. Di Patti for providing access to human specimens from San Teodoro 2 (Italy); P. Blaževičius for providing access to the Donkalnis human remains and the new radiocarbon dates; the Italian Ministry of Culture and Soprintendenza Archeologia Belle Arti e Paesaggio for the Provinces of Verona, Rovigo, and Vicenza for granting access to the human remains of Tagliente 2; F. Fontana, who carries out investigations of the Riparo Tagliente site (Italy); the Friuli Venezia Giulia Superintendency for providing access to the human tooth Pradis 1; and the Soprintendenza Archeologia Belle Arti e Paesaggio for the Provinces of Barletta-Andria-Trani and Foggia for providing access to the Paglicci human remains. This project has received funding by the European Research Council under the European Union’s Horizon 2020 research and innovation programme under grant agreements no. 803147-RESOLUTION (to S.T.), no. 771234-PALEoRIDER (to W.H.), no. 864358 (to K.M.), no. 724703 and no. 101019659 (to K.H.). K.H. is also supported by the Deutsche Forschungsgemeinschaft (DFG FOR 2237). E.A. has received funding from the Van de Kamp fonds. PACEA co-authors of this research benefited from the scientific framework of the University of Bordeaux’s IdEx Investments for the Future programme/GPR Human Past. A.G.-O. is supported by a Ramón y Cajal fellowship (RYC-2017-22558). L. Sineo, M.L. and D.C. have received funding from the Italian Ministry of University and Research (MUR) PRIN 2017 grants 20177PJ9XF and 20174BTC4R_002. H. Rougier received support from the College of Social and Behavioral Sciences of CSUN and the CSUN Competition for RSCA Awards. C.L.S. and T. Saupe received support from the European Union through the European Regional Development Fund (project no. 2014-2020.4.01.16-0030) and C.L.S. received support from the Estonian Research Council grant PUT (PRG243). S. Shnaider received support from the Russian Science Foundation (no. 19-78-10053)., 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
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119. The diverse genetic origins of a Classical period Greek army

Author

Laurie J. Reitsema, Alissa Mittnik, Britney Kyle, Giulio Catalano, Pier Francesco Fabbri, Adam C. S. Kazmi, Katherine L. Reinberger, Luca Sineo, Stefano Vassallo, Rebecca Bernardos, Nasreen Broomandkhoshbacht, Kim Callan, Francesca Candilio, Olivia Cheronet, Elizabeth Curtis, Daniel Fernandes, Martina Lari, Ann Marie Lawson, Matthew Mah, Swapan Mallick, Kirsten Mandl, Adam Micco, Alessandra Modi, Jonas Oppenheimer, Kadir Toykan Özdogan, Nadin Rohland, Kristin Stewardson, Stefania Vai, Chiara Vergata, J. Noah Workman, Fatma Zalzala, Valentina Zaro, Alessandro Achilli, Achilles Anagnostopoulos, Cristian Capelli, Varnavas Constantinou, Hovirag Lancioni, Anna Olivieri, Anastasia Papadopoulou, Nikoleta Psatha, Ornella Semino, John Stamatoyannopoulos, Ioanna Valliannou, Evangelia Yannaki, Iosif Lazaridis, Nick Patterson, Harald Ringbauer, David Caramelli, Ron Pinhasi, David Reich, Reitsema, Laurie J, Mittnik, Alissa, Kyle, Britney, Catalano, Giulio, Fabbri, Pier Francesco, Kazmi, Adam C S, Reinberger, Katherine L, Sineo, Luca, Vassallo, Stefano, Bernardos, Rebecca, Broomandkhoshbacht, Nasreen, Callan, Kim, Candilio, Francesca, Cheronet, Olivia, Curtis, Elizabeth, Fernandes, Daniel, Lari, Martina, Lawson, Ann Marie, Mah, Matthew, Mallick, Swapan, Mandl, Kirsten, Micco, Adam, Modi, Alessandra, Oppenheimer, Jona, Özdogan, Kadir Toykan, Rohland, Nadin, Stewardson, Kristin, Vai, Stefania, Vergata, Chiara, Workman, J Noah, Zalzala, Fatma, Zaro, Valentina, Achilli, Alessandro, Anagnostopoulos, Achille, Capelli, Cristian, Constantinou, Varnava, Lancioni, Hovirag, Olivieri, Anna, Papadopoulou, Anastasia, Psatha, Nikoleta, Semino, Ornella, Stamatoyannopoulos, John, Valliannou, Ioanna, Yannaki, Evangelia, Lazaridis, Iosif, Patterson, Nick, Ringbauer, Harald, Caramelli, David, Pinhasi, Ron, and Reich, David

Subjects
Europe, Warfare, Multidisciplinary, Military Personnel, Archaeology, Greece, Classical world, Humans, history, Settore BIO/08 - Antropologia, ancient DNA, ancient warfare, History, Ancient
Abstract

Trade and colonization caused an unprecedented increase in Mediterranean human mobility in the first millennium BCE. Often seen as a dividing force, warfare is in fact another catalyst of culture contact. We provide insight into the demographic dynamics of ancient warfare by reporting genome-wide data from fifth-century soldiers who fought for the army of the Greek Sicilian colony of Himera, along with representatives of the civilian population, nearby indigenous settlements, and 96 present-day individuals from Italy and Greece. Unlike the rest of the sample, many soldiers had ancestral origins in northern Europe, the Steppe, and the Caucasus. Integrating genetic, archaeological, isotopic, and historical data, these results illustrate the significant role mercenaries played in ancient Greek armies and highlight how participation in war contributed to continental-scale human mobility in the Classical world.

Published
2022

120. Paleogenetic analysis and radiocarbon dating on skeletal remains from the Roman necropolis of Contrada Diana (Lipari Island, Sicily)

Author

Giulio Catalano, Alessandra Modi, Annunziata Ollà, Letterio Giordano, Umberto Spigo, Lucia Liccioli, Serena Barone, David Caramelli, Martina Lari, Luca Sineo, Catalano, Giulio, Modi, Alessandra, Ollà, Annunziata, Giordano, Letterio, Spigo, Umberto, Liccioli, Lucia, Barone, Serena, Caramelli, David, Lari, Martina, and Sineo, Luca

Subjects
Radiocarbon dating, Archeology, Anthropology, Settore BIO/08 - Antropologia, Palaeogenetics, Lipari, Roman Necropolis
Abstract

Lipari, the largest of the Aeolian Islands, is located in the southern Tyrrhenian Sea. Archeological evidence suggests an early human occupation starting from the Neolithic period. The island, favored by its volcanic history, was an important crossroads of cultures and commerce exchanges during prehistory up to Greek and Roman dominations. In this study, we present multidisciplinary analysis results on four skeletal remains from the necropolis of Contrada Diana attributed to the Roman period. By using Next Generation Sequencing technology we identified the biological sex and reconstructed the complete mitochondrial genome for two individuals. We retrieved the first ancient L3e5a lineage that is today present only in North and Central Africa. In addition, a 14C dating of 2,030 ± 45 years BP was obtained for one individual. A previous ancient DNA study has highlighted a genetic link between Sicily and the African continent at least from the Bronze Age. Our results, documenting the existence of contacts between Lipari and Africa during Roman influence, are particularly relevant to better understand the peopling of the Aeolian Archipelago when the island was a sea route of primary importance for the trade in the Mediterranean.

Published
2023

121. Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture

Author

Andrea Quagliariello, Alessandra Modi, Gabriel Innocenti, Valentina Zaro, Cecilia Conati Barbaro, Annamaria Ronchitelli, Francesco Boschin, Claudio Cavazzuti, Elena Dellù, Francesca Radina, Alessandra Sperduti, Luca Bondioli, Stefano Ricci, Miriam Lognoli, Maria Giovanna Belcastro, Valentina Mariotti, David Caramelli, Marta Mariotti Lippi, Emanuela Cristiani, Maria Elena Martino, Italo Maria Muntoni, Martina Lari, Quagliariello, Andrea, Modi, Alessandra, Innocenti, Gabriel, Zaro, Valentina, Conati Barbaro, Cecilia, Ronchitelli, Annamaria, Boschin, Francesco, Cavazzuti, Claudio, Dellù, Elena, Radina, Francesca, Sperduti, Alessandra, Bondioli, Luca, Ricci, Stefano, Lognoli, Miriam, Belcastro, Maria Giovanna, Mariotti, Valentina, Caramelli, David, Mariotti Lippi, Marta, Cristiani, Emanuela, Martino, Maria Elena, Muntoni, Italo Maria, and Lari, Martina

Subjects
Multidisciplinary, Farmers, Microbiota, palaeodiet, Paleolithic, Neolithic, Copper Age, oral microbiome, dental calculus, General Physics and Astronomy, Agriculture, General Chemistry, General Biochemistry, Genetics and Molecular Biology, ADna, Diet, oral microbiome, Italy, neolithic, Humans
Abstract

The human microbiome has recently become a valuable source of information about host life and health. To date little is known about how it may have evolved during key phases along our history, such as the Neolithic transition towards agriculture. Here, we shed light on the evolution experienced by the oral microbiome during this transition, comparing Palaeolithic hunter-gatherers with Neolithic and Copper Age farmers that populated a same restricted area in Italy. We integrate the analysis of 76 dental calculus oral microbiomes with the dietary information derived from the identification of embedded plant remains. We detect a stronger deviation from the hunter-gatherer microbiome composition in the last part of the Neolithic, while to a lesser extent in the early phases of the transition. Our findings demonstrate that the introduction of agriculture affected host microbiome, supporting the hypothesis of a gradual transition within the investigated populations.

Published
2022

122. Genetic structure and differentiation from early bronze age in the mediterranean island of sicily: Insights from ancient mitochondrial genomes

Author

Alessandra Modi, Maria Teresa Vizzari, Giulio Catalano, Rajiv Boscolo Agostini, Stefania Vai, Martina Lari, Chiara Vergata, Valentina Zaro, Lucia Liccioli, Mariaelena Fedi, Serena Barone, Lorenzo Nigro, Hovirag Lancioni, Alessandro Achilli, Luca Sineo, David Caramelli, Silvia Ghirotto, Modi, Alessandra, Vizzari, Maria Teresa, Catalano, Giulio, Boscolo Agostini, Rajiv, Vai, Stefania, Lari, Martina, Vergata, Chiara, Zaro, Valentina, Liccioli, Lucia, Fedi, Mariaelena, Barone, Serena, Nigro, Lorenzo, Lancioni, Hovirag, Achilli, Alessandro, Sineo, Luca, Caramelli, David, and Ghirotto, Silvia

Subjects
ANCIENT DNA, mitochondrial genomes, genetic structure, coalescent simulations, approximate bayesian computation, a DNA, Sicily, Mediterranean, Early Bronze Age, Motya, Mediterranean, Settore BIO/08 - Antropologia, Motya, coalescent simulations, mitochondrial genomes, Genetics, Early Bronze Age, genetic structure, Molecular Medicine, ANCIENT DNA, a DNA, Sicily, Genetics (clinical), approximate bayesian computation
Abstract

Sicily is one of the main islands of the Mediterranean Sea, and it is characterized by a variety of archaeological records, material culture and traditions, reflecting the history of migrations and populations’ interaction since its first colonization, during the Paleolithic. These deep and complex demographic and cultural dynamics should have affected the genomic landscape of Sicily at different levels; however, the relative impact of these migrations on the genomic structure and differentiation within the island remains largely unknown. The available Sicilian modern genetic data gave a picture of the current genetic structure, but the paucity of ancient data did not allow so far to make predictions about the level of historical variation. In this work, we sequenced and analyzed the complete mitochondrial genomes of 36 individuals from five different locations in Sicily, spanning from Early Bronze Age to Iron Age, and with different cultural backgrounds. The comparison with coeval groups from the Mediterranean Basin highlighted structured genetic variation in Sicily since Early Bronze Age, thus supporting a demic impact of the cultural transitions within the Island. Explicit model testing through Approximate Bayesian Computation allowed us to make predictions about the origin of Sicanians, one of the three indigenous peoples of Sicily, whose foreign origin from Spain, historically attributed, was not confirmed by our analysis of genetic data. Sicilian modern mitochondrial data show a different, more homogeneous, genetic composition, calling for a recent genetic replacement in the Island of pre-Iron Age populations, that should be further investigated.

Published
2022

123. First bronze age human mitogenomes from calabria (Grotta della monaca, southern italy)

Author

Stefania Sarno, Francesco Fontani, Adam J. Andrews, Elisabetta Cilli, Adriana Latorre, Paolo Abondio, Felice Larocca, Martina Lari, Donata Luiselli, Alessandra Modi, Sara De Fanti, Emanuela Gualdi-Russo, Fabiola Arena, David Caramelli, Fontani, Francesco, Cilli, Elisabetta, Arena, Fabiola, Sarno, Stefania, Modi, Alessandra, De Fanti, Sara, Andrews, Adam Jon, Latorre, Adriana, Abondio, Paolo, Larocca, Felice, Lari, Martina, Caramelli, David, Gualdi-Russo, Emanuela, and Luiselli, Donata

Subjects
0301 basic medicine, Bronze Age, Population, Socio-culturale, mitochondrial DNA, QH426-470, Article, Ancient DNA, Archaeology, Human, Italy, Mitochondrial DNA, Paleogenomics, Evolution, Molecular, Humans, DNA, Ancient, Genome, Human, Genome, Mitochondrial, Prehistory, 03 medical and health sciences, 0302 clinical medicine, Cave, Beaker, Peninsula, Genetics, human, education, ancient DNA, Genetics (clinical), geography, education.field_of_study, geography.geographical_feature_category, paleogenomic, paleogenomics, archaeology, language.human_language, 030104 developmental biology, language, Sicilian, 030217 neurology & neurosurgery
Abstract

The Italian peninsula was host to a strong history of migration processes that shaped its genomic variability since prehistoric times. During the Metal Age, Sicily and Southern Italy were the protagonists of intense trade networks and settlements along the Mediterranean. Nonetheless, ancient DNA studies in Southern Italy are, at present, still limited to prehistoric and Roman Apulia. Here, we present the first mitogenomes from a Middle Bronze Age cave burial in Calabria to address this knowledge gap. We adopted a hybridization capture approach, which enabled the recovery of one complete and one partial mitochondrial genome. Phylogenetic analysis assigned these two individuals to the H1e and H5 subhaplogroups, respectively. This preliminary phylogenetic analysis supports affinities with coeval Sicilian populations, along with Linearbandkeramik and Bell Beaker cultures maternal lineages from Central Europe and Iberia. Our work represents a starting point which contributes to the comprehension of migrations and population dynamics in Southern Italy, and highlights this knowledge gap yet to be filled by genomic studies.

Published
2021

124. The genetic history of Ice Age Europe

Author

Alexander Peltzer, Dorothée G. Drucker, Annamaria Ronchitelli, Stephan Schiffels, Maria Teschler-Nicola, Swapan Mallick, Svante Pääbo, Michael P. Richards, Daniel Fernandes, Martin Petr, Manuel R. González Morales, Marco Peresani, Jiří Svoboda, V. S. Slavinsky, Janet Kelso, David Reich, Isabelle Crevecoeur, Pontus Skoglund, E. Vacca, Francesco Mallegni, Donato Coppola, Oana Teodora Moldovan, Cosimo Posth, Nadin Rohland, Kurt Wehrberger, Anatoly P. Derevianko, Birgit Nickel, A. A. Tsybankov, Viviane Slon, Nicholas J. Conard, Stefano Ricci, Christine Neugebauer-Maresch, Corinne Thevenet, Qiaomei Fu, Lawrence Guy Straus, Vyacheslav Moiseyev, Frédérique Valentin, Johannes Krause, Iain Mathieson, Silviu Constantin, Mateja Hajdinjak, Sahra Talamo, Bernard Gély, Renata Grifoni Cremonesi, Dan Grigorescu, David Caramelli, Mark Lipson, Matthias Meyer, Damien Flas, Stefano Benazzi, Alissa Mittnik, Nick Patterson, Iosif Lazaridis, Martina Lari, Hervé Bocherens, Wolfgang Haak, Katerina Harvati, Patrick Semal, Christophe Cupillard, Hélène Rougier, Ron Pinhasi, Marcello A. Mannino, Anja Furtwängler, Nikolai I. Drozdov, Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Harvard School of Public Health, School of Archaeology [Dublin], University College Dublin [Dublin] (UCD), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Université libre de Bruxelles (ULB), Department of Evolutianory Genetics, Max-Planck-Institut, Sackler Faculty of Medicine, Tel Aviv University (TAU), Department of Human Evolution [Leipzig], Nuffield Department of Medicine, Service régional de l'Archéologie Rhône-Alpes, Ministère de la Culture et de la Communication (MCC), Laboratory of Excellence for Financial Regulation (LABEX ReFi), Université Paris-Sud - Paris 11 (UP11), Institutul de Speologie ‘Emil Racoviţă', Str. Frumoasă 31, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Università degli Studi di Ferrara = University of Ferrara (UniFE), Università degli Studi di Firenze = University of Florence (UniFI), Department of Information Engineering [Firenze], U.R. Ecologia Preistorica, Dipartimento di Scienze Ambientali ', Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Museum Ulm, De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Service Anthropologie et Préhistoire [Bruxelles], Institut Royal des Sciences Naturelles de Belgique (IRSNB), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, University of Tübingen, Faculty of Science [Brno] (SCI / MUNI), Masaryk University [Brno] (MUNI), Department of Physics, University of Sussex, Department of Animal Biology and Genetics, School of Archaeology, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Centre International de Recherche Archéologique sur la Polynésie (CIRAP), Université de la Polynésie Française (UPF), Tel Aviv University [Tel Aviv], Università degli Studi di Ferrara (UniFE), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Max Planck Institute for Evolutionary Anthropology, Eberhard Karls Universität Tübingen, Max-Planck-Institut für evolutionäre Anthropologie (MPI-EVA), University College of London [London] (UCL), Laboratoire Chrono-environnement - CNRS - UFC (UMR 6249) (LCE), Department of Archaeogenetics [Jena] (DAG), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), University of Bologna, Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente., Università degli Studi di Siena = University of Siena (UNISI), Laboratoire d'Anthropologie et de Préhistoire, Institut royal des Sciences naturelles de Belgique (IRSNB), Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), Ministère de la Culture et de la Communication (MCC)-École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Centre National de la Recherche Scientifique (CNRS), Institut Royal des Sciences naturelles de Belgique, Univ Tubingen, Senckenberg Ctr Human Evolut & Palaeoecol, Palaeoanthropol, Tubingen, Germany, Laboratorio di Antropologia, Università degli Studi di Firenze = University of Florence [Firenze], Qiaomei, Fu, Posth, Cosimo, Hajdinjak, Mateja, Petr, Martin, Mallick, Swapan, Fernandes, Daniel, Furtwängler, Anja, Haak, Wolfgang, Meyer, Matthia, Mittnik, Alissa, Nickel, Birgit, Peltzer, Alexander, Rohland, Nadin, Slon, Viviane, Talamo, Sahra, Lazaridis, Iosif, Lipson, Mark, Mathieson, Iain, Schiffels, Stephan, Skoglund, Pontu, Derevianko, Anatoly P., Drozdov, Nikolai, Slavinsky, Vyacheslav, Tsybankov, Alexander, Cremonesi, Renata Grifoni, Mallegni, Francesco, Gély, Bernard, Vacca, Eligio, Morales, Manuel R. González, Straus, Lawrence G., Neugebauer Maresch, Christine, Teschler Nicola, Maria, Constantin, Silviu, Moldovan, Oana Teodora, Benazzi, Stefano, Peresani, Marco, Coppola, Donato, Lari, Martina, Ricci, Stefano, Ronchitelli, Annamaria, Valentin, Frédérique, Thevenet, Corinne, Wehrberger, Kurt, Grigorescu, Dan, Rougier, Hélène, Crevecoeur, Isabelle, Flas, Damien, Semal, Patrick, Mannino, Marcello A., Cupillard, Christophe, Bocherens, Hervé, Conard, Nicholas J., Harvati, Katerina, Moiseyev, Vyacheslav, Drucker, Dorothée G., Svoboda, Jiří, Richards, Michael P., Caramelli, David, Pinhasi, Ron, Kelso, Janet, Patterson, Nick, Krause, Johanne, Pääbo, Svante, and Reich, David

Subjects
0301 basic medicine, Male, Neanderthal, Time Factors, [SDV]Life Sciences [q-bio], Population Dynamics, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Neanderthal genome project, migration, Ancient Modern Humans, [SHS]Humanities and Social Sciences, 0302 clinical medicine, Ice Cover, History, Ancient, Phylogeny, ComputingMilieux_MISCELLANEOUS, Modern Humans, Neanderthals, Genetics, education.field_of_study, Multidisciplinary, Ancient DNA, Human migration, Biological Evolution, Founder Effect, Pleistocene, Europe, Ethnology, Female, Ancient DNA, Ancient Modern Humans, Neanderthals, Human, Animals, DNA, European Continental Ancestry Group, Genetics, Population, Human Migration, Humans, Middle East, Selection, Genetic, Sequence Analysis, DNA, Medicine (all), Archaeogenetics, Time Factor, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Modern Humans, Genetics, Pleistocene, Europe, migration, culture, Europe glaciaire, Population, Socio-culturale, Biology, Article, White People, Prehistory, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], biology.animal, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, Population Dynamic, Homo sapiens, Animal, business.industry, culture, 030104 developmental biology, [ SHS.ARCHEO ] Humanities and Social Sciences/Archaeology and Prehistory, business, génome humain, 030217 neurology & neurosurgery, Founder effect
Abstract

Modern humans arrived in Europe ∼45,000 years ago, but little is known about their genetic composition before the start of farming ∼8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ∼45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3-6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ∼37,000 and ∼14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ∼35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ∼19,000 years ago. During the major warming period after ∼14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.

Published
2016

125. DNA methylation analysis of multiple genes in thymic epithelial tumors.

Author

Nicolì V, Giangreco M, Pardini E, Petrini I, Bacchin D, Aprile V, Melfi F, Lucchi M, Guida M, Ricciardi R, Maestri M, Lari M, Migliore L, Stoccoro A, and Coppedè F

Abstract

Aim: To investigate DNA methylation levels of a panel of genes in thymic epithelial tumors (TETs). Materials & methods: We selected 15 genes among the most promising epigenetic biomarkers of TETs and evaluated their methylation levels in 71 TET samples. Results: thymic carcinomas (TCs) showed hypermethylation of GHSR and ELF3 genes and reduced IL1RN methylation levels compared with thymomas (TMs) and healthy thymic tissues. RAG1 was hypomethylated in TMs compared with healthy thymic tissues. No difference in the methylation levels of the investigated genes was seen among TM stages and subtypes. No changes in blood methylation levels of the investigated genes were seen among TET subtypes. Conclusion: The present study confirms GHSR, ELF3, IL1RN and RAG1 as TET epigenetic biomarkers.

Published
2024
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126. Associations between Circulating Biomarkers of One-Carbon Metabolism and Mitochondrial D-Loop Region Methylation Levels.

Author

Stoccoro A, Lari M, Migliore L, and Coppedè F

Abstract

Background/objectives: One-carbon metabolism is a critical pathway for epigenetic mechanisms. Circulating biomarkers of one-carbon metabolism have been associated with changes in nuclear DNA methylation levels in individuals affected by age-related diseases. More and more studies are showing that even mitochondrial DNA (mtDNA) could be methylated. In particular, methylation of the mitochondrial displacement (D-loop) region modulates the gene expression and replication of mtDNA and, when altered, can contribute to the development of human illnesses. However, no study until now has demonstrated an association between circulating biomarkers of one-carbon metabolism and D-loop methylation levels., Methods: In the study presented herein, we searched for associations between circulating one-carbon metabolism biomarkers, including folate, homocysteine, and vitamin B12, and the methylation levels of the D-loop region in DNA obtained from the peripheral blood of 94 elderly voluntary subjects., Results: We observed a positive correlation between D-loop methylation and vitamin B12 (r = 0.21; p = 0.03), while no significant correlation was observed with folate (r = 0.02; p = 0.80) or homocysteine levels (r = 0.02; p = 0.82). Moreover, D-loop methylation was increased in individuals with high vitamin B12 levels compared to those with normal vitamin B12 levels ( p = 0.04)., Conclusions: This is the first study suggesting an association between vitamin B12 circulating levels and mtDNA methylation in human subjects. Given the potential implications of altered one-carbon metabolism and mitochondrial epigenetics in human diseases, a deeper understanding of their interaction could inspire novel interventions with beneficial effects for human health.

Published
2024
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127. The role of emerging elites in the formation and development of communities after the fall of the Roman Empire.

Author

Tian Y, Koncz I, Defant S, Giostra C, Vyas DN, Sołtysiak A, Pejrani Baricco L, Fetner R, Posth C, Brandt G, Bedini E, Modi A, Lari M, Vai S, Francalacci P, Fernandes R, Steinhof A, Pohl W, Caramelli D, Krause J, Izdebski A, Geary PJ, and Veeramah KR

Subjects
Humans, Italy, History, Medieval, Human Migration history, History, Ancient, Archaeology, Roman World history
Abstract

Elites played a pivotal role in the formation of post-Roman Europe on both macro- and microlevels during the Early Medieval period. History and archaeology have long focused on their description and identification based on written sources or through their archaeological record. We provide a different perspective on this topic by integrating paleogenomic, archaeological, and isotopic data to gain insights into the role of one such elite group in a Langobard period community near Collegno, Italy dated to the 6-8th centuries CE. Our analysis of 28 newly sequenced genomes together with 24 previously published ones combined with isotope (Sr, C, N) measurements revealed that this community was established by and organized around a network of biologically and socially related individuals likely composed of multiple elite families that over time developed into a single extended pedigree. The community also included individuals with diverse genetic ancestries, maintaining its diversity by integrating newcomers and groups in later stages of its existence. This study highlights how shifts in political power and migration impacted the formation and development of a small rural community within a key region of the former Western Roman Empire after its dissolution and the emergence of a new kingdom. Furthermore, it suggests that Early Medieval elites had the capacity to incorporate individuals from varied backgrounds and that these elites were the result of (political) agency rather than belonging to biologically homogeneous groups., Competing Interests: Competing interests statement:The authors declare no competing interest.

Published
2024
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128. The Illumina Sequencing Protocol and the NovaSeq 6000 System.

Author

Modi A, Vai S, Caramelli D, and Lari M

Subjects
Genomic Library, Research Design, Workflow, Genomics instrumentation, High-Throughput Nucleotide Sequencing instrumentation, Sequence Analysis, DNA instrumentation
Abstract

The NovaSeq 6000 is a sequencing platform from Illumina that enables the sequencing of short reads with an output up to 6 Tb. The NovaSeq 6000 uses the typical Illumina sequencing workflow based on library preparation, cluster generation by in situ amplification, and sequencing by synthesis. Flexibility is one of the major features of the NovaSeq 6000. Several types of sequencing kits coupled with dual flow cell mode enable high scalability of sequencing outputs to match a wide range of applications from complete genome sequencing to metagenomics analysis. In this chapter, after explaining how to assemble a normalized pool of libraries for sequencing, we will describe the experimental steps required to run the pools on the NovaSeq 6000 platform.

Published
2021
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129. Specific inactivation of two immunomodulatory SIGLEC genes during human evolution.

Author

Wang X, Mitra N, Secundino I, Banda K, Cruz P, Padler-Karavani V, Verhagen A, Reid C, Lari M, Rizzi E, Balsamo C, Corti G, De Bellis G, Longo L, Beggs W, Caramelli D, Tishkoff SA, Hayakawa T, Green ED, Mullikin JC, Nizet V, Bui J, and Varki A

Subjects
Animals, Gene Deletion, Humans, Immune System, Primates, Sialic Acid Binding Immunoglobulin-like Lectins, Evolution, Molecular, Gene Silencing, Lectins genetics
Abstract

Sialic acid-recognizing Ig-like lectins (Siglecs) are signaling receptors that modulate immune responses, and are targeted for interactions by certain pathogens. We describe two primate Siglecs that were rendered nonfunctional by single genetic events during hominin evolution after our common ancestor with the chimpanzee. SIGLEC13 was deleted by an Alu-mediated recombination event, and a single base pair deletion disrupted the ORF of SIGLEC17. Siglec-13 is expressed on chimpanzee monocytes, innate immune cells that react to bacteria. The human SIGLEC17P pseudogene mRNA is still expressed at high levels in human natural killer cells, which bridge innate and adaptive immune responses. As both resulting pseudogenes are homozygous in all human populations, we resurrected the originally encoded proteins and examined their functions. Chimpanzee Siglec-13 and the resurrected human Siglec-17 recruit a signaling adapter and bind sialic acids. Expression of either Siglec in innate immune cells alters inflammatory cytokine secretion in response to Toll-like receptor-4 stimulation. Both Siglecs can also be engaged by two potentially lethal sialylated bacterial pathogens of newborns and infants, agents with a potential impact on reproductive fitness. Neanderthal and Denisovan genomes show human-like sequences at both loci, corroborating estimates that the initial pseudogenization events occurred in the common ancestral population of these hominins. Both loci also show limited polymorphic diversity, suggesting selection forces predating the origin of modern humans. Taken together, these data suggest that genetic elimination of Siglec-13 and/or Siglec-17 represents signatures of infectious and/or other inflammatory selective processes contributing to population restrictions during hominin origins.

Published
2012
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130. Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans.

Author

Caramelli D, Lalueza-Fox C, Vernesi C, Lari M, Casoli A, Mallegni F, Chiarelli B, Dupanloup I, Bertranpetit J, Barbujani G, and Bertorelle G

Subjects
Animals, Base Sequence, DNA Primers, DNA, Mitochondrial genetics, Europe, Humans, Molecular Sequence Data, Biological Evolution, Hominidae genetics
Abstract

During the late Pleistocene, early anatomically modern humans coexisted in Europe with the anatomically archaic Neandertals for some thousand years. Under the recent variants of the multiregional model of human evolution, modern and archaic forms were different but related populations within a single evolving species, and both have contributed to the gene pool of current humans. Conversely, the Out-of-Africa model considers the transition between Neandertals and anatomically modern humans as the result of a demographic replacement, and hence it predicts a genetic discontinuity between them. Following the most stringent current standards for validation of ancient DNA sequences, we typed the mtDNA hypervariable region I of two anatomically modern Homo sapiens sapiens individuals of the Cro-Magnon type dated at about 23 and 25 thousand years ago. Here we show that the mtDNAs of these individuals fall well within the range of variation of today's humans, but differ sharply from the available sequences of the chronologically closer Neandertals. This discontinuity is difficult to reconcile with the hypothesis that both Neandertals and early anatomically modern humans contributed to the current European gene pool.

Published
2003
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