40 results on '"Marquès-Bonet, Tomás"'
Search Results
2. Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr)
- Author
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Mochales-Riaño, Gabriel, Fontsere, Claudia, de Manuel, Marc, Talavera, Adrián, Burriel-Carranza, Bernat, Tejero-Cicuéndez, Héctor, AlGethami, Raed Hamoud M., Shobrak, Mohammed, Marques-Bonet, Tomas, and Carranza, Salvador
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- 2023
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3. Schizophrenia-associated somatic copy-number variants from 12,834 cases reveal recurrent NRXN1 and ABCB11 disruptions
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Marshall, Christian R., Merico, Daniele, Thiruvahindrapuram, Bhooma, Wang, Zhouzhi, Scherer, Stephen W., Howrigan, Daniel P, Ripke, Stephan, Bulik-Sullivan, Brendan, Farh, Kai-How, Fromer, Menachem, Goldstein, Jacqueline I., Huang, Hailiang, Lee, Phil, Daly, Mark J., Neale, Benjamin M., Belliveau, Richard A., Jr., Bergen, Sarah E., Bevilacqua, Elizabeth, Chambert, Kimberley D., O'Dushlaine, Colm, Scolnick, Edward M., Smoller, Jordan W., Moran, Jennifer L., Palotie, Aarno, Petryshen, Tracey L., Wu, Wenting, Greer, Douglas S., Antaki, Danny, Shetty, Aniket, Gujral, Madhusudan, Brandler, William M., Malhotra, Dheeraj, Fuentes Fajarado, Karin V., Maile, Michelle S., Holmans, Peter A., Carrera, Noa, Craddock, Nick, Escott-Price, Valentina, Georgieva, Lyudmila, Hamshere, Marian L., Kavanagh, David, Legge, Sophie E., Pocklington, Andrew J., Richards, Alexander L., Ruderfer, Douglas M., Williams, Nigel M., Kirov, George, Owen, Michael J., Pinto, Dalila, Cai, Guiqing, Davis, Kenneth L., Drapeau, Elodie, Friedman, Joseph I, Haroutunian, Vahram, Parkhomenko, Elena, Reichenberg, Abraham, Silverman, Jeremy M., Buxbaum, Joseph D., Domenici, Enrico, Agartz, Ingrid, Djurovic, Srdjan, Mattingsdal, Morten, Melle, Ingrid, Andreassen, Ole A., Jönsson, Erik G., Söderman, Erik, Albus, Margot, Alexander, Madeline, Laurent, Claudine, Levinson, Douglas F., Amin, Farooq, Atkins, Joshua, Cairns, Murray J., Scott, Rodney J., Tooney, Paul A., Wu, Jing Qin, Bacanu, Silviu A., Bigdeli, Tim B., Reimers, Mark A., Webb, Bradley T., Wolen, Aaron R., Wormley, Brandon K., Kendler, Kenneth S., Riley, Brien P., Kähler, Anna K., Magnusson, Patrik K.E., Hultman, Christina M., Bertalan, Marcelo, Hansen, Thomas, Olsen, Line, Rasmussen, Henrik B., Werge, Thomas, Mattheisen, Manuel, Black, Donald W., Bruggeman, Richard, Buccola, Nancy G., Buckner, Randy L., Roffman, Joshua L., Byerley, William, Cahn, Wiepke, Kahn, René S, Strengman, Eric, Ophoff, Roel A., Carr, Vaughan J., Catts, Stanley V., Henskens, Frans A., Loughland, Carmel M., Michie, Patricia T., Pantelis, Christos, Schall, Ulrich, Jablensky, Assen V., Kelly, Brian J., Campion, Dominique, Cantor, Rita M., Cheng, Wei, Cloninger, C. Robert, Svrakic, Dragan M, Cohen, David, Cormican, Paul, Donohoe, Gary, Morris, Derek W., Corvin, Aiden, Gill, Michael, Crespo-Facorro, Benedicto, Crowley, James J., Farrell, Martilias S., Giusti-Rodríguez, Paola, Kim, Yunjung, Szatkiewicz, Jin P., Williams, Stephanie, Curtis, David, Pimm, Jonathan, Gurling, Hugh, McQuillin, Andrew, Davidson, Michael, Weiser, Mark, Degenhardt, Franziska, Forstner, Andreas J., Herms, Stefan, Hoffmann, Per, Hofman, Andrea, Cichon, Sven, Nöthen, Markus M., Del Favero, Jurgen, DeLisi, Lynn E., McCarley, Robert W., Levy, Deborah L., Mesholam-Gately, Raquelle I., Seidman, Larry J., Dikeos, Dimitris, Papadimitriou, George N., Dinan, Timothy, Duan, Jubao, Sanders, Alan R., Gejman, Pablo V., Gershon, Elliot S., Dudbridge, Frank, Eichhammer, Peter, Eriksson, Johan, Salomaa, Veikko, Essioux, Laurent, Fanous, Ayman H., Knowles, James A., Pato, Michele T., Pato, Carlos N., Frank, Josef, Meier, Sandra, Schulze, Thomas G., Strohmaier, Jana, Witt, Stephanie H., Rietschel, Marcella, Franke, Lude, Karjalainen, Juha, Freedman, Robert, Olincy, Ann, Freimer, Nelson B., Purcell, Shaun M., Roussos, Panos, Stahl, Eli A., Sklar, Pamela, Giegling, Ina, Hartmann, Annette M., Konte, Bettina, Rujescu, Dan, Godard, Stephanie, Hirschhorn, Joel N., Pers, Tune H., Price, Alkes, Esko, Tõnu, Gratten, Jacob, Lee, S. Hong, Visscher, Peter M., Wray, Naomi R., Mowry, Bryan J., de Haan, Lieuwe, Meijer, Carin J., Hansen, Mark, Ikeda, Masashi, Iwata, Nakao, Joa, Inge, Kalaydjieva, Luba, Keller, Matthew C., Kennedy, James L., Zai, Clement C., Knight, Jo, Lerer, Bernard, Liang, Kung-Yee, Lieberman, Jeffrey, Stroup, T. Scott, Lönnqvist, Jouko, Suvisaari, Jaana, Maher, Brion S., Maier, Wolfgang, Mallet, Jacques, McDonald, Colm, McIntosh, Andrew M., Blackwood, Douglas H.R., Metspalu, Andres, Milani, Lili, Milanova, Vihra, Mokrab, Younes, Collier, David A., Müller-Myhsok, Bertram, Murphy, Kieran C., Murray, Robin M., Powell, John, Myin-Germeys, Inez, Van Os, Jim, Nenadic, Igor, Nertney, Deborah A., Nestadt, Gerald, Pulver, Ann E., Nicodemus, Kristin K., Nisenbaum, Laura, Nordin, Annelie, Adolfsson, Rolf, O'Callaghan, Eadbhard, Oh, Sang-Yun, O'Neill, F. Anthony, Paunio, Tiina, Pietiläinen, Olli, Perkins, Diana O., Quested, Digby, Savitz, Adam, Li, Qingqin S., Schwab, Sibylle G., Shi, Jianxin, Spencer, Chris C.A., Thirumalai, Srinivas, Veijola, Juha, Waddington, John, Walsh, Dermot, Wildenauer, Dieter B., Bramon, Elvira, Darvasi, Ariel, Posthuma, Danielle, St. Clair, David, Shanta, Omar, Klein, Marieke, Park, Peter J., Weinberger, Daniel, Moran, John V., Gage, Fred H., Vaccarino, Flora M., Gleeson, Joseph, Mathern, Gary, Courchesne, Eric, Roy, Subhojit, Bizzotto, Sara, Coulter, Michael, Dias, Caroline, D'Gama, Alissa, Ganz, Javier, Hill, Robert, Huang, August Yue, Khoshkhoo, Sattar, Kim, Sonia, Lodato, Michael, Miller, Michael, Borges-Monroy, Rebeca, Rodin, Rachel, Zhou, Zinan, Bohrson, Craig, Chu, Chong, Cortes-Ciriano, Isidro, Dou, Yanmei, Galor, Alon, Gulhan, Doga, Kwon, Minseok, Luquette, Joe, Viswanadham, Vinay, Jones, Attila, Rosenbluh, Chaggai, Cho, Sean, Langmead, Ben, Thorpe, Jeremy, Erwin, Jennifer, Jaffe, Andrew, McConnell, Michael, Narurkar, Rujuta, Paquola, Apua, Shin, Jooheon, Straub, Richard, Abyzov, Alexej, Bae, Taejeong, Jang, Yeongjun, Wang, Yifan, Gage, Fred, Linker, Sara, Reed, Patrick, Wang, Meiyan, Urban, Alexander, Zhou, Bo, Zhu, Xiaowei, Pattni, Reenal, Amero, Aitor Serres, Juan, David, Lobon, Irene, Marques-Bonet, Tomas, Moruno, Manuel Solis, Perez, Raquel Garcia, Povolotskaya, Inna, Soriano, Eduardo, Averbuj, Dan, Ball, Laurel, Breuss, Martin, Yang, Xiaoxu, Chung, Changuk, Emery, Sarah B., Flasch, Diane A., Kidd, Jeffrey M., Kopera, Huira C., Kwan, Kenneth Y., Mills, Ryan E., Moldovan, John B., Sun, Chen, Zhao, Xuefang, Zhou, Weichen, Frisbie, Trenton J., Cherskov, Adriana, Fasching, Liana, Jourdon, Alexandre, Pochareddy, Sirisha, Scuderi, Soraya, Sestan, Nenad, Maury, Eduardo A., Sherman, Maxwell A., Genovese, Giulio, Gilgenast, Thomas G., Kamath, Tushar, Burris, S.J., Rajarajan, Prashanth, Flaherty, Erin, Akbarian, Schahram, Chess, Andrew, McCarroll, Steven A., Loh, Po-Ru, Phillips-Cremins, Jennifer E., Brennand, Kristen J., Macosko, Evan Z., Walters, James T.R., O’Donovan, Michael, Sullivan, Patrick, Sebat, Jonathan, Lee, Eunjung A., and Walsh, Christopher A.
- Published
- 2023
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4. Population dynamics and genetic connectivity in recent chimpanzee history
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Fontsere, Claudia, Kuhlwilm, Martin, Morcillo-Suarez, Carlos, Alvarez-Estape, Marina, Lester, Jack D., Gratton, Paolo, Schmidt, Joshua M., Dieguez, Paula, Aebischer, Thierry, Álvarez-Varona, Paula, Agbor, Anthony, Angedakin, Samuel, Assumang, Alfred K., Ayimisin, Emmanuel A., Bailey, Emma, Barubiyo, Donatienne, Bessone, Mattia, Carretero-Alonso, Andrea, Chancellor, Rebecca, Cohen, Heather, Danquah, Emmanuel, Deschner, Tobias, Dunn, Andrew, Dupain, Jef, Egbe, Villard E., Feliu, Olga, Goedmakers, Annemarie, Granjon, Anne-Céline, Head, Josephine, Hedwig, Daniela, Hermans, Veerle, Hernandez-Aguilar, R. Adriana, Imong, Inaoyom, Jones, Sorrel, Junker, Jessica, Kadam, Parag, Kaiser, Mike, Kambere, Mbangi, Kambale, Magloire V., Kalan, Ammie K., Kienast, Ivonne, Kujirakwinja, Deo, Langergraber, Kevin, Lapuente, Juan, Larson, Bradley, Laudisoit, Anne, Lee, Kevin, Llana, Manuel, Llorente, Miquel, Marrocoli, Sergio, Morgan, David, Mulindahabi, Felix, Murai, Mizuki, Neil, Emily, Nicholl, Sonia, Nixon, Stuart, Normand, Emma, Orbell, Chris, Ormsby, Lucy J., Pacheco, Liliana, Piel, Alex, Riera, Laura, Robbins, Martha M., Rundus, Aaron, Sanz, Crickette, Sciaky, Lilah, Sommer, Volker, Stewart, Fiona A., Tagg, Nikki, Tédonzong, Luc Roscelin, Ton, Els, van Schijndel, Joost, Vergnes, Virginie, Wessling, Erin G., Willie, Jacob, Wittig, Roman M., Yuh, Yisa G., Yurkiw, Kyle, Zuberbuehler, Klaus, Hecht, Jochen, Vigilant, Linda, Boesch, Christophe, Andrés, Aida M., Hughes, David A., Kühl, Hjalmar S., Lizano, Esther, Arandjelovic, Mimi, and Marques-Bonet, Tomas
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- 2022
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5. The era of reference genomes in conservation genomics
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Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlos, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Čiampor, Fedor, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Hoglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per, Pampoulie, Christophe, Ruiz-López, María José, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Goujie, Mazzoni, Camila J., Jarvis, Erich, Bálint, Miklós, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Berg, Paul R., Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe, Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Waterhouse, Robert M., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Höglund, Jacob, Palsbøll, Per J., Ruiz-López, María J., Zhang, Guojie, and Jarvis, Erich D.
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- 2022
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6. The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS
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Orkin, Joseph D., Montague, Michael J., Tejada-Martinez, Daniela, de Manuel, Marc, del Campo, Javier, Hernandez, Saul Cheves, Di Fiore, Anthony, Fontsere, Claudia, Hodgson, Jason A., Janiak, Mareike C., Kuderna, Lukas F. K., Lizano, Esther, Martin, Maria Pia, Niimura, Yoshihito, Perry, George H., Valverde, Carmen Soto, Tang, Jia, Warren, Wesley C., de Magalhães, João Pedro, Kawamura, Shoji, Marquès-Bonet, Tomàs, Krawetz, Roman, and Melin, Amanda D.
- Published
- 2021
7. The evolutionary history of extinct and living lions
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de Manuel, Marc, Barnett, Ross, Sandoval-Velasco, Marcela, Yamaguchi, Nobuyuki, Vieira, Filipe Garrett, Mendoza, M. Lisandra Zepeda, Liu, Shiping, Martin, Michael D., Sinding, Mikkel-Holger S., Mak, Sarah S. T., Carøe, Christian, Liu, Shanlin, Guo, Chunxue, Zheng, Jiao, Zazula, Grant, Baryshnikov, Gennady, Eizirik, Eduardo, Koepfli, Klaus-Peter, Johnson, Warren E., Antunes, Agostinho, Sicheritz-Ponten, Thomas, Gopalakrishnan, Shyam, Larson, Greger, Yang, Huanming, O’Brien, Stephen J., Hansen, Anders J., Zhang, Guojie, Marques-Bonet, Tomas, and Gilbert, M. Thomas P.
- Published
- 2020
8. Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts
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de-Dios, Toni, Carrión, Pablo, Olalde, Iñigo, Llovera Nadal, Laia, Lizano, Esther, Pàmies, Dídac, Marques-Bonet, Tomas, Balloux, François, van Dorp, Lucy, and Lalueza-Fox, Carles
- Published
- 2021
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9. Origins of de novo genes in human and chimpanzee
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Ruiz-Orera, Jorge, Hernandez-Rodriguez, Jessica, Chiva, Cristina, Sabidó, Eduard, Kondova, Ivanela, Bontrop, Ronald, Marqués-Bonet, Tomàs, and Albà, M. Mar
- Subjects
Quantitative Biology - Genomics - Abstract
The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that do not contain any gene or gene copy. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process we have performed in-depth sequencing of the transcriptomes of four mammalian species, human, chimpanzee, macaque and mouse, and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new transcriptional multiexonic events in human and/or chimpanzee that are not observed in the rest of species. By comparative genomics we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. We also find that the coding potential of the new genes is higher than expected by chance, consistent with the presence of protein-coding genes in the dataset. Using available human tissue proteomics and ribosome profiling data we identify several de novo genes with translation evidence. These genes show significant purifying selection signatures, indicating that they are probably functional. Taken together, the data supports a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins., Comment: 25 pages, 4 figures, 2 tables
- Published
- 2015
10. Genetic diagnosis of autoinflammatory disease patients using clinical exome sequencing
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Batlle-Masó, Laura, Mensa-Vilaró, Anna, Solís-Moruno, Manuel, Marquès-Bonet, Tomàs, Arostegui, Juan I., and Casals, Ferran
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- 2020
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11. Spatiotemporal transcriptomic divergence across human and macaque brain development
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Zhu, Ying, Sousa, André M. M., Gao, Tianliuyun, Skarica, Mario, Li, Mingfeng, Santpere, Gabriel, Esteller-Cucala, Paula, Juan, David, Ferrández-Peral, Luis, Gulden, Forrest O., Yang, Mo, Miller, Daniel J., Marques-Bonet, Tomas, Kawasawa, Yuka Imamura, Zhao, Hongyu, and Sestan, Nenad
- Published
- 2018
12. Late-replicating CNVs as a source of new genes
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Juan, David, Rico, Daniel, Marques-Bonet, Tomas, Fernandez-Capetillo, Oscar, and Valencia, Alfonso
- Subjects
Quantitative Biology - Genomics - Abstract
Asynchronous replication of the genome has been associated with different rates of point mutation and copy number variation (CNV) in human populations. Here, we explored if the bias in the generation of CNV that is associated to DNA replication timing might have conditioned the birth of new protein-coding genes during evolution. We show that genes that were duplicated during primate evolution are more commonly found among the human genes located in late-replicating CNV regions. We traced the relationship between replication timing and the evolutionary age of duplicated genes. Strikingly, we found that there is a significant enrichment of evolutionary younger duplicates in late replicating regions of the human and mouse genome. Indeed, the presence of duplicates in late replicating regions gradually decreases as the evolutionary time since duplication extends. Our results suggest that the accumulation of recent duplications in late replicating CNV regions is an active process influencing genome evolution., Comment: 43 pages, 5 figures and 4 figure supplements (two new figure supplements); added references and text in Introduction and Discussion, corrected typos; results unchanged
- Published
- 2013
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13. Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs
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Freedman, Adam H., Schweizer, Rena M., Gronau, Ilan, Han, Eunjung, Vecchyo, Diego Ortega-Del, Silva, Pedro M., Galaverni, Marco, Fan, Zhenxin, Marx, Peter, Lorente-Galdos, Belen, Beale, Holly, Ramirez, Oscar, Hormozdiari, Farhad, Alkan, Can, Vilà, Carles, Squire, Kevin, Geffen, Eli, Kusak, Josip, Boyko, Adam R., Parker, Heidi G., Lee, Clarence, Tadigotla, Vasisht, Siepel, Adam, Bustamante, Carlos D., Harkins, Timothy T., Nelson, Stanley F., Ostrander, Elaine A., Marques-Bonet, Tomas, Wayne, Robert K., and Novembre, John
- Subjects
Quantitative Biology - Genomics - Abstract
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we analyzed novel high-quality genome sequences of three gray wolves, one from each of three putative centers of dog domestication, two ancient dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. We find dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow, which confounds previous inferences of dog origins. In dogs, the domestication bottleneck was severe involving a 17 to 49-fold reduction in population size, a much stronger bottleneck than estimated previously from less intensive sequencing efforts. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was far larger than represented by modern wolf populations. Conditional on mutation rate, we narrow the plausible range for the date of initial dog domestication to an interval from 11 to 16 thousand years ago. This period predates the rise of agriculture, implying that the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that surprisingly, none of the extant wolf lineages from putative domestication centers are more closely related to dogs, and the sampled wolves instead form a sister monophyletic clade. This result, in combination with our finding of dog-wolf admixture during the process of domestication, suggests a re-evaluation of past hypotheses of dog origin is necessary. Finally, we also detect signatures of selection, including evidence for selection on genes implicated in morphology, metabolism, and neural development. Uniquely, we find support for selective sweeps at regulatory sites suggesting gene regulatory changes played a critical role in dog domestication., Comment: 24 pages, 5 figures. To download the Supporting Information file, use the following link: https://www.dropbox.com/s/2yoytspv1iods7s/Freedman_etal_SupportingInfo_arxiv.pdf
- Published
- 2013
14. Molecular and cellular reorganization of neural circuits in the human lineage
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Sousa, André M. M., Zhu, Ying, Raghanti, Mary Ann, Kitchen, Robert R., Onorati, Marco, Tebbenkamp, Andrew T. N., Stutz, Bernardo, Meyer, Kyle A., Li, Mingfeng, Kawasawa, Yuka Imamura, Liu, Fuchen, Perez, Raquel Garcia, Mele, Marta, Carvalho, Tiago, Skarica, Mario, Gulden, Forrest O., Pletikos, Mihovil, Shibata, Akemi, Stephenson, Alexa R., Edler, Melissa K., Ely, John J., Elsworth, John D., Horvath, Tamas L., Hof, Patrick R., Hyde, Thomas M., Kleinman, Joel E., Weinberger, Daniel R., Reimers, Mark, Lifton, Richard P., Mane, Shrikant M., Noonan, James P., State, Matthew W., Lein, Ed S., Knowles, James A., Marques-Bonet, Tomas, Sherwood, Chet C., Gerstein, Mark B., and Sestan, Nenad
- Published
- 2017
15. Ancient genomic changes associated with domestication of the horse
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Librado, Pablo, Gamba, Cristina, Gaunitz, Charleen, Sarkissian, Clio Der, Pruvost, Mélanie, Albrechtsen, Anders, Fages, Antoine, Khan, Naveed, Schubert, Mikkel, Jagannathan, Vidhya, Serres-Armero, Aitor, Kuderna, Lukas F. K., Povolotskaya, Inna S., Seguin-Orlando, Andaine, Lepetz, Sébastien, Neuditschko, Markus, Thèves, Catherine, Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled, Rieder, Stefan, Samashev, Zainolla, Francfort, Henri-Paul, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Keyser, Christine, Marques-Bonet, Tomas, Ludes, Bertrand, Crubézy, Eric, Leeb, Tosso, Willerslev, Eske, and Orlando, Ludovic
- Published
- 2017
16. Evidence that the rate of strong selective sweeps increases with population size in the great apes
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Nam, Kiwoong, Munch, Kasper, Mailund, Thomas, Nater, Alexander, Greminger, Maja Patricia, Krützen, Michael, Marquès-Bonet, Tomàs, and Schierup, Mikkel Heide
- Published
- 2017
17. Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros
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Sánchez-Barreiro, Fátima, primary, De Cahsan, Binia, additional, Westbury, Michael V, additional, Sun, Xin, additional, Margaryan, Ashot, additional, Fontsere, Claudia, additional, Bruford, Michael W, additional, Russo, Isa-Rita M, additional, Kalthoff, Daniela C, additional, Sicheritz-Pontén, Thomas, additional, Petersen, Bent, additional, Dalén, Love, additional, Zhang, Guojie, additional, Marquès-Bonet, Tomás, additional, Gilbert, M Thomas P, additional, and Moodley, Yoshan, additional
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- 2023
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18. Historic Sampling of a Vanishing Beast:Population Structure and Diversity in the Black Rhinoceros
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Sánchez-Barreiro, Fátima, De Cahsan, Binia, Westbury, Michael V., Sun, Xin, Margaryan, Ashot, Fontsere, Claudia, Bruford, Michael W., Russo, Isa-Rita M., Kalthoff, Daniela C., Sicheritz-Pontén, Thomas, Petersen, Bent, Dalén, Love, Zhang, Guojie, Marquès-Bonet, Tomás, Gilbert, M. Thomas P., Moodley, Yoshan, Sánchez-Barreiro, Fátima, De Cahsan, Binia, Westbury, Michael V., Sun, Xin, Margaryan, Ashot, Fontsere, Claudia, Bruford, Michael W., Russo, Isa-Rita M., Kalthoff, Daniela C., Sicheritz-Pontén, Thomas, Petersen, Bent, Dalén, Love, Zhang, Guojie, Marquès-Bonet, Tomás, Gilbert, M. Thomas P., and Moodley, Yoshan
- Abstract
The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
- Published
- 2023
19. Chimpanzee genomic diversity reveals ancient admixture with bonobos
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de Manuel, Marc, Kuhlwilm, Martin, Frandsen, Peter, Sousa, Vitor C., Desai, Tariq, Prado-Martinez, Javier, Hernandez-Rodriguez, Jessica, Dupanloup, Isabelle, Lao, Oscar, Hallast, Pille, Schmidt, Joshua M., Heredia-Genestar, José María, Benazzo, Andrea, Barbujani, Guido, Peter, Benjamin M., Kuderna, Lukas F. K., Casals, Ferran, Angedakin, Samuel, Arandjelovic, Mimi, Boesch, Christophe, Kühl, Hjalmar, Vigilant, Linda, Langergraber, Kevin, Novembre, John, Gut, Marta, Gut, Ivo, Navarro, Arcadi, Carlsen, Frauds, Andres, Aida M., Siegismund, Hans. R., Scally, Aylwyn, Excoffier, Laurent, Tyler-Smith, Chris, Castellano, Sergi, Xue, Yali, Hvilsom, Christina, and Marques-Bonet, Tomas
- Published
- 2016
20. Whole mitochondrial genomes illuminate ancient intercontinental dispersals of grey wolves (Canis lupus)
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Koblmüller, Stephan, Vilá, Carles, Lorente-Galdos, Belen, Dabad, Marc, Ramirez, Oscar, Marques-Bonet, Tomas, Wayne, Robert K., and Leonard, Jennifer A.
- Published
- 2016
21. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs
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Marsden, Clare D., Vecchyo, Diego Ortega-Del, O’Brien, Dennis P., Taylor, Jeremy F., Ramirez, Oscar, Vilà, Carles, Marques-Bonet, Tomas, Schnabel, Robert D., Wayne, Robert K., and Lohmueller, Kirk E.
- Published
- 2016
22. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments
- Author
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Librado, Pablo, Sarkissian, Clio Der, Ermini, Luca, Schubert, Mikkel, Jónsson, Hákon, Albrechtsen, Anders, Fumagalli, Matteo, Yang, Melinda A., Gamba, Cristina, Seguin-Orlando, Andaine, Mortensen, Cecilie D., Petersen, Bent, Hoover, Cindi A., Lorente-Galdos, Belen, Nedoluzhko, Artem, Boulygina, Eugenia, Tsygankova, Svetlana, Neuditschko, Markus, Jagannathan, Vidhya, Thèves, Catherine, Alfarhan, Ahmed H., Alquraishi, Saleh A., Al-Rasheid, Khaled A. S., Sicheritz-Ponten, Thomas, Popov, Ruslan, Grigoriev, Semyon, Alekseev, Anatoly N., Rubin, Edward M., McCue, Molly, Rieder, Stefan, Leeb, Tosso, Tikhonov, Alexei, Crubézy, Eric, Slatkin, Montgomery, Marques-Bonet, Tomas, Nielsen, Rasmus, Willerslev, Eske, Kantanen, Juha, Prokhortchouk, Egor, and Orlando, Ludovic
- Published
- 2015
23. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding
- Author
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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
- Published
- 2015
24. Prehistoric genomes reveal the genetic foundation and cost of horse domestication
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Schubert, Mikkel, Jónsson, Hákon, Chang, Dan, Der Sarkissian, Clio, Ermini, Luca, Ginolhac, Aurélien, Albrechtsen, Anders, Dupanloup, Isabelle, Foucal, Adrien, Petersen, Bent, Fumagalli, Matteo, Raghavan, Maanasa, Seguin-Orlando, Andaine, Komeliussen, Thorfinn S., Velazquez, Amhed M. V., Stenderup, Jesper, Hoover, Cindi A., Rubin, Carl-Johan, Alfarhan, Ahmed H., Alquraishi, Saleh A., Al-Rasheid, Khaled A. S., MacHugh, David E., Kalbfleisch, Ted, MacLeod, James N., Rubin, Edward M., Sicheritz-Ponten, Thomas, Andersson, Leif, Hofreiter, Michael, Marques-Bonet, Tomas, Thomas, M., Gilbert, P., Nielsen, Rasmus, Excoffier, Laurent, Willerslev, Eske, Shapiro, Beth, and Orlando, Ludovic
- Published
- 2014
25. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication
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Montague, Michael J., Li, Gang, Gandolfi, Barbara, Khan, Razib, Aken, Bronwen L., Searle, Steven M. J., Minx, Patrick, Hillier, LaDeana W., Koboldt, Daniel C., Davis, Brian W., Driscoll, Carlos A., Barr, Christina S., Blackistone, Kevin, Quilez, Javier, Lorente-Galdos, Belen, Marques-Bonet, Tomas, Alkan, Can, Thomas, Gregg W. C., Hahn, Matthew W., Menotti-Raymond, Marilyn, O'Brien, Stephen J., Wilson, Richard K., Lyons, Leslie A., Murphy, William J., and Warren, Wesley C.
- Published
- 2014
26. Rates and patterns of great ape retrotransposition
- Author
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Great Ape Genome Project, Hormozdiari, Fereydoun, Konkel, Miriam K., Prado-Martinez, Javier, Chiatante, Giorgia, Herraez, Irene Hernando, Walker, Jerilyn A., Nelson, Benjamin, Alkan, Can, Sudmant, Peter H., Huddleston, John, Catacchio, Claudia R., Ko, Arthur, Malig, Maika, Baker, Carl, Marques-Bonet, Tomas, Ventura, Mario, Batzer, Mark A., and Eichler, Evan E.
- Published
- 2013
27. The genome of melon (Cucumis melo L.)
- Author
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Garcia-Mas, Jordi, Benjak, Andrej, Sanseverino, Walter, Bourgeois, Michael, Mir, Gisela, González, Víctor M., Hénaff, Elizabeth, Câmara, Francisco, Cozzuto, Luca, Lowy, Ernesto, Alioto, Tyler, Capella-Gutiérrez, Salvador, Blanca, Jose, Cañizares, Joaquín, Ziarsolo, Pello, Gonzalez-Ibeas, Daniel, Rodríguez-Moreno, Luis, Droege, Marcus, Du, Lei, Alvarez-Tejado, Miguel, Lorente-Galdos, Belen, Melé, Marta, Yang, Luming, Weng, Yiqun, Navarro, Arcadi, Marques-Bonet, Tomas, Aranda, Miguel A., Nuez, Fernando, Picó, Belén, Gabaldón, Toni, Roma, Guglielmo, Guigó, Roderic, Casacuberta, Josep M., Arús, Pere, and Puigdomènech, Pere
- Published
- 2012
28. A Draft Sequence of the Neandertal Genome
- Author
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Green, Richard E., Krause, Johannes, Briggs, Adrian W., Marcic, Tomislav, Stenzel, Udo, Kircher, Martin, Patterson, Nick, Li, Heng, Zhai, Weiwei, Fritz, Markus Hsi-Yang, Hansen, Nancy F., Durand, Eric Y., Malaspinas, Anna-Sapfo, Jensen, Jeffrey D., Marques-Bonet, Tomas, Alkan, Can, Prüfer, kay, Meyer, Matthias, Burbano, Hernán A., Good, Jeffrey M., Schultz, Rigo, Aximu-Petri, Ayinuer, Butthof, Anne, Höber, Barbara, Höffner, Barbara, Siegemund, Madlen, Weihmann, Antje, Nusbaum, Chad, Lander, Eric S., Russ, Carsten, Novod, Nathaniel, Affourtit, Jason, Egholm, Michael, Verna, Christine, Rudan, Pavao, Brajkovic, Dejana, Kucan, Zeljko, Gusic, Ivan, Doronichev, Vladimir B., Golovanova, Liubov V., Lalueza-Fox, Carles, de la Rasilla, Marco, Fortea, Javier, Rosas, Antonio, Schmitz, Ralf W., Johnson, Philip L F., Eichler, Evan E., Falush, Daniel, Birney, Ewan, Mullikin, James, Slatkin, Montgomery, Nielsen, Rasmus, Kelso, Janet, Lachmann, Michael, Reich, David, and Pääbo, Svante
- Published
- 2010
29. Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros ( Ceratotherium simum )
- Author
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Sánchez‐Barreiro, Fátima, primary, Gopalakrishnan, Shyam, additional, Ramos‐Madrigal, Jazmín, additional, Westbury, Michael V., additional, de Manuel, Marc, additional, Margaryan, Ashot, additional, Ciucani, Marta M., additional, Vieira, Filipe G., additional, Patramanis, Yannis, additional, Kalthoff, Daniela C., additional, Timmons, Zena, additional, Sicheritz‐Pontén, Thomas, additional, Dalén, Love, additional, Ryder, Oliver A., additional, Zhang, Guojie, additional, Marquès‐Bonet, Tomás, additional, Moodley, Yoshan, additional, and Gilbert, M. Thomas P., additional
- Published
- 2021
- Full Text
- View/download PDF
30. Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros ( Ceratotherium simum )
- Author
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Sánchez‐Barreiro, Fátima, Gopalakrishnan, Shyam, Ramos‐Madrigal, Jazmín, Westbury, Michael V., Manuel, Marc, Margaryan, Ashot, Ciucani, Marta M., Vieira, Filipe G., Patramanis, Yannis, Kalthoff, Daniela C., Timmons, Zena, Sicheritz‐Pontén, Thomas, Dalén, Love, Ryder, Oliver A., Zhang, Guojie, Marquès‐Bonet, Tomás, Moodley, Yoshan, Gilbert, M. Thomas P., Sánchez‐Barreiro, Fátima, Gopalakrishnan, Shyam, Ramos‐Madrigal, Jazmín, Westbury, Michael V., Manuel, Marc, Margaryan, Ashot, Ciucani, Marta M., Vieira, Filipe G., Patramanis, Yannis, Kalthoff, Daniela C., Timmons, Zena, Sicheritz‐Pontén, Thomas, Dalén, Love, Ryder, Oliver A., Zhang, Guojie, Marquès‐Bonet, Tomás, Moodley, Yoshan, and Gilbert, M. Thomas P.
- Abstract
Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.
- Published
- 2021
- Full Text
- View/download PDF
31. Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet
- Author
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Gelabert, Pere, Sandoval-Velasco, Marcela, Serres, Aitor, de Manuel, Marc, Renom, Pere, Margaryan, Ashot, Stiller, Josefin, de-Dios, Toni, Fang, Qi, Feng, Shaohong, Mañosa, Santi, Pacheco, George, Ferrando-Bernal, Manuel, Shi, Guolin, Hao, Fei, Chen, Xianqing, Petersen, Bent, Olsen, Remi-André, Navarro, Arcadi, Deng, Yuan, Dalén, Love, Marquès-Bonet, Tomàs, Zhang, Guojie, Antunes, Agostinho, Gilbert, M. Thomas P., and Lalueza-Fox, Carles
- Published
- 2020
- Full Text
- View/download PDF
32. Whole-Genomes From the Extinct Xerces Blue Butterfly Reveal Low Diversity and Long-Term Population Decline
- Author
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de-Dios, Toni, primary, Fontsere, Claudia, additional, Renom, Pere, additional, Stiller, Josefin, additional, Llovera Nadal, Laia, additional, Uliano-Silva, Marcela, additional, Wright, Charlotte, additional, Lizano, Esther, additional, Navarro, Arcadi, additional, Robbins, Robert, additional, Blaxter, Mark, additional, Marquès-Bonet, Tomás, additional, Vila, Roger, additional, and Lalueza-Fox, Carles, additional
- Published
- 2021
- Full Text
- View/download PDF
33. Ancient Salmonella Enterica from a Soldier of the 1652-Siege of Barcelona (Spain) Supports Historical Epidemic Contacts Across the Atlantic
- Author
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de-Dios, Toni, primary, Carrión, Pablo, additional, Olalde, Iñigo, additional, Llovera Nadal, Laia, additional, Lizano, Esther, additional, Pàmies, Didac, additional, Marquès-Bonet, Tomás, additional, Balloux, François, additional, van Dorp, Lucy, additional, and Lalueza-Fox, Carles, additional
- Published
- 2021
- Full Text
- View/download PDF
34. Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)
- Author
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Sánchez-Barreiro, Fátima, primary, Gopalakrishnan, Shyam, additional, Ramos-Madrigal, Jazmín, additional, Westbury, Michael V., additional, de Manuel, Marc, additional, Margaryan, Ashot, additional, Ciucani, Marta M., additional, Vieira, Filipe G., additional, Patramanis, Yannis, additional, Kalthoff, Daniela C., additional, Timmons, Zena, additional, Sicheritz-Pontén, Thomas, additional, Dalén, Love, additional, Ryder, Oliver A., additional, Zhang, Guojie, additional, Marquès-Bonet, Tomás, additional, Moodley, Yoshan, additional, and Gilbert, M. Thomas P., additional
- Published
- 2020
- Full Text
- View/download PDF
35. Historical Population Declines Prompted Significant Genomic Erosion in the Northern and Southern White Rhinoceros ( Ceratotherium simum)
- Author
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Sánchez Barreiro, Fátima, primary, Gopalakrishnan, Shyam, additional, Ramos-Madrigal, Jazmín, additional, Westbury, Michael Vincent, additional, de Manuel, Marc, additional, Margaryan, Ashot, additional, Ciucani, Marta Maria, additional, Vieira, Filipe Garrett, additional, Patramanis, Yannis, additional, Kalthoff, Daniela, additional, Timmons, Zena, additional, Sicheritz-Pontén, Thomas, additional, Dalén, Love, additional, Ryder, Oliver, additional, Zhang, Guojie, additional, Marquès-Bonet, Tomás, additional, Moodley, Yoshan, additional, and Gilbert, Marcus Thomas Pius, additional
- Published
- 2020
- Full Text
- View/download PDF
36. A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures
- Author
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Olalde, Iñigo, Schroeder, Hannes, Sandoval Velasco, Marcela, Vinner, Lasse, Lobón, Irene, Ramirez, Oscar, Civit, Sergi, Borja, Pablo García, Salazar-García, Domingo C., Talamo, Sahra, Fullola, Josep María, Oms, Francesc Xavier, Pedro, Mireia, Martínez, Pablo, Sanz, Montserrat, Daura, Joan, Zilhão, João, Marquès-Bonet, Tomás, Gilbert, M. Thomas P., Lalueza-Fox, Carles, Olalde, Iñigo, Schroeder, Hannes, Sandoval Velasco, Marcela, Vinner, Lasse, Lobón, Irene, Ramirez, Oscar, Civit, Sergi, Borja, Pablo García, Salazar-García, Domingo C., Talamo, Sahra, Fullola, Josep María, Oms, Francesc Xavier, Pedro, Mireia, Martínez, Pablo, Sanz, Montserrat, Daura, Joan, Zilhão, João, Marquès-Bonet, Tomás, Gilbert, M. Thomas P., and Lalueza-Fox, Carles
- Published
- 2015
37. Rivers as possible landmarks in the orientation flight of Miniopterus schreibersii
- Author
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Serra-Cobo, Jordi, primary, López-Roig, Marc, additional, Marquès-Bonet, Tomás, additional, and Lahuerta, Eva, additional
- Published
- 2000
- Full Text
- View/download PDF
38. Genomic legacy of the African cheetah, Acinonyx jubatus
- Author
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Dobrynin, Pavel, Liu, Shiping, Tamazian, Gaik, Xiong, Zijun, Yurchenko, Andrey A., Krasheninnikova, Ksenia, Kliver, Sergey, Schmidt-Küntzel, Anne, Koepfli, Klaus-Peter, Johnson, Warren, Kuderna, Lukas F.K., García-Pérez, Raquel, Manuel, Marc de, Godinez, Ricardo, Komissarov, Aleksey, Makunin, Alexey, Brukhin, Vladimir, Qiu, Weilin, Zhou, Long, Li, Fang, Yi, Jian, Driscoll, Carlos, Antunes, Agostinho, Oleksyk, Taras K., Eizirik, Eduardo, Perelman, Polina, Roelke, Melody, Wildt, David, Diekhans, Mark, Marques-Bonet, Tomas, Marker, Laurie, Bhak, Jong, Wang, Jun, Zhang, Guojie, and O’Brien, Stephen J.
- Subjects
Genetic diversity ,Conservation biology ,Population biology - Abstract
Background: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. Results: Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years ago coincident with cheetah migrations out of the Americas and into Eurasia and Africa, and a second 11,084–12,589 years ago in Africa coincident with late Pleistocene large mammal extinctions. MHC class I gene loss and dramatic reduction in functional diversity of MHC genes would explain why cheetahs ablate skin graft rejection among unrelated individuals. Significant excess of non-synonymous mutations in AKAP4 (p<0.02), a gene mediating spermatozoon development, indicates cheetah fixation of five function-damaging amino acid variants distinct from AKAP4 homologues of other Felidae or mammals; AKAP4 dysfunction may cause the cheetah’s extremely high (>80 %) pleiomorphic sperm. Conclusions: The study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species’ natural history, physiological adaptations and unique reproductive disposition. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0837-4) contains supplementary material, which is available to authorized users.
- Published
- 2015
- Full Text
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39. Gibbon genome and the fast karyotype evolution of small apes
- Author
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Carbone, Lucia, Harris, R. Alan, Gnerre, Sante, Veeramah, Krishna R., Lorente-Galdos, Belen, Huddleston, John, Meyer, Thomas J., Herrero, Javier, Roos, Christian, Aken, Bronwen, Anaclerio, Fabio, Archidiacono, Nicoletta, Baker, Carl, Barrell, Daniel, Batzer, Mark A., Beal, Kathryn, Blancher, Antoine, Bohrson, Craig L., Brameier, Markus, Campbell, Michael S., Capozzi, Oronzo, Casola, Claudio, Chiatante, Giorgia, Cree, Andrew, Damert, Annette, de Jong, Pieter J., Dumas, Laura, Fernandez-Callejo, Marcos, Flicek, Paul, Fuchs, Nina V., Gut, Marta, Gut, Ivo, Hahn, Matthew W., Hernandez-Rodriguez, Jessica, Hillier, LaDeana W., Hubley, Robert, Ianc, Bianca, Izsvák, Zsuzsanna, Jablonski, Nina G., Johnstone, Laurel M., Karimpour-Fard, Anis, Konkel, Miriam K., Kostka, Dennis, Lazar, Nathan H., Lee, Sandra L., Lewis, Lora R., Liu, Yue, Locke, Devin P., Mallick, Swapan, Mendez, Fernando L., Muffato, Matthieu, Nazareth, Lynne V., Nevonen, Kimberly A., O,Bleness, Majesta, Ochis, Cornelia, Odom, Duncan T., Pollard, Katherine S., Quilez, Javier, Reich, David, Rocchi, Mariano, Schumann, Gerald G., Searle, Stephen, Sikela, James M., Skollar, Gabriella, Smit, Arian, Sonmez, Kemal, Hallers, Boudewijn ten, Terhune, Elizabeth, Thomas, Gregg W.C., Ullmer, Brygg, Ventura, Mario, Walker, Jerilyn A., Wall, Jeffrey D., Walter, Lutz, Ward, Michelle C., Wheelan, Sarah J., Whelan, Christopher W., White, Simon, Wilhelm, Larry J., Woerner, August E., Yandell, Mark, Zhu, Baoli, Hammer, Michael F., Marques-Bonet, Tomas, Eichler, Evan E., Fulton, Lucinda, Fronick, Catrina, Muzny, Donna M., Warren, Wesley C., Worley, Kim C., Rogers, Jeffrey, Wilson, Richard K., and Gibbs, Richard A.
- Abstract
Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation ~5 million years ago, coincident with major geographical changes in Southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat.
- Published
- 2014
- Full Text
- View/download PDF
40. Great ape genetic diversity and population history
- Author
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Prado-Martinez, Javier, Sudmant, Peter H., Kidd, Jeffrey M., Li, Heng, Kelley, Joanna L., Lorente-Galdos, Belen, Veeramah, Krishna R., Woerner, August E., O’Connor, Timothy D., Santpere, Gabriel, Cagan, Alexander, Theunert, Christoph, Casals, Ferran, Laayouni, Hafid, Munch, Kasper, Hobolth, Asger, Halager, Anders E., Malig, Maika, Hernandez-Rodriguez, Jessica, Hernando-Herraez, Irene, Prüfer, Kay, Pybus, Marc, Johnstone, Laurel, Lachmann, Michael, Alkan, Can, Twigg, Dorina, Petit, Natalia, Baker, Carl, Hormozdiari, Fereydoun, Fernandez-Callejo, Marcos, Dabad, Marc, Wilson, Michael L., Stevison, Laurie, Camprubí, Cristina, Carvalho, Tiago, Ruiz-Herrera, Aurora, Vives, Laura, Mele, Marta, Abello, Teresa, Kondova, Ivanela, Bontrop, Ronald E., Pusey, Anne, Lankester, Felix, Kiyang, John A., Bergl, Richard A., Lonsdorf, Elizabeth, Myers, Simon, Ventura, Mario, Gagneux, Pascal, Comas, David, Siegismund, Hans, Blanc, Julie, Agueda-Calpena, Lidia, Gut, Marta, Fulton, Lucinda, Tishkoff, Sarah A., Mullikin, James C., Wilson, Richard K., Gut, Ivo G., Gonder, Mary Katherine, Ryder, Oliver A., Hahn, Beatrice H., Navarro, Arcadi, Akey, Joshua M., Bertranpetit, Jaume, Reich, David, Mailund, Thomas, Schierup, Mikkel H., Hvilsom, Christina, Andrés, Aida M., Wall, Jeffrey D., Bustamante, Carlos D., Hammer, Michael F., Eichler, Evan E., and Marques-Bonet, Tomas
- Published
- 2013
- Full Text
- View/download PDF
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