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1. Identification of constrained sequence elements across 239 primate genomes

Author: Kuderna, Lukas F. K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rouselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N. F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marques Bonet, Tomas, and Farh, Kyle Kai-How
Published: 2024
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2. Comprehensive identification of somatic nucleotide variants in human brain tissue

Author: Wang, Yifan, Bae, Taejeong, Thorpe, Jeremy, Sherman, Maxwell A, Jones, Attila G, Cho, Sean, Daily, Kenneth, Dou, Yanmei, Ganz, Javier, Galor, Alon, Lobon, Irene, Pattni, Reenal, Rosenbluh, Chaggai, Tomasi, Simone, Tomasini, Livia, Yang, Xiaoxu, Zhou, Bo, Akbarian, Schahram, Ball, Laurel L, Bizzotto, Sara, Emery, Sarah B, Doan, Ryan, Fasching, Liana, Jang, Yeongjun, Juan, David, Lizano, Esther, Luquette, Lovelace J, Moldovan, John B, Narurkar, Rujuta, Oetjens, Matthew T, Rodin, Rachel E, Sekar, Shobana, Shin, Joo Heon, Soriano, Eduardo, Straub, Richard E, Zhou, Weichen, Chess, Andrew, Gleeson, Joseph G, Marquès-Bonet, Tomas, Park, Peter J, Peters, Mette A, Pevsner, Jonathan, Walsh, Christopher A, Weinberger, Daniel R, Vaccarino, Flora M, Moran, John V, Urban, Alexander E, Kidd, Jeffrey M, Mills, Ryan E, and Abyzov, Alexej
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Neurosciences, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Alleles, Brain, Chromosome Mapping, Computational Biology, Genetic Association Studies, Genetic Variation, Genomics, Germ Cells, High-Throughput Nucleotide Sequencing, Humans, Organ Specificity, Polymorphism, Single Nucleotide, Brain Somatic Mosaicism Network, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract: BackgroundPost-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells.ResultsHere, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees.ConclusionsThis study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.
Published: 2021

3. Identification of constrained sequence elements across 239 primate genomes

Author: Natural Environment Research Council (UK), UK Research and Innovation, National Human Genome Research Institute (US), Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fonds de la Recherche Scientifique (Fédération Wallonie-Bruxelles), Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, Ministry of Science and Technology of Vietnam, Agencia Estatal de Investigación (España), Generalitat de Catalunya, Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Wenner-Gren Foundation, Leakey Foundation, National Science Foundation (US), National Geographic Society, National Institute on Aging (US), Swedish Research Council, National Research Foundation Singapore, European Research Council, Ministerio de Ciencia e Innovación (España), Ministerio de Ciencia, Innovación y Universidades (España), Kuderna, Lukas F. K. [0000-0002-9992-9295], Kuhlwilm, Martin [0000-0002-0115-1797], Valenzuela, Alejandro [0000-0001-6120-6246], Juan, David [0000-0003-1912-9667], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Kuderna, Lukas F. K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Farh, Kyle Kai-How, Natural Environment Research Council (UK), UK Research and Innovation, National Human Genome Research Institute (US), Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fonds de la Recherche Scientifique (Fédération Wallonie-Bruxelles), Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, Ministry of Science and Technology of Vietnam, Agencia Estatal de Investigación (España), Generalitat de Catalunya, Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Wenner-Gren Foundation, Leakey Foundation, National Science Foundation (US), National Geographic Society, National Institute on Aging (US), Swedish Research Council, National Research Foundation Singapore, European Research Council, Ministerio de Ciencia e Innovación (España), Ministerio de Ciencia, Innovación y Universidades (España), Kuderna, Lukas F. K. [0000-0002-9992-9295], Kuhlwilm, Martin [0000-0002-0115-1797], Valenzuela, Alejandro [0000-0001-6120-6246], Juan, David [0000-0003-1912-9667], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Kuderna, Lukas F. K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marqués-Bonet, Tomàs, and Farh, Kyle Kai-How
Abstract: Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3,4,5,6,7,8,9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
Published: 2024

4. Population dynamics and genetic connectivity in recent chimpanzee history

Author: 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
Published: 2022
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5. Current challenges and best practices for cell-free long RNA biomarker discovery

Author: Cabús, Lluc, Lagarde, Julien, Curado, Joao, Lizano, Esther, and Pérez-Boza, Jennifer
Published: 2022
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6. Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition

Author: García-Fernández, Carla, Lizano, Esther, Telford, Marco, Olalde, Íñigo, de Cid, Rafael, Larmuseau, Maarten H. D., M. de Pancorbo, Marian, and Calafell, Francesc
Published: 2022
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7. The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS

Author: 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

8. Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

Author: Krueger, Johanna, primary, Fong Zazueta, Ricardo, additional, Alba, David M., additional, Aymerich, Xenia, additional, Beck, Robin M.D., additional, Cappellini, Enrico, additional, Carrillo Martin, Guillermo, additional, Cirilli, Omar, additional, Clark, Nathan, additional, Cornejo, Omar E., additional, Farh, Kyle, additional, Ferrandez-Peral, Luis, additional, Juan, David, additional, Kelley, Joanna L., additional, Kuderna, Lukas F. K., additional, Little, Jordan, additional, Orkin, Joseph D., additional, Paterson, Ryan S., additional, Pawar, Harvinder, additional, Marques-Bonet, Tomas, additional, and Lizano, Esther, additional
Published: 2024
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9. Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts

Author: 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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10. Identification of constrained sequence elements across 239 primate genomes

Author: Kuderna, Lukas F.K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rouselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marques Bonet, Tomas, Farh, Kyle Kai How, Kuderna, Lukas F.K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rouselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marques Bonet, Tomas, and Farh, Kyle Kai How
Abstract: Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3,4,5,6,7,8,9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals., Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3–9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
Published: 2024

11. Whole-genomes from the extinct Xerces Blue butterfly reveal low diversity and long-term population decline

Author: Lalueza-Fox, Carles, primary, de-Dios, Toni, additional, Fontsere, Claudia, additional, Renom, Pere, additional, Stiller, Josefin, additional, Llovera, Laia, additional, Uliano-Silva, Marcela, additional, Wright, Charlotte, additional, Lizano, Esther, additional, Navarro, Arcadi, additional, Robbins, Robert, additional, Blaxter, Mark, additional, Marquès-Bonet, Tomas, additional, and Vila, Roger, additional
Published: 2024
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12. Identification of constrained sequence elements across 239 primate genomes

Author: Kuderna, Lukas F. K., primary, Ulirsch, Jacob C., additional, Rashid, Sabrina, additional, Ameen, Mohamed, additional, Sundaram, Laksshman, additional, Hickey, Glenn, additional, Cox, Anthony J., additional, Gao, Hong, additional, Kumar, Arvind, additional, Aguet, Francois, additional, Christmas, Matthew J., additional, Clawson, Hiram, additional, Haeussler, Maximilian, additional, Janiak, Mareike C., additional, Kuhlwilm, Martin, additional, Orkin, Joseph D., additional, Bataillon, Thomas, additional, Manu, Shivakumara, additional, Valenzuela, Alejandro, additional, Bergman, Juraj, additional, Rouselle, Marjolaine, additional, Silva, Felipe Ennes, additional, Agueda, Lidia, additional, Blanc, Julie, additional, Gut, Marta, additional, de Vries, Dorien, additional, Goodhead, Ian, additional, Harris, R. Alan, additional, Raveendran, Muthuswamy, additional, Jensen, Axel, additional, Chuma, Idriss S., additional, Horvath, Julie E., additional, Hvilsom, Christina, additional, Juan, David, additional, Frandsen, Peter, additional, Schraiber, Joshua G., additional, de Melo, Fabiano R., additional, Bertuol, Fabrício, additional, Byrne, Hazel, additional, Sampaio, Iracilda, additional, Farias, Izeni, additional, Valsecchi, João, additional, Messias, Malu, additional, da Silva, Maria N. F., additional, Trivedi, Mihir, additional, Rossi, Rogerio, additional, Hrbek, Tomas, additional, Andriaholinirina, Nicole, additional, Rabarivola, Clément J., additional, Zaramody, Alphonse, additional, Jolly, Clifford J., additional, Phillips-Conroy, Jane, additional, Wilkerson, Gregory, additional, Abee, Christian, additional, Simmons, Joe H., additional, Fernandez-Duque, Eduardo, additional, Kanthaswamy, Sree, additional, Shiferaw, Fekadu, additional, Wu, Dongdong, additional, Zhou, Long, additional, Shao, Yong, additional, Zhang, Guojie, additional, Keyyu, Julius D., additional, Knauf, Sascha, additional, Le, Minh D., additional, Lizano, Esther, additional, Merker, Stefan, additional, Navarro, Arcadi, additional, Nadler, Tilo, additional, Khor, Chiea Chuen, additional, Lee, Jessica, additional, Tan, Patrick, additional, Lim, Weng Khong, additional, Kitchener, Andrew C., additional, Zinner, Dietmar, additional, Gut, Ivo, additional, Melin, Amanda D., additional, Guschanski, Katerina, additional, Schierup, Mikkel Heide, additional, Beck, Robin M. D., additional, Karakikes, Ioannis, additional, Wang, Kevin C., additional, Umapathy, Govindhaswamy, additional, Roos, Christian, additional, Boubli, Jean P., additional, Siepel, Adam, additional, Kundaje, Anshul, additional, Paten, Benedict, additional, Lindblad-Toh, Kerstin, additional, Rogers, Jeffrey, additional, Marques Bonet, Tomas, additional, and Farh, Kyle Kai-How, additional
Published: 2023
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13. Targeted conservation genetics of the endangered chimpanzee

Author: Frandsen, Peter, Fontsere, Claudia, Nielsen, Svend Vendelbo, Hanghøj, Kristian, Castejon-Fernandez, Natalia, Lizano, Esther, Hughes, David, Hernandez-Rodriguez, Jessica, Korneliussen, Thorfinn Sand, Carlsen, Frands, Siegismund, Hans Redlef, Mailund, Thomas, Marques-Bonet, Tomas, and Hvilsom, Christina
Published: 2020
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14. Y chromosome sequence and epigenomic reconstruction across human populations

Author: Fundación la Caixa, European Research Council, European Commission, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Kuderna, Lukas F. K. [0000-0002-9992-9295], Lizano, Esther [0000-0003-3304-9807], Juan, David [0000-0003-1912-9667], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Esteller-Cucala, Paula, Palmada-Flores, Marc, Kuderna, Lukas F. K., Fontsere, Claudia, Serres-Armero, Aitor, Dabad, Marc, Torralvo, María, Faella, Armida, Ferrández-Peral, Luis, Llovera, Laia, Fornas, Oscar, Julià, Eva, Ramírez, Erika, González, Irene, Hecht, Jochen, Lizano, Esther, Juan, David, Marqués-Bonet, Tomàs, Fundación la Caixa, European Research Council, European Commission, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Kuderna, Lukas F. K. [0000-0002-9992-9295], Lizano, Esther [0000-0003-3304-9807], Juan, David [0000-0003-1912-9667], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Esteller-Cucala, Paula, Palmada-Flores, Marc, Kuderna, Lukas F. K., Fontsere, Claudia, Serres-Armero, Aitor, Dabad, Marc, Torralvo, María, Faella, Armida, Ferrández-Peral, Luis, Llovera, Laia, Fornas, Oscar, Julià, Eva, Ramírez, Erika, González, Irene, Hecht, Jochen, Lizano, Esther, Juan, David, and Marqués-Bonet, Tomàs
Abstract: Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). Native DNA was sequenced on a MinION Oxford Nanopore Technologies sequencing device to generate genome assemblies for seven major chrY human haplogroups. We analyzed and compared the chrY enrichment of sequencing data obtained using two different selective sequencing approaches: adaptive sampling and flow cytometry chromosome sorting. We show that adaptive sampling can produce data to create assemblies comparable to chromosome sorting while being a less expensive and time-consuming technique. We also assessed haplogroup-specific structural variants, which would be otherwise difficult to study using short-read sequencing data only. Finally, we took advantage of this technology to detect and profile epigenetic modifications among the considered haplogroups. Altogether, we provide a framework to study complex genomic regions with a simple, fast, and affordable methodology that could be applied to larger population genomics datasets.
Published: 2023

15. The landscape of tolerated genetic variation in humans and primates

Author: EMBO, National Institutes of Health (US), Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), International Primatological Society, Rufford Foundation, Margot Marsh Biodiversity Foundation, Primate Conservation, Mamirauá Institute for Sustainable Development, Gordon and Betty Moore Foundation, Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, National Science Foundation (US), Ministry of Science and Technology of Vietnam, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Illumina, Natural Environment Research Council (UK), San Diego Zoo Wildlife Alliance, Wenner-Gren Foundation, Leakey Foundation, National Geographic Society, National Institute on Aging (US), National Research Foundation Singapore, Swedish Research Council, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad (España), Juan, David [0000-0003-1912-9667], Valenzuela, Alejandro [0000-0001-6120-6246], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Gao, Hong, Hamp, Tobias, Ede, Jeffrey, Schraiber, Joshua G., McRae, Jeremy, Singer-Berk, Moriel, Yang, Yanshen, Dietrich, Anastasia S. D., Fiziev, Petko P., Kuderna, Lukas F. K., Sundaram, Laksshman, Wu, Yibing, Adhikari, Aashish, Field, Yair, Chen, Chen, Batzoglou, Serafim, Aguet, Francois, Lemire, Gabrielle, Reimers, Rebecca, Balick, Daniel, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Amaral, João Valsecchi do, Messias, Mariluce, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Bataillon, Thomas, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda, Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Lek, Monkol, Sunyaev, Shamil, O’Donnell-Luria, Anne, Rehm, Heidi L., Xu, Jinbo, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Farh, Kyle Kai-How, EMBO, National Institutes of Health (US), Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), International Primatological Society, Rufford Foundation, Margot Marsh Biodiversity Foundation, Primate Conservation, Mamirauá Institute for Sustainable Development, Gordon and Betty Moore Foundation, Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, National Science Foundation (US), Ministry of Science and Technology of Vietnam, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Illumina, Natural Environment Research Council (UK), San Diego Zoo Wildlife Alliance, Wenner-Gren Foundation, Leakey Foundation, National Geographic Society, National Institute on Aging (US), National Research Foundation Singapore, Swedish Research Council, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad (España), Juan, David [0000-0003-1912-9667], Valenzuela, Alejandro [0000-0001-6120-6246], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Gao, Hong, Hamp, Tobias, Ede, Jeffrey, Schraiber, Joshua G., McRae, Jeremy, Singer-Berk, Moriel, Yang, Yanshen, Dietrich, Anastasia S. D., Fiziev, Petko P., Kuderna, Lukas F. K., Sundaram, Laksshman, Wu, Yibing, Adhikari, Aashish, Field, Yair, Chen, Chen, Batzoglou, Serafim, Aguet, Francois, Lemire, Gabrielle, Reimers, Rebecca, Balick, Daniel, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Amaral, João Valsecchi do, Messias, Mariluce, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Bataillon, Thomas, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda, Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Lek, Monkol, Sunyaev, Shamil, O’Donnell-Luria, Anne, Rehm, Heidi L., Xu, Jinbo, Rogers, Jeffrey, Marqués-Bonet, Tomàs, and Farh, Kyle Kai-How
Abstract: [INTRODUCTION] Millions of people have received genome and exome sequencing to date, a collective effort that has illuminated for the first time the vast catalog of small genetic differences that distinguish us as individuals within our species. However, the effects of most of these genetic variants remain unknown, limiting their clinical utility and actionability. New approaches that can accurately discern disease-causing from benign mutations and interpret genetic variants on a genome-wide scale would constitute a meaningful initial step towards realizing the potential of personalized genomic medicine., [RATIONALE] As a result of the short evolutionary distance between humans and nonhuman primates, our proteins share near-perfect amino acid sequence identity. Hence, the effects of a protein-altering mutation found in one species are likely to be concordant in the other species. By systematically cataloging common variants of nonhuman primates, we aimed to annotate these variants as being unlikely to cause human disease as they are tolerated by natural selection in a closely related species. Once collected, the resulting resource may be applied to infer the effects of unobserved variants across the genome using machine learning., [RESULTS] Following the strategy outlined above we obtained whole-genome sequencing data for 809 individuals from 233 primate species and cataloged 4.3 million common missense variants. We confirmed that human missense variants seen in at least one nonhuman primate species were annotated as benign in the ClinVar clinical variant database in 99% of cases. By contrast, common variants from mammals and vertebrates outside the primate lineage were substantially less likely to be benign in the ClinVar database (71 to 87% benign), restricting this strategy to nonhuman primates. Overall, we reclassified more than 4 million human missense variants of previously unknown consequence as likely benign, resulting in a greater than 50-fold increase in the number of annotated missense variants compared to existing clinical databases. To infer the pathogenicity of the remaining missense variants in the human genome, we constructed PrimateAI-3D, a semisupervised 3D-convolutional neural network that operates on voxelized protein structures. We trained PrimateAI-3D to separate common primate variants from matched control variants in 3D space as a semisupervised learning task. We evaluated the trained PrimateAI-3D model alongside 15 other published machine learning methods on their ability to distinguish between benign and pathogenic variants in six different clinical benchmarks and demonstrated that PrimateAI-3D outperformed all other classifiers in each of the tasks., [CONCLUSION] Our study addresses one of the key challenges in the variant interpretation field, namely, the lack of sufficient labeled data to effectively train large machine learning models. By generating the most comprehensive primate sequencing dataset to date and pairing this resource with a deep learning architecture that leverages 3D protein structures, we were able to achieve meaningful improvements in variant effect prediction across multiple clinical benchmarks.
Published: 2023

16. Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs

Author: Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, European Research Council, European Commission, Ministerio de Ciencia e Innovación (España), Fundación la Caixa, Alvarez-Estape, Marina [0000-0001-8242-1092], Fontsere, Claudia [0000-0003-2233-6026], Lizano, Esther [0000-0003-3304-9807], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Alvarez-Estape, Marina, Pawar, Harvinder, Fontsere, Claudia, Trujillo, Amber E., Gunson, Jessica L., Bergl, Richard A., Bermejo, Magdalena, Linder, Joshua M., McFarland, Kelley, Oates, John F., Sunderland-Groves, Jacqueline L., Orkin, Joseph D., Higham, James P., Viaud-Martinez, Karine A., Lizano, Esther, Marqués-Bonet, Tomàs, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, European Research Council, European Commission, Ministerio de Ciencia e Innovación (España), Fundación la Caixa, Alvarez-Estape, Marina [0000-0001-8242-1092], Fontsere, Claudia [0000-0003-2233-6026], Lizano, Esther [0000-0003-3304-9807], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Alvarez-Estape, Marina, Pawar, Harvinder, Fontsere, Claudia, Trujillo, Amber E., Gunson, Jessica L., Bergl, Richard A., Bermejo, Magdalena, Linder, Joshua M., McFarland, Kelley, Oates, John F., Sunderland-Groves, Jacqueline L., Orkin, Joseph D., Higham, James P., Viaud-Martinez, Karine A., Lizano, Esther, and Marqués-Bonet, Tomàs
Abstract: The critically endangered western gorillas (Gorilla gorilla) are divided into two subspecies: the western lowland (G. g. gorilla) and the Cross River (G. g. diehli) gorilla. Given the difficulty in sampling wild great ape populations and the small estimated size of the Cross River gorilla population, only one whole genome of a Cross River gorilla has been sequenced to date, hindering the study of this subspecies at the population level. In this study, we expand the number of whole genomes available for wild western gorillas, generating 41 new genomes (25 belonging to Cross River gorillas) using single shed hairs collected from gorilla nests. By combining these genomes with publicly available wild gorilla genomes, we confirm that Cross River gorillas form three population clusters. We also found little variation in genome-wide heterozygosity among them. Our analyses reveal long runs of homozygosity (>10 Mb), indicating recent inbreeding in Cross River gorillas. This is similar to that seen in mountain gorillas but with a much more recent bottleneck. We also detect past gene flow between two Cross River sites, Afi Mountain Wildlife Sanctuary and the Mbe Mountains. Furthermore, we observe past allele sharing between Cross River gorillas and the northern western lowland gorilla sites, as well as with the eastern gorilla species. This is the first study using single shed hairs from a wild species for whole genome sequencing to date. Taken together, our results highlight the importance of implementing conservation measures to increase connectivity among Cross River gorilla sites.
Published: 2023

17. A global catalog of whole-genome diversity from 233 primate species

Author: Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), International Primatological Society, Rufford Foundation, Margot Marsh Biodiversity Foundation, Primate Conservation, Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, National Science Foundation (US), Ministry of Science and Technology of Vietnam, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, European Research Council, Natural Environment Research Council (UK), UK Research and Innovation, Department of Biotechnology (India), San Diego Zoo Wildlife Alliance, Wenner-Gren Foundation, Leakey Foundation, National Geographic Society, National Institute on Aging (US), National Institutes of Health (US), Swedish Research Council, National Research Foundation Singapore, Government of Singapore, Kuderna, Lukas F. K. [0000-0002-9992-9295], Kuhlwilm, Martin [0000-0002-0115-1797], Orkin, Joseph D. [0000-0001-6922-2072], Valenzuela, Alejandro [0000-0001-6120-6246], Juan, David [0000-0003-1912-9667], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Kuderna, Lukas F. K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai-How, Marqués-Bonet, Tomàs, Fundación la Caixa, Vienna Science and Technology Fund, European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), International Primatological Society, Rufford Foundation, Margot Marsh Biodiversity Foundation, Primate Conservation, Fundação de Amparo à Pesquisa do Estado do Amazonas, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), German Research Foundation, National Science Foundation (US), Ministry of Science and Technology of Vietnam, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, European Research Council, Natural Environment Research Council (UK), UK Research and Innovation, Department of Biotechnology (India), San Diego Zoo Wildlife Alliance, Wenner-Gren Foundation, Leakey Foundation, National Geographic Society, National Institute on Aging (US), National Institutes of Health (US), Swedish Research Council, National Research Foundation Singapore, Government of Singapore, Kuderna, Lukas F. K. [0000-0002-9992-9295], Kuhlwilm, Martin [0000-0002-0115-1797], Orkin, Joseph D. [0000-0001-6922-2072], Valenzuela, Alejandro [0000-0001-6120-6246], Juan, David [0000-0003-1912-9667], Lizano, Esther [0000-0003-3304-9807], Navarro, Arcadi [0000-0003-2162-8246], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Kuderna, Lukas F. K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, Vries, Dorien de, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., Melo, Fabiano R. de, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, Silva, Maria N. F. da, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai-How, and Marqués-Bonet, Tomàs
Abstract: The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
Published: 2023

18. A new assemblage of late Neanderthal remains from Cova Simanya (NE Iberia)

Author: Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Agència de Gestió d'Ajuts Universitaris i de Recerca, Generalitat de Catalunya, Diputación de Barcelona, Fundación Palarq, Universidad Autónoma de Madrid, Ministerio de Universidades (España), Universidad de Alicante, European Commission, Xunta de Galicia, European Research Council, Martín-Perea, David Manuel [0000-0002-3238-0904], García-Tabernero, Antonio [0000-0001-5400-5630], Lizano, Esther [0000-0003-3304-9807], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Lalueza-Fox, Carles [0000-0002-1730-5914], Morales, Juan I., Cebriá, Artur, Soto, María, Rodríguez-Hidalgo, Antonio, Hernando, Raquel, Moreno-Ribas, Elena, Lombao, Diego, Rabuñal, José R., Martín-Perea, David Manuel, García-Tabernero, Antonio, Allué, Ethel, García-Basanta, Andrea, Lizano, Esther, Marqués-Bonet, Tomàs, Talamo, Sahra, Tassoni, Laura, Lalueza-Fox, Carles, Fullola, Josep M., Rosas, Antonio, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Agència de Gestió d'Ajuts Universitaris i de Recerca, Generalitat de Catalunya, Diputación de Barcelona, Fundación Palarq, Universidad Autónoma de Madrid, Ministerio de Universidades (España), Universidad de Alicante, European Commission, Xunta de Galicia, European Research Council, Martín-Perea, David Manuel [0000-0002-3238-0904], García-Tabernero, Antonio [0000-0001-5400-5630], Lizano, Esther [0000-0003-3304-9807], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Lalueza-Fox, Carles [0000-0002-1730-5914], Morales, Juan I., Cebriá, Artur, Soto, María, Rodríguez-Hidalgo, Antonio, Hernando, Raquel, Moreno-Ribas, Elena, Lombao, Diego, Rabuñal, José R., Martín-Perea, David Manuel, García-Tabernero, Antonio, Allué, Ethel, García-Basanta, Andrea, Lizano, Esther, Marqués-Bonet, Tomàs, Talamo, Sahra, Tassoni, Laura, Lalueza-Fox, Carles, Fullola, Josep M., and Rosas, Antonio
Abstract: This study presents an exceptional collection of 54 Late Pleistocene human remains that correspond to at least three Neanderthal individuals from Simanya Gran, the main gallery of Cova Simanya, located in the northeastern Iberian Peninsula. The collection comprised 53 unpublished remains that were unearthed during the 1970s and an additional tooth discovered during 2021 excavations. The specimens represent an adult with a small stature, a periadolescent aged approximately 11.5 years, and an immature individual aged approximately 7.7 years, thus offering a more complete demographic perspective. The collection encompasses diverse anatomical parts including upper and lower dentition, mandible, vertebrae, and limb bones from both the upper and lower extremities. Attempts to extract aDNA were unsuccessful. Renewed archaeological investigations at Cova Simanya have facilitated the reevaluation of the original stratigraphic context of these remains, leading to the discovery of the additional tooth, aligning with the periadolescent individual. This assemblage is currently the most extensive Neanderthal collection from the northeastern Mediterranean Iberia, offering invaluable insights into the morphology and evolutionary trajectory of Late Pleistocene hominins. Hence, Simanya Neanderthals will enhance our understanding of Neanderthal demographics and evolution, paving the way for an in-depth examination of the morphological diversity and evolutionary context of Iberian Neanderthals.
Published: 2023

19. DataSheet1_A new assemblage of late Neanderthal remains from Cova Simanya (NE Iberia).docx

Author: Martín-Perea, David Manuel [0000-0002-3238-0904], García-Tabernero, Antonio [0000-0001-5400-5630], Lizano, Esther [0000-0003-3304-9807], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Lalueza-Fox, Carles [0000-0002-1730-5914], Morales, Juan I., Cebriá, Artur, Soto, María, Rodríguez-Hidalgo, Antonio, Hernando, Raquel, Moreno-Ribas, Elena, Lombao, Diego, Rabuñal, José R., Martín-Perea, David Manuel, García-Tabernero, Antonio, Allué, Ethel, García-Basanta, Andrea, Lizano, Esther, Marqués-Bonet, Tomàs, Talamo, Sahra, Tassoni, Laura, Lalueza-Fox, Carles, Fullola, Josep M., Rosas, Antonio, Martín-Perea, David Manuel [0000-0002-3238-0904], García-Tabernero, Antonio [0000-0001-5400-5630], Lizano, Esther [0000-0003-3304-9807], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Lalueza-Fox, Carles [0000-0002-1730-5914], Morales, Juan I., Cebriá, Artur, Soto, María, Rodríguez-Hidalgo, Antonio, Hernando, Raquel, Moreno-Ribas, Elena, Lombao, Diego, Rabuñal, José R., Martín-Perea, David Manuel, García-Tabernero, Antonio, Allué, Ethel, García-Basanta, Andrea, Lizano, Esther, Marqués-Bonet, Tomàs, Talamo, Sahra, Tassoni, Laura, Lalueza-Fox, Carles, Fullola, Josep M., and Rosas, Antonio
Abstract: This study presents an exceptional collection of 54 Late Pleistocene human remains that correspond to at least three Neanderthal individuals from Simanya Gran, the main gallery of Cova Simanya, located in the northeastern Iberian Peninsula. The collection comprised 53 unpublished remains that were unearthed during the 1970s and an additional tooth discovered during 2021 excavations. The specimens represent an adult with a small stature, a periadolescent aged approximately 11.5 years, and an immature individual aged approximately 7.7 years, thus offering a more complete demographic perspective. The collection encompasses diverse anatomical parts including upper and lower dentition, mandible, vertebrae, and limb bones from both the upper and lower extremities. Attempts to extract aDNA were unsuccessful. Renewed archaeological investigations at Cova Simanya have facilitated the reevaluation of the original stratigraphic context of these remains, leading to the discovery of the additional tooth, aligning with the periadolescent individual. This assemblage is currently the most extensive Neanderthal collection from the northeastern Mediterranean Iberia, offering invaluable insights into the morphology and evolutionary trajectory of Late Pleistocene hominins. Hence, Simanya Neanderthals will enhance our understanding of Neanderthal demographics and evolution, paving the way for an in-depth examination of the morphological diversity and evolutionary context of Iberian Neanderthals.
Published: 2023

20. A new assemblage of late Neanderthal remains from Cova Simanya (NE Iberia)

Author: Morales, Juan I., primary, Cebrià, Artur, additional, Soto, María, additional, Rodríguez-Hidalgo, Antonio, additional, Hernando, Raquel, additional, Moreno-Ribas, Elena, additional, Lombao, Diego, additional, Rabuñal, José R., additional, Martín-Perea, David M., additional, García-Tabernero, Antonio, additional, Allué, Ethel, additional, García-Basanta, Andrea, additional, Lizano, Esther, additional, Marquès-Bonet, Tomàs, additional, Talamo, Sahra, additional, Tassoni, Laura, additional, Lalueza-Fox, Carles, additional, Fullola, Josep M., additional, and Rosas, Antonio, additional
Published: 2023
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21. Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species

Author: de-Dios, Toni, primary, Fontsere, Claudia, additional, Renom, Pere, additional, Stiller, Josefin, additional, Llovera, Laia, additional, Uliano-Silva, Marcela, additional, Sánchez-Gracia, Alejandro, additional, Wright, Charlotte, additional, Lizano, Esther, additional, Caballero, Berta, additional, Navarro, Arcadi, additional, Civit, Sergi, additional, Robbins, Robert K., additional, Blaxter, Mark, additional, Marquès-Bonet, Tomàs, additional, Vila, Roger, additional, and Lalueza-Fox, Carles, additional
Published: 2023
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22. Whole genome approach to the structure and dynamics ofCacajaowild populations

Author: Hermosilla-Albala, Nuria, primary, Silva, Felipe Ennes, additional, Cuadros-Espinoza, Sebastian, additional, Fontsere, Claudia, additional, Valenzuela-Seba, Alejandro, additional, Gut, Marta, additional, Kelley, Joanna L., additional, Ruibal-Puertas, Sandra, additional, Alentorn-Moron, Pol, additional, Faella, Armida, additional, Lizano, Esther, additional, Farias, Izeni, additional, Hrbek, Tomas, additional, Valsecchi, Joao, additional, Gut, Ivo G., additional, Rogers, Jeffrey, additional, Farh, Kyle Kai-How, additional, Kuderna, Lukas F. K., additional, Boubli, Jean P., additional, and Marques-Bonet, Tomas, additional
Published: 2023
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23. Enamel proteins reveal biological sex and genetic variability within southern AfricanParanthropus

Author: Madupe, Palesa P., primary, Koenig, Claire, additional, Patramanis, Ioannis, additional, Rüther, Patrick L., additional, Hlazo, Nomawethu, additional, Mackie, Meaghan, additional, Tawane, Mirriam, additional, Krueger, Johanna, additional, Taurozzi, Alberto J., additional, Troché, Gaudry, additional, Kibii, Job, additional, Pickering, Robyn, additional, Dickinson, Marc, additional, Sahle, Yonatan, additional, Kgotleng, Dipuo, additional, Musiba, Charles, additional, Manthi, Fredrick, additional, Bell, Liam, additional, DuPlessis, Michelle, additional, Gilbert, Catherine, additional, Zipfel, Bernhard, additional, Kuderna, Lukas F. K., additional, Lizano, Esther, additional, Welker, Frido, additional, Kyriakidou, Pelagia, additional, Cox, Jürgen, additional, Mollereau, Catherine, additional, Tokarski, Caroline, additional, Blackburn, Jonathan, additional, Ramos-Madrigal, Jazmín, additional, Marques-Bonet, Tomas, additional, Penkman, Kirsty, additional, Zanolli, Clément, additional, Schroeder, Lauren, additional, Racimo, Fernando, additional, Olsen, Jesper V., additional, Ackermann, Rebecca R., additional, and Cappellini, Enrico, additional
Published: 2023
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24. Y chromosome sequence and epigenomic reconstruction across human populations

Author: Esteller-Cucala, Paula, primary, Palmada-Flores, Marc, additional, Kuderna, Lukas F. K., additional, Fontsere, Claudia, additional, Serres-Armero, Aitor, additional, Dabad, Marc, additional, Torralvo, María, additional, Faella, Armida, additional, Ferrández-Peral, Luis, additional, Llovera, Laia, additional, Fornas, Oscar, additional, Julià, Eva, additional, Ramírez, Erika, additional, González, Irene, additional, Hecht, Jochen, additional, Lizano, Esther, additional, Juan, David, additional, and Marquès-Bonet, Tomàs, additional
Published: 2023
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25. A global catalog of whole-genome diversity from 233 primate species

Author: Kuderna, Lukas F. K., primary, Gao, Hong, additional, Janiak, Mareike C., additional, Kuhlwilm, Martin, additional, Orkin, Joseph D., additional, Bataillon, Thomas, additional, Manu, Shivakumara, additional, Valenzuela, Alejandro, additional, Bergman, Juraj, additional, Rousselle, Marjolaine, additional, Silva, Felipe Ennes, additional, Agueda, Lidia, additional, Blanc, Julie, additional, Gut, Marta, additional, de Vries, Dorien, additional, Goodhead, Ian, additional, Harris, R. Alan, additional, Raveendran, Muthuswamy, additional, Jensen, Axel, additional, Chuma, Idrissa S., additional, Horvath, Julie E., additional, Hvilsom, Christina, additional, Juan, David, additional, Frandsen, Peter, additional, Schraiber, Joshua G., additional, de Melo, Fabiano R., additional, Bertuol, Fabrício, additional, Byrne, Hazel, additional, Sampaio, Iracilda, additional, Farias, Izeni, additional, Valsecchi, João, additional, Messias, Malu, additional, da Silva, Maria N. F., additional, Trivedi, Mihir, additional, Rossi, Rogerio, additional, Hrbek, Tomas, additional, Andriaholinirina, Nicole, additional, Rabarivola, Clément J., additional, Zaramody, Alphonse, additional, Jolly, Clifford J., additional, Phillips-Conroy, Jane, additional, Wilkerson, Gregory, additional, Abee, Christian, additional, Simmons, Joe H., additional, Fernandez-Duque, Eduardo, additional, Kanthaswamy, Sree, additional, Shiferaw, Fekadu, additional, Wu, Dongdong, additional, Zhou, Long, additional, Shao, Yong, additional, Zhang, Guojie, additional, Keyyu, Julius D., additional, Knauf, Sascha, additional, Le, Minh D., additional, Lizano, Esther, additional, Merker, Stefan, additional, Navarro, Arcadi, additional, Nadler, Tilo, additional, Khor, Chiea Chuen, additional, Lee, Jessica, additional, Tan, Patrick, additional, Lim, Weng Khong, additional, Kitchener, Andrew C., additional, Zinner, Dietmar, additional, Gut, Ivo, additional, Melin, Amanda D., additional, Guschanski, Katerina, additional, Schierup, Mikkel Heide, additional, Beck, Robin M. D., additional, Umapathy, Govindhaswamy, additional, Roos, Christian, additional, Boubli, Jean P., additional, Rogers, Jeffrey, additional, Farh, Kyle Kai-How, additional, and Marques Bonet, Tomas, additional
Published: 2023
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26. The landscape of tolerated genetic variation in humans and primates

Author: Gao, Hong, primary, Hamp, Tobias, additional, Ede, Jeffrey, additional, Schraiber, Joshua G., additional, McRae, Jeremy, additional, Singer-Berk, Moriel, additional, Yang, Yanshen, additional, Dietrich, Anastasia S. D., additional, Fiziev, Petko P., additional, Kuderna, Lukas F. K., additional, Sundaram, Laksshman, additional, Wu, Yibing, additional, Adhikari, Aashish, additional, Field, Yair, additional, Chen, Chen, additional, Batzoglou, Serafim, additional, Aguet, Francois, additional, Lemire, Gabrielle, additional, Reimers, Rebecca, additional, Balick, Daniel, additional, Janiak, Mareike C., additional, Kuhlwilm, Martin, additional, Orkin, Joseph D., additional, Manu, Shivakumara, additional, Valenzuela, Alejandro, additional, Bergman, Juraj, additional, Rousselle, Marjolaine, additional, Silva, Felipe Ennes, additional, Agueda, Lidia, additional, Blanc, Julie, additional, Gut, Marta, additional, de Vries, Dorien, additional, Goodhead, Ian, additional, Harris, R. Alan, additional, Raveendran, Muthuswamy, additional, Jensen, Axel, additional, Chuma, Idriss S., additional, Horvath, Julie E., additional, Hvilsom, Christina, additional, Juan, David, additional, Frandsen, Peter, additional, de Melo, Fabiano R., additional, Bertuol, Fabrício, additional, Byrne, Hazel, additional, Sampaio, Iracilda, additional, Farias, Izeni, additional, do Amaral, João Valsecchi, additional, Messias, Mariluce, additional, da Silva, Maria N. F., additional, Trivedi, Mihir, additional, Rossi, Rogerio, additional, Hrbek, Tomas, additional, Andriaholinirina, Nicole, additional, Rabarivola, Clément J., additional, Zaramody, Alphonse, additional, Jolly, Clifford J., additional, Phillips-Conroy, Jane, additional, Wilkerson, Gregory, additional, Abee, Christian, additional, Simmons, Joe H., additional, Fernandez-Duque, Eduardo, additional, Kanthaswamy, Sree, additional, Shiferaw, Fekadu, additional, Wu, Dongdong, additional, Zhou, Long, additional, Shao, Yong, additional, Zhang, Guojie, additional, Keyyu, Julius D., additional, Knauf, Sascha, additional, Le, Minh D., additional, Lizano, Esther, additional, Merker, Stefan, additional, Navarro, Arcadi, additional, Bataillon, Thomas, additional, Nadler, Tilo, additional, Khor, Chiea Chuen, additional, Lee, Jessica, additional, Tan, Patrick, additional, Lim, Weng Khong, additional, Kitchener, Andrew C., additional, Zinner, Dietmar, additional, Gut, Ivo, additional, Melin, Amanda, additional, Guschanski, Katerina, additional, Schierup, Mikkel Heide, additional, Beck, Robin M. D., additional, Umapathy, Govindhaswamy, additional, Roos, Christian, additional, Boubli, Jean P., additional, Lek, Monkol, additional, Sunyaev, Shamil, additional, O’Donnell-Luria, Anne, additional, Rehm, Heidi L., additional, Xu, Jinbo, additional, Rogers, Jeffrey, additional, Marques-Bonet, Tomas, additional, and Farh, Kyle Kai-How, additional
Published: 2023
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27. A global catalog of whole-genome diversity from 233 primate species

Author: Kuderna, Lukas F.K., primary, Gao, Hong, additional, Janiak, Mareike C., additional, Kuhlwilm, Martin, additional, Orkin, Joseph D., additional, Bataillon, Thomas, additional, Manu, Shivakumara, additional, Valenzuela, Alejandro, additional, Bergman, Juraj, additional, Rouselle, Marjolaine, additional, Silva, Felipe Ennes, additional, Agueda, Lidia, additional, Blanc, Julie, additional, Gut, Marta, additional, de Vries, Dorien, additional, Goodhead, Ian, additional, Harris, R. Alan, additional, Raveendran, Muthuswamy, additional, Jensen, Axel, additional, Chuma, Idriss S., additional, Horvath, Julie, additional, Hvilsom, Christina, additional, Juan, David, additional, Frandsen, Peter, additional, Schraiber, Joshua G., additional, de Melo, Fabiano R., additional, Bertuol, Fabricio, additional, Byrne, Hazel, additional, Sampaio, Iracilda, additional, Farias, Izeni, additional, Valsecchi do Amaral, Joao, additional, Messias, Malu, additional, da Silva, Maria N. F., additional, Trivedi, Mihir, additional, Rossi, Rogerio, additional, Hrbek, Tomas, additional, Andriaholinirina, Nicole, additional, Rabarivola, Clement J., additional, Zaramody, Alphonse, additional, Jolly, Clifford J., additional, Phillips-Conroy, Jane, additional, Wilkerson, Gregory, additional, Abee, Christian, additional, Simmons, Joe H., additional, Fernandez-Duque, Eduardo, additional, Kanthaswamy, Sree, additional, Shiferaw, Fekadu, additional, Wu, Dongdong, additional, Zhou, Long, additional, Shao, Yong, additional, Zhang, Guojie, additional, Keyyu, Julius D., additional, Knauf, Sascha, additional, Le, Minh D., additional, Lizano, Esther, additional, Merker, Stefan, additional, Navarro, Arcadi, additional, Nadler, Tilo, additional, Khor, Chiea Chuen, additional, Lee, Jessica, additional, Tan, Patrick, additional, Lim, Weng Khong, additional, Kitchener, Andrew C., additional, Zinner, Dietmar, additional, Gut, Ivo, additional, Melin, Amanda, additional, Guschanski, Katerina, additional, Schierup, Mikkel Heide, additional, Beck, Robin M. D., additional, Umapathy, Govindhaswamy, additional, Roos, Christian, additional, Boubli, Jean P., additional, Rogers, Jeffrey, additional, Farh, Kyle, additional, and Marques Bonet, Tomas, additional
Published: 2023
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28. Differential DNA methylation of vocal and facial anatomy genes in modern humans

Author: Gokhman, David, Nissim-Rafinia, Malka, Agranat-Tamir, Lily, Housman, Genevieve, García-Pérez, Raquel, Lizano, Esther, Cheronet, Olivia, Mallick, Swapan, Nieves-Colón, Maria A., Li, Heng, Alpaslan-Roodenberg, Songül, Novak, Mario, Gu, Hongcang, Osinski, Jason M., Ferrando-Bernal, Manuel, Gelabert, Pere, Lipende, Iddi, Mjungu, Deus, Kondova, Ivanela, Bontrop, Ronald, Kullmer, Ottmar, Weber, Gerhard, Shahar, Tal, Dvir-Ginzberg, Mona, Faerman, Marina, Quillen, Ellen E., Meissner, Alexander, Lahav, Yonatan, Kandel, Leonid, Liebergall, Meir, Prada, María E., Vidal, Julio M., Gronostajski, Richard M., Stone, Anne C., Yakir, Benjamin, Lalueza-Fox, Carles, Pinhasi, Ron, Reich, David, Marques-Bonet, Tomas, Meshorer, Eran, and Carmel, Liran
Published: 2020
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29. Selective single molecule sequencing and assembly of a human Y chromosome of African origin

Author: Kuderna, Lukas F. K., Lizano, Esther, Julià, Eva, Gomez-Garrido, Jessica, Serres-Armero, Aitor, Kuhlwilm, Martin, Alandes, Regina Antoni, Alvarez-Estape, Marina, Juan, David, Simon, Heath, Alioto, Tyler, Gut, Marta, Gut, Ivo, Schierup, Mikkel Heide, Fornas, Oscar, and Marques-Bonet, Tomas
Published: 2019
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30. Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs

Author: Alvarez-Estape, Marina, primary, Pawar, Harvinder, additional, Fontsere, Claudia, additional, Trujillo, Amber E., additional, Gunson, Jessica L., additional, Bergl, Richard A., additional, Bermejo, Magdalena, additional, Linder, Joshua M., additional, McFarland, Kelley, additional, Oates, John F., additional, Sunderland-Groves, Jacqueline L., additional, Orkin, Joseph, additional, Higham, James P., additional, Viaud-Martinez, Karine A., additional, Lizano, Esther, additional, and Marques-Bonet, Tomas, additional
Published: 2023
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31. A global catalog of whole-genome diversity from 233 primate species

Author: Kuderna, Lukas F. K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabricio, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, Joao, Messias, Malu, da Silva, Maria N. F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clement J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dong-dong, Zhou, Long, Shao, Yong, Zhang, Guoji, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai-How, Bonet, Tomas Marques, Kuderna, Lukas F. K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabricio, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, Joao, Messias, Malu, da Silva, Maria N. F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clement J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dong-dong, Zhou, Long, Shao, Yong, Zhang, Guoji, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai-How, and Bonet, Tomas Marques
Abstract: The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage wholegenome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
Published: 2023
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32. The landscape of tolerated genetic variation in humans and primates

Author: Gao, Hong, Hamp, Tobias, Ede, Jeffrey, Schraiber, Joshua G., McRae, Jeremy, Singer-Berk, Moriel, Yang, Yanshen, Dietrich, Anastasia S. D., Fiziev, Petko P., Kuderna, Lukas F. K., Sundaram, Laksshman, Wu, Yibing, Adhikari, Aashish, Field, Yair, Chen, Chen, Batzoglou, Serafim, Aguet, Francois, Lemire, Gabrielle, Reimers, Rebecca, Balick, Daniel, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, de Melo, Fabiano R., Bertuol, Fabricio, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, do Amaral, Joao Valsecchi, Messias, Mariluce, da Silva, Maria N. F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clement J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Bataillon, Thomas, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda, Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Lek, Monkol, Sunyaev, Shamil, O'Donnell-Luria, Anne, Rehm, Heidi L., Xu, Jinbo, Rogers, Jeffrey, Marques-Bonet, Tomas, Farh, Kyle Kai-How, Gao, Hong, Hamp, Tobias, Ede, Jeffrey, Schraiber, Joshua G., McRae, Jeremy, Singer-Berk, Moriel, Yang, Yanshen, Dietrich, Anastasia S. D., Fiziev, Petko P., Kuderna, Lukas F. K., Sundaram, Laksshman, Wu, Yibing, Adhikari, Aashish, Field, Yair, Chen, Chen, Batzoglou, Serafim, Aguet, Francois, Lemire, Gabrielle, Reimers, Rebecca, Balick, Daniel, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, de Melo, Fabiano R., Bertuol, Fabricio, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, do Amaral, Joao Valsecchi, Messias, Mariluce, da Silva, Maria N. F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clement J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Bataillon, Thomas, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda, Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M. D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Lek, Monkol, Sunyaev, Shamil, O'Donnell-Luria, Anne, Rehm, Heidi L., Xu, Jinbo, Rogers, Jeffrey, Marques-Bonet, Tomas, and Farh, Kyle Kai-How
Abstract: Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases., INTRODUCTION: Millions of people have received genome and exome sequencing to date, a collective effort that has illuminated for the first time the vast catalog of small genetic differences that distinguish us as individuals within our species. However, the effects of most of these genetic variants remain unknown, limiting their clinical utility and actionability. New approaches that can accurately discern disease-causing from benign mutations and interpret genetic variants on a genome-wide scale would constitute a meaningful initial step towards realizing the potential of personalized genomic medicine. RATIONALE: As a result of the short evolutionary distance between humans and nonhuman primates, our proteins share near-perfect amino acid sequence identity. Hence, the effects of a protein-altering mutation found in one species are likely to be concordant in the other species. By systematically cataloging common variants of nonhuman primates, we aimed to annotate these variants as being unlikely to cause human disease as they are tolerated by natural selection in a closely related species. Once collected, the resulting resource may be applied to infer the effects of unobserved variants across the genome using machine learning. RESULTS: Following the strategy outlined above we obtained whole-genome sequencing data for 809 individuals from 233 primate species and cataloged 4.3 million common missense variants. We confirmed that human missense variants seen in at least one nonhuman primate species were annotated as benign in the ClinVar clinical variant database in 99% of cases. By contrast, common variants from mammals and vertebrates outside the primate lineage were substantially less likely to be benign in the ClinVar database (71 to 87% benign), restricting this strategy to nonhuman primates. Overall, we reclassified more than 4 million human missense variants of previously unknown consequence as likely benign, resulting in a greater than 50-fold increase in the nu
Published: 2023
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33. A new assemblage of late Neanderthal remains from Cova Simanya (NE Iberia)

Author: Morales, Juan I., Cebrià, Artur, Soto, María, Rodríguez Hidalgo, Antonio, Hernando, Raquel, Moreno Ribas, Elena, Lombao, Diego, Rabuñal, José R., Martín Perea, David Manuel, García Tabernero, Antonio, Allué, Ethel, García Basanta, Andrea, Lizano, Esther, Marquès Bonet, Tomàs, Talamo, Sahra, Tassoni, Laura, Lalueza Fox, Carles, Fullola, Josep María, Rosas González, Antonio, Morales, Juan I., Cebrià, Artur, Soto, María, Rodríguez Hidalgo, Antonio, Hernando, Raquel, Moreno Ribas, Elena, Lombao, Diego, Rabuñal, José R., Martín Perea, David Manuel, García Tabernero, Antonio, Allué, Ethel, García Basanta, Andrea, Lizano, Esther, Marquès Bonet, Tomàs, Talamo, Sahra, Tassoni, Laura, Lalueza Fox, Carles, Fullola, Josep María, and Rosas González, Antonio
Abstract: This study presents an exceptional collection of 54 Late Pleistocene human remains that correspond to at least three Neanderthal individuals from Simanya Gran, the main gallery of Cova Simanya, located in the northeastern Iberian Peninsula. The collection comprised 53 unpublished remains that were unearthed during the 1970s and an additional tooth discovered during 2021 excavations. The specimens represent an adult with a small stature, a periadolescent aged approximately 11.5 years, and an immature individual aged approximately 7.7 years, thus offering a more complete demographic perspective. The collection encompasses diverse anatomical parts including upper and lower dentition, mandible, vertebrae, and limb bones from both the upper and lower extremities. Attempts to extract aDNA were unsuccessful. Renewed archaeological investigations at Cova Simanya have facilitated the reevaluation of the original stratigraphic context of these remains, leading to the discovery of the additional tooth, aligning with the periadolescent individual. This assemblage is currently the most extensive Neanderthal collection from the northeastern Mediterranean Iberia, offering invaluable insights into the morphology and evolutionary trajectory of Late Pleistocene hominins. Hence, Simanya Neanderthals will enhance our understanding of Neanderthal demographics and evolution, paving the way for an in-depth examination of the morphological diversity and evolutionary context of Iberian Neanderthals., Ministerio de Ciencia e Innovación, Generalitat de Catalunya, Diputació de Barcelona, Fundación Palarq, UAM Tomás y Valiente Program, European Union, Ministerio de Universidades, Xunta de Galicia, European Research Council, Depto. de Geodinámica, Estratigrafía y Paleontología, Fac. de Ciencias Geológicas, TRUE, pub
Published: 2023

34. A new assemblage of late Neanderthal remains from Cova Simanya (NE Iberia)

Author: Universidad de Alicante. Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Morales, Juan Ignacio, Cebrià, Artur, Soto, María, Rodríguez-Hidalgo, Antonio, Hernando, Raquel, Moreno-Ribas, Elena, Lombao, Diego, Rabuñal, José Ramón, Martín-Perea, David M., García Tabernero, Antonio, Allué, Ethel, García-Basanta, Andrea, Lizano, Esther, Marquès-Bonet, Tomàs, Talamo, Sahra, Tassoni, Laura, Lalueza-Fox, Carles, Fullola, Josep Maria, Rosas, Antonio, Universidad de Alicante. Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Morales, Juan Ignacio, Cebrià, Artur, Soto, María, Rodríguez-Hidalgo, Antonio, Hernando, Raquel, Moreno-Ribas, Elena, Lombao, Diego, Rabuñal, José Ramón, Martín-Perea, David M., García Tabernero, Antonio, Allué, Ethel, García-Basanta, Andrea, Lizano, Esther, Marquès-Bonet, Tomàs, Talamo, Sahra, Tassoni, Laura, Lalueza-Fox, Carles, Fullola, Josep Maria, and Rosas, Antonio
Abstract: This study presents an exceptional collection of 54 Late Pleistocene human remains that correspond to at least three Neanderthal individuals from Simanya Gran, the main gallery of Cova Simanya, located in the northeastern Iberian Peninsula. The collection comprised 53 unpublished remains that were unearthed during the 1970s and an additional tooth discovered during 2021 excavations. The specimens represent an adult with a small stature, a periadolescent aged approximately 11.5 years, and an immature individual aged approximately 7.7 years, thus offering a more complete demographic perspective. The collection encompasses diverse anatomical parts including upper and lower dentition, mandible, vertebrae, and limb bones from both the upper and lower extremities. Attempts to extract aDNA were unsuccessful. Renewed archaeological investigations at Cova Simanya have facilitated the reevaluation of the original stratigraphic context of these remains, leading to the discovery of the additional tooth, aligning with the periadolescent individual. This assemblage is currently the most extensive Neanderthal collection from the northeastern Mediterranean Iberia, offering invaluable insights into the morphology and evolutionary trajectory of Late Pleistocene hominins. Hence, Simanya Neanderthals will enhance our understanding of Neanderthal demographics and evolution, paving the way for an in-depth examination of the morphological diversity and evolutionary context of Iberian Neanderthals.
Published: 2023

35. Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs

Author: Alvarez-Estape, Marina, Pawar, Harvinder, Fontsere, Claudia, Trujillo, Amber E., Gunson, Jessica L., Bergl, Richard A., Bermejo, Magdalena, Linder, Joshua M., McFarland, Kelley, Oates, John F., Sunderland-Groves, Jacqueline L., Orkin, Joseph, Higham, James P., Viaud-Martinez, Karine A., Lizano, Esther, Marques-Bonet, Tomas, Alvarez-Estape, Marina, Pawar, Harvinder, Fontsere, Claudia, Trujillo, Amber E., Gunson, Jessica L., Bergl, Richard A., Bermejo, Magdalena, Linder, Joshua M., McFarland, Kelley, Oates, John F., Sunderland-Groves, Jacqueline L., Orkin, Joseph, Higham, James P., Viaud-Martinez, Karine A., Lizano, Esther, and Marques-Bonet, Tomas
Abstract: The critically endangered western gorillas (Gorilla gorilla) are divided into two subspecies: the western lowland (G. g. gorilla) and the Cross River (G. g. diehli) gorilla. Given the difficulty in sampling wild great ape populations and the small estimated size of the Cross River gorilla population, only one whole genome of a Cross River gorilla has been sequenced to date, hindering the study of this subspecies at the population level. In this study, we expand the number of whole genomes available for wild western gorillas, generating 41 new genomes (25 belonging to Cross River gorillas) using single shed hairs collected from gorilla nests. By combining these genomes with publicly available wild gorilla genomes, we confirm that Cross River gorillas form three population clusters. We also found little variation in genome-wide heterozygosity among them. Our analyses reveal long runs of homozygosity (>10 Mb), indicating recent inbreeding in Cross River gorillas. This is similar to that seen in mountain gorillas but with a much more recent bottleneck. We also detect past gene flow between two Cross River sites, Afi Mountain Wildlife Sanctuary and the Mbe Mountains. Furthermore, we observe past allele sharing between Cross River gorillas and the northern western lowland gorilla sites, as well as with the eastern gorilla species. This is the first study using single shed hairs from a wild species for whole genome sequencing to date. Taken together, our results highlight the importance of implementing conservation measures to increase connectivity among Cross River gorilla sites.
Published: 2023

36. Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species

Author: Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, European Research Council, Generalitat de Catalunya, Wellcome Trust, Dios Martínez, Antonio de, Fontsere, Claudia, Renom, P., Stiller, Josefin, Llovera, Laia, Uliano-Silva, Marcela, Sánchez-Gracia, Alejandro, Wright, Charlotte, Lizano, Esther, Caballero, Berta, Navarro, Arcadi, Civit, Sergi, Robbins, Robert K., Blaxter, Mark, Marqués-Bonet, Tomàs, Vila, Roger, Lalueza-Fox, Carles, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, European Research Council, Generalitat de Catalunya, Wellcome Trust, Dios Martínez, Antonio de, Fontsere, Claudia, Renom, P., Stiller, Josefin, Llovera, Laia, Uliano-Silva, Marcela, Sánchez-Gracia, Alejandro, Wright, Charlotte, Lizano, Esther, Caballero, Berta, Navarro, Arcadi, Civit, Sergi, Robbins, Robert K., Blaxter, Mark, Marqués-Bonet, Tomàs, Vila, Roger, and Lalueza-Fox, Carles
Published: 2023

37. A global catalog of whole-genome diversity from 233 primate species

Author: Kuderna, Lukas F.K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai How, Marques Bonet, Tomas, Kuderna, Lukas F.K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai How, and Marques Bonet, Tomas
Abstract: The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research., The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
Published: 2023

38. Y chromosome sequence and epigenomic reconstruction across human populations

Author: Esteller-Cucala, Paula, primary, Palmada-Flores, Marc, additional, Kuderna, Lukas F. K., additional, Fontsere, Claudia, additional, Serres-Armero, Aitor, additional, Dabad, Marc, additional, Torralvo, María, additional, Faella, Armida, additional, Ferrández-Peral, Luis, additional, Llovera, Laia, additional, Fornas, Oscar, additional, Julià, Eva, additional, Ramírez, Erika, additional, González, Irene, additional, Hecht, Jochen, additional, Lizano, Esther, additional, Juan, David, additional, and Marquès-Bonet, Tomàs, additional
Published: 2022
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39. Variation in predicted COVID‐19 risk among lemurs and lorises

Author: Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Natural Environment Research Council (UK), Ministerio de Ciencia, Innovación y Universidades (España), Instituto de Salud Carlos III, Agencia Estatal de Investigación (España), Ministerio de Economía y Competitividad (España), European Commission, Generalitat de Catalunya, Fundación la Caixa, Howard Hughes Medical Institute, National Institutes of Health (US), Rockefeller University, Melin, Amanda D. [0000-0002-0612-2514], Orkin, Joseph D. [0000-0001-6922-2072], Janiak, Mareike C. [0000-0002-7759-2556], Valenzuela, Alejandro [0000-0002-2252-3887], Kuderna, Lukas F. K. [0000-0002-9992-9295], Marrone, Frank [0000-0002-1735-0723], Ramangason, Hasinala [0000-0003-4222-7476], Horvath, Julie E. [0000-0002-6426-035X], Roos, Christian [0000-0003-0190-4266], Kitchener, Andrew C. [0000-0003-2594-0827], Khor, Chiea Chuen [0000-0002-1128-4729], Lim, Weng Khong [0000-0003-4391-1130], Umapathy, Govindhaswamy [0000-0003-4086-7445], Raveendran, Muthuswamy [0000-0001-6185-4059], Harris, R. Alan [0000-0002-7333-4752], Gut, Ivo [0000-0001-7219-632X], Gut, Marta [0000-0002-4063-7159], Lizano, Esther 0000-0003-3304-9807], Zinner, Dietmar [0000-0003-3967-8014], Manu, Sivakumara [0000-0002-9114-8793], Johnson, Steig E. [0000-0003-2257-8949], Fedrigo, Olivier [0000-0002-6450-7551], Farh, Kyle Kai-How [0000-0001-6947-8537], Rogers, Jeffrey [0000-0002-7374-6490], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Navarro, Arcadi [0000-0003-2162-8246], Juan, David [0000-0003-1912-9667], Arora, Paramjit S. [0000-0001-5315-401X], Higham, James P. [0000-0002-1133-2030], Melin, Amanda D., Orkin, Joseph D., Janiak, Mareike C., Valenzuela, Alejandro, Kuderna, Lukas F. K., Marrone, Frank, Ramangason, Hasinala, Horvath, Julie E., Roos, Christian, Kitchener, Andrew C., Khor, Chiea Chuen, Lim, Weng Khong, Lee, Jessica G. H., Tan, Patrick, Umapathy, Govindhaswamy, Raveendran, Muthuswamy, Harris, R. Alan, Gut, Ivo, Gut, Marta, Lizano, Esther, Nadler, Tilo, Zinner, Dietmar, Le, Minh D., Manu, Sivakumara, Rabarivola, Clément J., Zaramody, Alphonse, Andriaholinirina, Nicole, Johnson, Steig E., Jarvis, Erich D., Fedrigo, Olivier, Wu, Dongdong, Zhang, Guojie, Farh, Kyle Kai-How, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Navarro, Arcadi, Juan, David, Arora, Paramjit S., Higham, James P., Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Natural Environment Research Council (UK), Ministerio de Ciencia, Innovación y Universidades (España), Instituto de Salud Carlos III, Agencia Estatal de Investigación (España), Ministerio de Economía y Competitividad (España), European Commission, Generalitat de Catalunya, Fundación la Caixa, Howard Hughes Medical Institute, National Institutes of Health (US), Rockefeller University, Melin, Amanda D. [0000-0002-0612-2514], Orkin, Joseph D. [0000-0001-6922-2072], Janiak, Mareike C. [0000-0002-7759-2556], Valenzuela, Alejandro [0000-0002-2252-3887], Kuderna, Lukas F. K. [0000-0002-9992-9295], Marrone, Frank [0000-0002-1735-0723], Ramangason, Hasinala [0000-0003-4222-7476], Horvath, Julie E. [0000-0002-6426-035X], Roos, Christian [0000-0003-0190-4266], Kitchener, Andrew C. [0000-0003-2594-0827], Khor, Chiea Chuen [0000-0002-1128-4729], Lim, Weng Khong [0000-0003-4391-1130], Umapathy, Govindhaswamy [0000-0003-4086-7445], Raveendran, Muthuswamy [0000-0001-6185-4059], Harris, R. Alan [0000-0002-7333-4752], Gut, Ivo [0000-0001-7219-632X], Gut, Marta [0000-0002-4063-7159], Lizano, Esther 0000-0003-3304-9807], Zinner, Dietmar [0000-0003-3967-8014], Manu, Sivakumara [0000-0002-9114-8793], Johnson, Steig E. [0000-0003-2257-8949], Fedrigo, Olivier [0000-0002-6450-7551], Farh, Kyle Kai-How [0000-0001-6947-8537], Rogers, Jeffrey [0000-0002-7374-6490], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Navarro, Arcadi [0000-0003-2162-8246], Juan, David [0000-0003-1912-9667], Arora, Paramjit S. [0000-0001-5315-401X], Higham, James P. [0000-0002-1133-2030], Melin, Amanda D., Orkin, Joseph D., Janiak, Mareike C., Valenzuela, Alejandro, Kuderna, Lukas F. K., Marrone, Frank, Ramangason, Hasinala, Horvath, Julie E., Roos, Christian, Kitchener, Andrew C., Khor, Chiea Chuen, Lim, Weng Khong, Lee, Jessica G. H., Tan, Patrick, Umapathy, Govindhaswamy, Raveendran, Muthuswamy, Harris, R. Alan, Gut, Ivo, Gut, Marta, Lizano, Esther, Nadler, Tilo, Zinner, Dietmar, Le, Minh D., Manu, Sivakumara, Rabarivola, Clément J., Zaramody, Alphonse, Andriaholinirina, Nicole, Johnson, Steig E., Jarvis, Erich D., Fedrigo, Olivier, Wu, Dongdong, Zhang, Guojie, Farh, Kyle Kai-How, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Navarro, Arcadi, Juan, David, Arora, Paramjit S., and Higham, James P.
Abstract: The novel coronavirus SARS‐CoV‐2, which in humans leads to the disease COVID‐19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary target of SARS‐CoV‐2 is the cellular receptor angiotensin‐converting enzyme‐2 (ACE2). Recent sequence analyses of the ACE2 gene predict that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results while finding additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS‐CoV‐2 infection. Troublingly, some species, including the rare and endangered aye‐aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID‐19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS‐CoV‐2.
Published: 2021

40. tRNA

Author: Lizano, Esther and Mörl, Mario
Published: 2006
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41. Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Author: Ferrández-Peral, Luis, primary, Zhan, Xiaoyu, additional, Alvarez-Estape, Marina, additional, Chiva, Cristina, additional, Esteller-Cucala, Paula, additional, García-Pérez, Raquel, additional, Julià, Eva, additional, Lizano, Esther, additional, Fornas, Òscar, additional, Sabidó, Eduard, additional, Li, Qiye, additional, Marquès-Bonet, Tomàs, additional, Juan, David, additional, and Zhang, Guojie, additional
Published: 2022
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42. Recovering the genomes hidden in museum wet collections

Author: Ruiz‐Gartzia, Irune, primary, Lizano, Esther, additional, Marques‐Bonet, Tomas, additional, and Kelley, Joanna L., additional
Published: 2022
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43. Insights from the rescue and breeding management of Cuvier's gazelle (Gazella cuvieri) through whole-genome sequencing

Author: Alvarez-Estape, Marina, Fontsere, Claudia, Serres-Armero, Aitor, Kuderna, Lukas, Dobrynin, Pavel, Guidara, Héla, Pukazhenthi, Budhan S., Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Moreno, Eulalia, Lizano, Esther, Alvarez-Estape, Marina, Fontsere, Claudia, Serres-Armero, Aitor, Kuderna, Lukas, Dobrynin, Pavel, Guidara, Héla, Pukazhenthi, Budhan S., Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Moreno, Eulalia, and Lizano, Esther
Abstract: Captive breeding programmes represent the most intensive type of ex situ population management for threatened species. One example is the Cuvier's gazelle programme that started in 1975 with only four founding individuals, and after more than four decades of management in captivity, a reintroduction effort was undertaken in Tunisia in 2016, to establish a population in an area historically included within its range. Here, we aim to determine the genetic consequences of this reintroduction event by assessing the genetic diversity of the founder stock as well as of their descendants. We present the first whole-genome sequencing dataset of 30 Cuvier's gazelles including captive-bred animals, animals born in Tunisia after a reintroduction and individuals from a genetically unrelated Moroccan population. Our analyses revealed no difference between the founder and the offspring cohorts in genome-wide heterozygosity and inbreeding levels, and in the amount and length of runs of homozygosity. The captive but unmanaged Moroccan gazelles have the lowest genetic diversity of all genomes analysed. Our findings demonstrate that the Cuvier's gazelle captive breeding programme can serve as source populations for future reintroductions of this species. We believe that this study can serve as a starting point for global applications of genomics to the conservation plan of this species.
Published: 2022

44. YY-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition

Author: Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Ministerio de Ciencia e Innovación (España), Agència de Gestió d'Ajuts Universitaris i de Recerca, García-Fernández, Carla, Lizano, Esther, Telford, Marco, Olalde, Iñigo, Cid, Rafael de, Larmuseau, Maarten H. D., Pancorbo, Marian M. de, Calafell, Francesc, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Ministerio de Ciencia e Innovación (España), Agència de Gestió d'Ajuts Universitaris i de Recerca, García-Fernández, Carla, Lizano, Esther, Telford, Marco, Olalde, Iñigo, Cid, Rafael de, Larmuseau, Maarten H. D., Pancorbo, Marian M. de, and Calafell, Francesc
Abstract: The Y chromosome can yield a unique perspective into the study of human demographic history. However, due to the repetitive nature of part of its sequence, only a small set of regions are suitable for variant calling and discovery from short-read sequencing data. These regions combined represent 8.9 Mbp or 0.14% of a diploid human genome. Consequently, investing in whole-genome sequencing to resolve Y-chromosome questions is poorly efficient. Here we use, as an alternative, target enrichment technology to greatly increase sequencing effectiveness, validating and applying the technique to 181 males, for 162 of whom we obtained a positive result. Additionally, 75 samples sequenced for the whole genome were also included, for a total sample size of 237. These samples were chosen for their Y chromosome haplogroup: R1b-DF27. In the context of European populations, and particularly in Iberia, this haplogroup stands out for its high frequency and its demographic history. Current evidence indicates that the diffusion of this haplogroup is related to the population movements that mark the cultural Bronze Age transition, making it remarkably interesting for population geneticists. The results of this study show the effects of the rapid radiation of the haplogroup in Spain, as even with the higher discriminating power of whole sequences, most haplotypes still fall within the R1b-DF27* paragroup rather than in the main derived branches. However, we were able to refine the ISOGG 2019–2020 phylogeny, and its two main subbranches, namely L176.2 and Z272, which present geographical differentiation between the Atlantic and Mediterranean coasts of Iberia.
Published: 2022

45. Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Author: Chinese Academy of Sciences, International Science & Technology Cooperation (China), Carlsberg Foundation, Villum Fonden, Fundación la Caixa, Centre for Genomic Regulation (España), Universidad Pompeu Fabra, Instituto de Salud Carlos III, European Commission, Generalitat de Catalunya, European Research Council, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), National Institutes of Health (US), Ferrández-Peral, Luis, Zhang, Xiaoyu, Alvarez-Estape, Marina, Chiva, Cristina, Esteller-Cucala, Paula, García-Pérez, Raquel, Julià, Eva, Lizano, Esther, Fornas, Oscar, Sabidó, Eduard, Li, Qiye, Marqués-Bonet, Tomàs, Juan, David, Zhang, Guojie, Chinese Academy of Sciences, International Science & Technology Cooperation (China), Carlsberg Foundation, Villum Fonden, Fundación la Caixa, Centre for Genomic Regulation (España), Universidad Pompeu Fabra, Instituto de Salud Carlos III, European Commission, Generalitat de Catalunya, European Research Council, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), National Institutes of Health (US), Ferrández-Peral, Luis, Zhang, Xiaoyu, Alvarez-Estape, Marina, Chiva, Cristina, Esteller-Cucala, Paula, García-Pérez, Raquel, Julià, Eva, Lizano, Esther, Fornas, Oscar, Sabidó, Eduard, Li, Qiye, Marqués-Bonet, Tomàs, Juan, David, and Zhang, Guojie
Abstract: Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates. changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.
Published: 2022

46. Population dynamics and genetic connectivity in recent chimpanzee history

Author: Fundación la Caixa, Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Economía y Competitividad (España), European Commission, Vienna Science and Technology Fund, European Research Council, Howard Hughes Medical Institute, Generalitat de Catalunya, Wellcome Trust Centre for Human Genetics, Max Planck Society, Heinz L. Krekeler Foundation, Fontsere, Claudia, Kuhlwilm, Martin, Morcillo-Suárez, 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 Ayuk, Bailey, Emma, Barubiyo, Donatienne, Bessone, Mattia, Carretero-Alonso, Andrea, Chancellor, Rebecca, Cohen, Heather, Danquah, Emmanuel, Deschner, Tobias, Dunn, Andrew, Dupain, Jef, Egbe, Villard E., Feliú, 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 E., Lapuente, Juan, Larson, Bradley, Laudisoit, Anne, Lee, Kevin, Llana, Manuel, Llorente, Miquel, Marrocol, iSergio, Morgan, David, Mulindahabi, Felix, Murai, Mizuki, Neil, Emily, Nicholl, Sonia, Nixon, Stuart, Normand, Emma, Orbell, Chris, Ormsby, Lucy Jayne, Pacheco, Liliana, Piel, Alex, Riera, Laura, Robbins, Martha M., Rundus, Aaron, Sanz, Crickette, Sciaky, Lilah, Sommer, Volker, Stewart, Fiona, 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, Lizano, Esther, Arandjelovic, Mimi, Marqués-Bonet, Tomàs, Fundación la Caixa, Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Economía y Competitividad (España), European Commission, Vienna Science and Technology Fund, European Research Council, Howard Hughes Medical Institute, Generalitat de Catalunya, Wellcome Trust Centre for Human Genetics, Max Planck Society, Heinz L. Krekeler Foundation, Fontsere, Claudia, Kuhlwilm, Martin, Morcillo-Suárez, 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 Ayuk, Bailey, Emma, Barubiyo, Donatienne, Bessone, Mattia, Carretero-Alonso, Andrea, Chancellor, Rebecca, Cohen, Heather, Danquah, Emmanuel, Deschner, Tobias, Dunn, Andrew, Dupain, Jef, Egbe, Villard E., Feliú, 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 E., Lapuente, Juan, Larson, Bradley, Laudisoit, Anne, Lee, Kevin, Llana, Manuel, Llorente, Miquel, Marrocol, iSergio, Morgan, David, Mulindahabi, Felix, Murai, Mizuki, Neil, Emily, Nicholl, Sonia, Nixon, Stuart, Normand, Emma, Orbell, Chris, Ormsby, Lucy Jayne, Pacheco, Liliana, Piel, Alex, Riera, Laura, Robbins, Martha M., Rundus, Aaron, Sanz, Crickette, Sciaky, Lilah, Sommer, Volker, Stewart, Fiona, 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, Lizano, Esther, Arandjelovic, Mimi, and Marqués-Bonet, Tomàs
Abstract: Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.
Published: 2022

47. Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Author: Ferrández-Peral, Luis, Zhan, Xiaoyu, Alvarez-Estape, Marina, Chiva, Cristina, Esteller-Cucala, Paula, García-Pérez, Raquel, Julià, Eva, Lizano, Esther, Fornas, Òscar, Sabidó, Eduard, Li, Qiye, Marquès-Bonet, Tomàs, Juan, David, Zhang, Guojie, Ferrández-Peral, Luis, Zhan, Xiaoyu, Alvarez-Estape, Marina, Chiva, Cristina, Esteller-Cucala, Paula, García-Pérez, Raquel, Julià, Eva, Lizano, Esther, Fornas, Òscar, Sabidó, Eduard, Li, Qiye, Marquès-Bonet, Tomàs, Juan, David, and Zhang, Guojie
Abstract: Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.
Published: 2022

48. Recovering the genomes hidden in museum wet collections

Author: Ministerio de Ciencia e Innovación (España), Ruiz-Gartzia, Irune, Lizano, Esther, Marqués-Bonet, Tomàs, Kelley, Joanna L., Ministerio de Ciencia e Innovación (España), Ruiz-Gartzia, Irune, Lizano, Esther, Marqués-Bonet, Tomàs, and Kelley, Joanna L.
Abstract: Natural history museums hold vast collections of biomaterials. The collections in museums, often painstakingly sampled, are largely unexplored treasures that may help us better understand biodiversity on the planet. Museum collections can provide a unique window into the past of species long gone or currently declining due to human activity. From a molecular perspective, however, many museum samples are stored under conditions that hasten the damage of DNA, RNA and proteins. For example, samples in wet collections are those stored in liquid preservatives, typically ethanol. These ethanol-preserved tissues are often, although not always, formalin-fixed prior to storage, which may damage DNA. In this and recent issues of Molecular Ecology Resources, Straube et al (2021), O'Connell et al (2021) and Hahn et al (2022) explore different types of specimens from museum wet collections as new sources of DNA for scientific studies. All three articles found that for wet museum collections, overall specimen condition mattered most for recovering high-quality genomic DNA.
Published: 2022

49. Insights from the rescue and breeding management of Cuvier’s gazelle (Gazella cuvieri) through whole-genome sequencing

Author: Rancho Santa Fe Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Smithsonian Institution, European Research Council, European Commission, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Generalitat de Catalunya, Alvarez-Estape, Marina, Fontsere, Claudia, Serres-Armero, Aitor, Kuderna, Lukas F. K., Dobrynin, Pavel, Guidara, Héla, Pukazhenthi, Budhan S., Koepfli, Klaus-Peter, Marqués-Bonet, Tomàs, Moreno, Eulalia, Lizano, Esther, Rancho Santa Fe Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Smithsonian Institution, European Research Council, European Commission, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Generalitat de Catalunya, Alvarez-Estape, Marina, Fontsere, Claudia, Serres-Armero, Aitor, Kuderna, Lukas F. K., Dobrynin, Pavel, Guidara, Héla, Pukazhenthi, Budhan S., Koepfli, Klaus-Peter, Marqués-Bonet, Tomàs, Moreno, Eulalia, and Lizano, Esther
Abstract: Captive breeding programmes represent the most intensive type of ex situ population management for threatened species. One example is the Cuvier’s gazelle programme that started in 1975 with only four founding individuals, and after more than four decades of management in captivity, a reintroduction effort was undertaken in Tunisia in 2016, to establish a population in an area historically included within its range. Here, we aim to determine the genetic consequences of this reintroduction event by assessing the genetic diversity of the founder stock as well as of their descendants. We present the first whole-genome sequencing dataset of 30 Cuvier’s gazelles including captive-bred animals, animals born in Tunisia after a reintroduction and individuals from a genetically unrelated Moroccan population. Our analyses revealed no difference between the founder and the offspring cohorts in genome-wide heterozygosity and inbreeding levels, and in the amount and length of runs of homozygosity. The captive but unmanaged Moroccan gazelles have the lowest genetic diversity of all genomes analysed. Our findings demonstrate that the Cuvier’s gazelle captive breeding programme can serve as source populations for future reintroductions of this species. We believe that this study can serve as a starting point for global applications of genomics to the conservation plan of this species.
Published: 2022

50. Insights from the rescue and breeding management of Cuvier’s gazelle ( Gazella cuvieri ) through whole‐genome sequencing

Author: Alvarez‐Estape, Marina, primary, Fontsere, Claudia, additional, Serres‐Armero, Aitor, additional, Kuderna, Lukas F. K., additional, Dobrynin, Pavel, additional, Guidara, Héla, additional, Pukazhenthi, Budhan S., additional, Koepfli, Klaus‐Peter, additional, Marques‐Bonet, Tomas, additional, Moreno, Eulalia, additional, and Lizano, Esther, additional
Published: 2022
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