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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. 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

3. 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

4. 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
Full Text
View/download PDF

5. 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
Full Text
View/download PDF

6. 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
Full Text
View/download PDF

7. 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
Full Text
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8. 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

9. 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

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