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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. Ancient and historical DNA in conservation policy

Author: Jensen, Evelyn L., Díez-del-Molino, David, Gilbert, M. Thomas P., Bertola, Laura D., Borges, Filipa, Cubric-Curik, Vlatka, de Navascués, Miguel, Frandsen, Peter, Heuertz, Myriam, Hvilsom, Christina, Jiménez-Mena, Belén, Miettinen, Antti, Moest, Markus, Pečnerová, Patrícia, Barnes, Ian, and Vernesi, Cristiano
Published: 2022
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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. 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

5. 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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6. Genetic diagnosis of trisomy 21 in chimpanzees (Pan troglodytes)

Author: Frandsen, Peter, Johansen, Peter, Carlsen, Frands, and Hvilsom, Christina
Published: 2020
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7. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

Author: Xue, Yali, Prado-Martinez, Javier, Sudmant, Peter H, Narasimhan, Vagheesh, Ayub, Qasim, Szpak, Michal, Frandsen, Peter, Chen, Yuan, Yngvadottir, Bryndis, Cooper, David N, de Manuel, Marc, Hernandez-Rodriguez, Jessica, Lobon, Irene, Siegismund, Hans R, Pagani, Luca, Quail, Michael A, Hvilsom, Christina, Mudakikwa, Antoine, Eichler, Evan E, Cranfield, Michael R, Marques-Bonet, Tomas, Tyler-Smith, Chris, and Scally, Aylwyn
Subjects: Human Genome, Genetics, Biotechnology, Generic health relevance, Life on Land, Adaptation, Physiological, Animals, Biological Evolution, DNA Copy Number Variations, Democratic Republic of the Congo, Endangered Species, Female, Genetic Variation, Genome, Gorilla gorilla, Homozygote, Inbreeding, Linkage Disequilibrium, Male, Mutation, Population Dynamics, Rwanda, Selection, Genetic, Sequence Analysis, DNA, Species Specificity, Time Factors, General Science & Technology
Abstract: Mountain gorillas are an endangered great ape subspecies and a prominent focus for conservation, yet we know little about their genomic diversity and evolutionary past. We sequenced whole genomes from multiple wild individuals and compared the genomes of all four Gorilla subspecies. We found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation. A further recent decline in the mountain gorilla population has led to extensive inbreeding, such that individuals are typically homozygous at 34% of their sequence, leading to the purging of severely deleterious recessive mutations from the population. We discuss the causes of their decline and the consequences for their future survival.
Published: 2015

8. The genetic impact of an Ebola outbreak on a wild gorilla population

Author: Fontsere, Claudia, Frandsen, Peter, Hernandez-Rodriguez, Jessica, Niemann, Jonas, Scharff-Olsen, Camilla Hjorth, Vallet, Dominique, Le Gouar, Pascaline, Ménard, Nelly, Navarro, Arcadi, Siegismund, Hans R., Hvilsom, Christina, Gilbert, M. Thomas P., Kuhlwilm, Martin, Hughes, David, and Marques-Bonet, Tomas
Published: 2021
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9. Deep genetic substructure within bonobos

Author: Han, Sojung, de Filippo, Cesare, Parra, Genís, Meneu, Juan Ramon, Laurent, Romain, Frandsen, Peter, Hvilsom, Christina, Gronau, Ilan, Marques-Bonet, Tomas, Kuhlwilm, Martin, and Andrés, Aida M.
Published: 2024
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10. 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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11. More grist for the mill? Species delimitation in the genomic era and its implications for conservation

Author: Stanton, David W. G., Frandsen, Peter, Waples, Ryan K., Heller, Rasmus, Russo, Isa-Rita M., Orozco-terWengel, Pablo A., Pedersen, Casper-Emil Tingskov, Siegismund, Hans R., and Bruford, Michael W.
Published: 2019
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12. Genetics as a novel tool in mining impact assessment and biomonitoring of critically endangered western chimpanzees in the Nimba Mountains, Guinea

Author: Koops, Kathelijne, Humle, Tatyana, Frandsen, Peter, Fitzgerald, Maegan, D'Auvergne, Lucy, Jackson, Hazel A, Børsting, Claus, Siegismund, Hans R, Soumah, Aly Gaspard, Hvilsom, Christina, Koops, Kathelijne [0000-0001-7097-2698], Humle, Tatyana [0000-0002-1919-631X], Frandsen, Peter [0000-0001-7131-0944], Fitzgerald, Maegan [0000-0003-3769-1688], Jackson, Hazel A [0000-0001-9573-2025], Børsting, Claus [0000-0003-0421-7429], Siegismund, Hans R [0000-0001-5757-3131], Hvilsom, Christina [0000-0001-7870-6888], and Apollo - University of Cambridge Repository
Subjects: Global and Planetary Change, environmental impact assessment, Ecology, CONTRIBUTED PAPER, Pan troglodytes verus, UNESCO world heritage site, genetic censusing, Environmental Science (miscellaneous), 3105 Genetics, CONTRIBUTED PAPERS, 31 Biological Sciences, conservation management, Nature and Landscape Conservation
Abstract: Funder: Alfred Benzon Foundation; Id: http://dx.doi.org/10.13039/501100007469, Funder: Gates Cambridge Trust; Id: http://dx.doi.org/10.13039/501100005370, Funder: Graduate Teaching PhD Scholarship, University of Kent, Funder: Homerton College, University of Cambridge; Id: http://dx.doi.org/10.13039/501100008420, Funder: Mohamed bin Zayed Species Conservation Fund; Id: http://dx.doi.org/10.13039/501100011672, Funder: Newnham College, University of Cambridge; Id: http://dx.doi.org/10.13039/501100000663, Funder: Société des Mines de Fer de Guineé S.A. (Conakry, Guinea), Funder: Stichting Lucie Burgers, The Netherlands; Id: http://dx.doi.org/10.13039/501100013496, Western chimpanzees (Pan troglodytes verus) are Critically Endangered and Guinea is a key stronghold for this subspecies. However, Guinea is also rich in minerals with some of the highest‐grade iron‐ore deposits in the world. Specifically, the Nimba Mountains, home to western chimpanzees, is one of the sites under consideration for mining activities. To assess the impact of mining activities in the area, we used non‐invasive genetic sampling to estimate chimpanzee population size, sex ratio, community composition, and range boundaries on the western flank of the massif. The level of genetic diversity and affinity between communities was estimated and recommendations for future genetic censusing provided. Between 2003 and 2018, we collected 999 fecal samples of which 663 were analyzed using a panel of 26 microsatellites. We identified a minimum of 136 chimpanzees in four communities, with evidence of migratory events, a high level of shared ancestry and genetic diversity. We assessed sampling intensities and capture rates for each community. Saturation was reached in two communities with sampling between 3.2 and 4.3 times the estimated number of chimpanzees. Our findings highlight the utility of genetic censusing for temporal monitoring of ape abundance, as well as capturing migratory events and gauging genetic diversity and population viability over time. We recommend genetic sampling, combined with camera trapping, for use in future Environmental and Social Impact Assessments, as these methods can yield robust baselines for implementing the mitigation hierarchy, future biomonitoring and conservation management.
Published: 2023
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13. 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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14. 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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15. 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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16. 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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17. 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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18. 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

19. 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

20. Genetics as a novel tool in mining impact assessment and biomonitoring of critically endangered western chimpanzees in the Nimba Mountains, Guinea

Author: Koops, Kathelijne; https://orcid.org/0000-0001-7097-2698, Humle, Tatyana; https://orcid.org/0000-0002-1919-631X, Frandsen, Peter; https://orcid.org/0000-0001-7131-0944, Fitzgerald, Maegan; https://orcid.org/0000-0003-3769-1688, D'Auvergne, Lucy, Jackson, Hazel A; https://orcid.org/0000-0001-9573-2025, Børsting, Claus; https://orcid.org/0000-0003-0421-7429, Siegismund, Hans R; https://orcid.org/0000-0001-5757-3131, Soumah, Aly Gaspard, Hvilsom, Christina; https://orcid.org/0000-0001-7870-6888, Koops, Kathelijne; https://orcid.org/0000-0001-7097-2698, Humle, Tatyana; https://orcid.org/0000-0002-1919-631X, Frandsen, Peter; https://orcid.org/0000-0001-7131-0944, Fitzgerald, Maegan; https://orcid.org/0000-0003-3769-1688, D'Auvergne, Lucy, Jackson, Hazel A; https://orcid.org/0000-0001-9573-2025, Børsting, Claus; https://orcid.org/0000-0003-0421-7429, Siegismund, Hans R; https://orcid.org/0000-0001-5757-3131, Soumah, Aly Gaspard, and Hvilsom, Christina; https://orcid.org/0000-0001-7870-6888
Abstract: Western chimpanzees (Pan troglodytes verus) are Critically Endangered and Guinea is a key stronghold for this subspecies. However, Guinea is also rich in minerals with some of the highest‐grade iron‐ore deposits in the world. Specifically, the Nimba Mountains, home to western chimpanzees, is one of the sites under consideration for mining activities. To assess the impact of mining activities in the area, we used non‐invasive genetic sampling to estimate chimpanzee population size, sex ratio, community composition, and range boundaries on the western flank of the massif. The level of genetic diversity and affinity between communities was estimated and recommendations for future genetic censusing provided. Between 2003 and 2018, we collected 999 fecal samples of which 663 were analyzed using a panel of 26 microsatellites. We identified a minimum of 136 chimpanzees in four communities, with evidence of migratory events, a high level of shared ancestry and genetic diversity. We assessed sampling intensities and capture rates for each community. Saturation was reached in two communities with sampling between 3.2 and 4.3 times the estimated number of chimpanzees. Our findings highlight the utility of genetic censusing for temporal monitoring of ape abundance, as well as capturing migratory events and gauging genetic diversity and population viability over time. We recommend genetic sampling, combined with camera trapping, for use in future Environmental and Social Impact Assessments, as these methods can yield robust baselines for implementing the mitigation hierarchy, future biomonitoring and conservation management.
Published: 2023

21. 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

22. Chimpanzee genomic diversity reveals ancient admixture with bonobos

Author: de Manuel, Marc, Kuhlwilm, Martin, Frandsen, Peter, Sousa, Vitor C., Desai, Tariq, Prado-Martinez, Javier, Hernandez-Rodriguez, Jessica, Dupanloup, Isabelle, Lao, Oscar, Hallast, Pille, Schmidt, Joshua M., Heredia-Genestar, José María, Benazzo, Andrea, Barbujani, Guido, Peter, Benjamin M., Kuderna, Lukas F. K., Casals, Ferran, Angedakin, Samuel, Arandjelovic, Mimi, Boesch, Christophe, Kühl, Hjalmar, Vigilant, Linda, Langergraber, Kevin, Novembre, John, Gut, Marta, Gut, Ivo, Navarro, Arcadi, Carlsen, Frauds, Andres, Aida M., Siegismund, Hans. R., Scally, Aylwyn, Excoffier, Laurent, Tyler-Smith, Chris, Castellano, Sergi, Xue, Yali, Hvilsom, Christina, and Marques-Bonet, Tomas
Published: 2016

23. Is Diagnosability an Indicator of Speciation? Response to "Why One Century of Phenetics Is Enough"

Author: Heller, Rasmus, Frandsen, Peter, Lorenzen, Eline Deirdre, and Siegismund, Hans R.
Published: 2014

24. Dynamic Matrix Rank

Author: Frandsen, Gudmund Skovbjerg, Frandsen, Peter Frands, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Bugliesi, Michele, editor, Preneel, Bart, editor, Sassone, Vladimiro, editor, and Wegener, Ingo, editor
Published: 2006
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25. Are There Really Twice as Many Bovid Species as We Thought?

Author: Heller, Rasmus, Frandsen, Peter, Lorenzen, Eline D., and Siegismund, Hans R.
Published: 2013
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26. PRIMATE GENOMICS: Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

Author: Xue, Yali, Prado-Martinez, Javier, Sudmant, Peter H., Narasimhan, Vagheesh, Ayub, Qasim, Szpak, Michal, Frandsen, Peter, Chen, Yuan, Yngvadottir, Bryndis, Cooper, David N., de Manuel, Marc, Hernandez-Rodriguez, Jessica, Lobon, Irene, Siegismund, Hans R., Pagani, Luca, Quail, Michael A., Hvilsom, Christina, Mudakikwa, Antoine, Eichler, Evan E., Cranfield, Michael R., Marques-Bonet, Tomas, Tyler-Smith, Chris, and Scally, Aylwyn
Published: 2015
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27. Dynamic matrix rank

Author: Frandsen, Gudmund Skovbjerg and Frandsen, Peter Frands
Published: 2009
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28. Additional file 2 of The genetic impact of an Ebola outbreak on a wild gorilla population

Author: Fontsere, Claudia, Frandsen, Peter, Hernandez-Rodriguez, Jessica, Niemann, Jonas, Scharff-Olsen, Camilla Hjorth, Vallet, Dominique, Le Gouar, Pascaline, Ménard, Nelly, Navarro, Arcadi, Siegismund, Hans R., Hvilsom, Christina, Gilbert, M. Thomas P., Kuhlwilm, Martin, Hughes, David, and Marques-Bonet, Tomas
Subjects: Data_FILES
Abstract: Additional file 2.
Published: 2021
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29. High genetic diversity and low differentiation reflect the ecological versatility of the African leopard

Author: Pečnerová, Patrícia, Garcia-Erill, Genís, Liu, Xiaodong, Nursyifa, Casia, Waples, Ryan K., Santander, Cindy G., Quinn, Liam, Frandsen, Peter, Meisner, Jonas, Stæger, Frederik Filip, Rasmussen, Malthe Sebro, Brüniche-Olsen, Anna, Jørgensen, Christian Hviid Friis, da Fonseca, Rute R., Siegismund, Hans R., Albrechtsen, Anders, Heller, Rasmus, Moltke, Ida, Hanghøj, Kristian, Pečnerová, Patrícia, Garcia-Erill, Genís, Liu, Xiaodong, Nursyifa, Casia, Waples, Ryan K., Santander, Cindy G., Quinn, Liam, Frandsen, Peter, Meisner, Jonas, Stæger, Frederik Filip, Rasmussen, Malthe Sebro, Brüniche-Olsen, Anna, Jørgensen, Christian Hviid Friis, da Fonseca, Rute R., Siegismund, Hans R., Albrechtsen, Anders, Heller, Rasmus, Moltke, Ida, and Hanghøj, Kristian
Abstract: Large carnivores are generally sensitive to ecosystem changes because their specialized diet and position at the top of the trophic pyramid is associated with small population sizes. Accordingly, low genetic diversity at the whole-genome level has been reported for all big cat species, including the widely distributed leopard. However, all previous whole-genome analyses of leopards are based on the Far Eastern Amur leopards that live at the extremity of the species' distribution and therefore are not necessarily representative of the whole species. We sequenced 53 whole genomes of African leopards. Strikingly, we found that the genomic diversity in the African leopard is 2- to 5-fold higher than in other big cats, including the Amur leopard, likely because of an exceptionally high effective population size maintained by the African leopard throughout the Pleistocene. Furthermore, we detected ongoing gene flow and very low population differentiation within African leopards compared with those of other big cats. We corroborated this by showing a complete absence of an otherwise ubiquitous equatorial forest barrier to gene flow. This sets the leopard apart from most other widely distributed large African mammals, including lions. These results revise our understanding of trophic sensitivity and highlight the remarkable resilience of the African leopard, likely because of its extraordinary habitat versatility and broad dietary niche.
Published: 2021

30. The genetic impact of an Ebola outbreak on a wild gorilla population

Author: La Caixa, European Commission, Danish Council for Independent Research, Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Centre National de la Recherche Scientifique (France), University of Bristol, Fontsere, Claudia, Frandsen, Peter, Hernández-Rodríguez, Jessica, Niemann, Jonas, Hjorth Scharff-Olsen, Camila, Vallet, Dominique, Le Gouar, Pascaline, Ménard, Nelly, Navarro, Arcadi, Siegismund, Hans R., Hvilsom, Christina, Gilbert, M. Thomas P., Kuhlwilm, Martin, Hughes, D., Marqués-Bonet, Tomàs, La Caixa, European Commission, Danish Council for Independent Research, Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Centre National de la Recherche Scientifique (France), University of Bristol, Fontsere, Claudia, Frandsen, Peter, Hernández-Rodríguez, Jessica, Niemann, Jonas, Hjorth Scharff-Olsen, Camila, Vallet, Dominique, Le Gouar, Pascaline, Ménard, Nelly, Navarro, Arcadi, Siegismund, Hans R., Hvilsom, Christina, Gilbert, M. Thomas P., Kuhlwilm, Martin, Hughes, D., and Marqués-Bonet, Tomàs
Abstract: Background] Numerous Ebola virus outbreaks have occurred in Equatorial Africa over the past decades. Besides human fatalities, gorillas and chimpanzees have also succumbed to the fatal virus. The 2004 outbreak at the Odzala-Kokoua National Park (Republic of Congo) alone caused a severe decline in the resident western lowland gorilla (Gorilla gorilla gorilla) population, with a 95% mortality rate. Here, we explore the immediate genetic impact of the Ebola outbreak in the western lowland gorilla population. [Results] Associations with survivorship were evaluated by utilizing DNA obtained from fecal samples from 16 gorilla individuals declared missing after the outbreak (non-survivors) and 15 individuals observed before and after the epidemic (survivors). We used a target enrichment approach to capture the sequences of 123 genes previously associated with immunology and Ebola virus resistance and additionally analyzed the gut microbiome which could influence the survival after an infection. Our results indicate no changes in the population genetic diversity before and after the Ebola outbreak, and no significant differences in microbial community composition between survivors and non-survivors. However, and despite the low power for an association analysis, we do detect six nominally significant missense mutations in four genes that might be candidate variants associated with an increased chance of survival. [Conclusion] This study offers the first insight to the genetics of a wild great ape population before and after an Ebola outbreak using target capture experiments from fecal samples, and presents a list of candidate loci that may have facilitated their survival.
Published: 2021

31. The genetic impact of an Ebola outbreak on a wild gorilla population

Author: Fontsere, Claudia, primary, Frandsen, Peter, additional, Hernandez-Rodriguez, Jessica, additional, Niemann, Jonas, additional, Scharff-Olsen, Camilla Hjorth, additional, Vallet, Dominique, additional, Gouar, Pascaline Le, additional, Ménard, Nelly, additional, Navarro, Arcadi, additional, Siegismund, Hans R., additional, Hvilsom, Christina, additional, Gilbert, M. Thomas P., additional, Kuhlwilm, Martin, additional, Hughes, David, additional, and Marques-Bonet, Tomas, additional
Published: 2021
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32. High genetic diversity and low differentiation reflect the ecological versatility of the African leopard

Author: Pečnerová, Patrícia, primary, Garcia-Erill, Genís, additional, Liu, Xiaodong, additional, Nursyifa, Casia, additional, Waples, Ryan K., additional, Santander, Cindy G., additional, Quinn, Liam, additional, Frandsen, Peter, additional, Meisner, Jonas, additional, Stæger, Frederik Filip, additional, Rasmussen, Malthe Sebro, additional, Brüniche-Olsen, Anna, additional, Hviid Friis Jørgensen, Christian, additional, da Fonseca, Rute R., additional, Siegismund, Hans R., additional, Albrechtsen, Anders, additional, Heller, Rasmus, additional, Moltke, Ida, additional, and Hanghøj, Kristian, additional
Published: 2021
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33. Targeted conservation genetics of the endangered chimpanzee

Author: Innovation Fund Denmark, Candys Foundation, Carlsberg Foundation, HSE University, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Howard Hughes Medical Institute, Fundación la Caixa, Generalitat de Catalunya, Frandsen, Peter, Fontsere, Claudia, Nielsen, Svend Vendelbo, Hanghøj, Kristian, Castejón-Fernández, Natalia, Lizano, Esther, Hughes, David A., Hernández-Rodríguez, Jessica, Sand Korneliussen, Thorfinn, Carlsen, Frands, Redlef Siegismund, Hans, Mailund, Thomas, Marqués-Bonet, Tomàs, Hvilsom, Christina, Innovation Fund Denmark, Candys Foundation, Carlsberg Foundation, HSE University, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Howard Hughes Medical Institute, Fundación la Caixa, Generalitat de Catalunya, Frandsen, Peter, Fontsere, Claudia, Nielsen, Svend Vendelbo, Hanghøj, Kristian, Castejón-Fernández, Natalia, Lizano, Esther, Hughes, David A., Hernández-Rodríguez, Jessica, Sand Korneliussen, Thorfinn, Carlsen, Frands, Redlef Siegismund, Hans, Mailund, Thomas, Marqués-Bonet, Tomàs, and Hvilsom, Christina
Abstract: Populations of the common chimpanzee (Pan troglodytes) are in an impending risk of going extinct in the wild as a consequence of damaging anthropogenic impact on their natural habitat and illegal pet and bushmeat trade. Conservation management programmes for the chimpanzee have been established outside their natural range (ex situ), and chimpanzees from these programmes could potentially be used to supplement future conservation initiatives in the wild (in situ). However, these programmes have often suffered from inadequate information about the geographical origin and subspecies ancestry of the founders. Here, we present a newly designed capture array with ~60,000 ancestry informative markers used to infer ancestry of individual chimpanzees in ex situ populations and determine geographical origin of confiscated sanctuary individuals. From a test panel of 167 chimpanzees with unknown origins or subspecies labels, we identify 90 suitable non-admixed individuals in the European Association of Zoos and Aquaria (EAZA) Ex situ Programme (EEP). Equally important, another 46 individuals have been identified with admixed subspecies ancestries, which therefore over time, should be naturally phased out of the breeding populations. With potential for future re-introduction to the wild, we determine the geographical origin of 31 individuals that were confiscated from the illegal trade and demonstrate the promises of using non-invasive sampling in future conservation action plans. Collectively, our genomic approach provides an exemplar for ex situ management of endangered species and offers an efficient tool in future in situ efforts to combat the illegal wildlife trade.
Published: 2020

34. Dynamic Matrix Rank

Author: Frandsen, Gudmund Skovbjerg, primary and Frandsen, Peter Frands, additional
Published: 2006
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35. Expected Long-Term Outcome after a Tibial Shaft Fracture

Author: Faergemann, Christian, Frandsen, Peter A., and Rock, Niels Dieter
Published: 1999

36. Residual Impairment after Lower Extremity Fracture

Author: Faergemann, Christian, Frandsen, Peter, and Rock, Niels
Published: 1998

37. Demographic history and population structure of chimpanzees (Pan troglodytes) with implacations for global conservation strategies

Author: Frandsen, Peter, Manuel, Marc de, Fontsere, Claudia, Hernandez, Jessica, Kuhlwilm, Martin, Chimpanzee Diversity Consortium, and Marqués-Bonet, Tomàs
Abstract: Frandsen, Peter et al.-- Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2016), celebrada en Gold Coast (Queensland, Australia) del 3 al 7 de julio de 2016., Large-scale population genomics have recently provided novel insight to the diversity and evolutionary history of the great apes, including our own closest living relative, the chimpanzee. However, limited by a lack of precise geographical information, our knowledge on the local demographic history and fine-scale population structure of chimpanzees is still incomplete. Such knowledge is crucial when setting future conservation strategies for chimpanzees, both in situ and ex situ.To fill this knowledge gap, we have analyzed a comprehensive dataset of 60 wild born chimpanzee genomes, covering all four subspecies sampled across their natural distribution range. From this project, we present an unpreceded fine scale inference of complex demographic histories and a tight link between geography and local layers of genetic population structure. Apart from valuable insights to the local evolutionary past of the chimpanzee, these findings have allowed us to ide ntify ancestry informative markers (AIM). We will show how this panel of AIMs can be used to re-assign confiscated individuals to their geographical origin, demonstrating a novel tool to combat illegal trafficking of chimpanzees along with the means to provide an accurate genetic guidance for global ex situ conservation management plans.
Published: 2016

38. Studies on the Reactions of Limax Maximus to Directive Stimuli

Author: Frandsen, Peter
Published: 1901
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39. Hybrid Classification in the Common Chimpanzee

Author: Albrechtsen, Anders, Frandsen, Peter, Mailund, Thomas, Lowe, Abigail Daisy, Albrechtsen, Anders, Frandsen, Peter, Mailund, Thomas, and Lowe, Abigail Daisy
Abstract: —Wild populations of all four subspecies of the common chimpanzee - Pan troglodytes - are increasingly threatened. In order to combat this, conservation programmes - both ex-situ and in-situ - require our focus. However, the studbooks that guide the captive management of the ex-situ programmes,are in need of improvement, as they are built on assumptions which are not provably accurate. This study analyses 34,203SNPs from a total of 161 chimpanzees, both wild-born geo- referenced individuals, and captive individuals from European zoos and African sanctuaries with unknown subspecies status. Here, two novel methods are introduced that aim to classify captive individuals in terms of their subspecies ancestry. This will allow identification of individuals suited for use in the captive breeding programme. Both methods are extremely accurate when classifying non-admixed individuals from a single subspecies, yet more refinement is needed in order to provide clarity on the ancestral composition of hybrid individuals.
Published: 2016

40. Time clustered sampling can inflate the inferred substitution rate in foot-and-mouth disease virus analyses

Author: Pedersen, Casper-Emil Tingskov, Frandsen, Peter, Wekesa, Sabenzia N., Heller, Rasmus, Sangula, Abraham K., Wadsworth, Jemma, Knowles, Nick J., Muwanika, Vincent B., Siegismund, Hans Redlef, Pedersen, Casper-Emil Tingskov, Frandsen, Peter, Wekesa, Sabenzia N., Heller, Rasmus, Sangula, Abraham K., Wadsworth, Jemma, Knowles, Nick J., Muwanika, Vincent B., and Siegismund, Hans Redlef
Abstract: With the emergence of analytical software for the inference of viral evolution, a number of studies have focused on estimating important parameters such as the substitution rate and the time to the most recent common ancestor (tMRCA) for rapidly evolving viruses. Coupled with an increasing abundance of sequence data sampled under widely different schemes, an effort to keep results consistent and comparable is needed. This study emphasizes commonly disregarded problems in the inference of evolutionary rates in viral sequence data when sampling is unevenly distributed on a temporal scale through a study of the foot-and-mouth (FMD) disease virus serotypes SAT 1 and SAT 2. Our study shows that clustered temporal sampling in phylogenetic analyses of FMD viruses will strongly bias the inferences of substitution rates and tMRCA because the inferred rates in such data sets reflect a rate closer to the mutation rate rather than the substitution rate. Estimating evolutionary parameters from viral sequences should be performed with due consideration of the differences in short-term and longer-term evolutionary processes occurring within sets of temporally sampled viruses, and studies should carefully consider how samples are combined.
Published: 2015

41. Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses

Author: Pedersen, Casper-Emil T., primary, Frandsen, Peter, additional, Wekesa, Sabenzia N., additional, Heller, Rasmus, additional, Sangula, Abraham K., additional, Wadsworth, Jemma, additional, Knowles, Nick J., additional, Muwanika, Vincent B., additional, and Siegismund, Hans R., additional
Published: 2015
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42. Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes

Author: Hvilsom, Christina, Frandsen, Peter, Børsting, Claus, Carlsen, F., Sallé, B., Simonsen, Bo Thisted, Siegismund, Hans Redlef, Hvilsom, Christina, Frandsen, Peter, Børsting, Claus, Carlsen, F., Sallé, B., Simonsen, Bo Thisted, and Siegismund, Hans Redlef
Abstract: Despite ample focus on this endangered species, conservation planning for chimpanzees residing outside Africa has proven a challenge because of the lack of ancestry information. Here, we analysed the largest number of chimpanzee samples to date, examining microsatellites in >100 chimpanzees from the range of the species in Africa, and 20% of the European zoo population. We applied the knowledge about subspecies differentiation throughout equatorial Africa to assign origin to chimpanzees in the largest conservation management programme globally. A total of 63% of the genotyped chimpanzees from the European zoos could be assigned to one of the recognized subspecies. The majority being of West African origin (40%) will help consolidate the current breeding programme for this subspecies and the identification of individuals belonging to the two other subspecies so far found in European zoos can form the basis for breeding programmes for these. Individuals of various degree of mixed ancestry made up 37% of the genotyped European zoo population and thus highlight the need for appropriate management programmes guided by genetic analysis to preserve maximum genetic diversity and reduce hybridization among subspecies.
Published: 2013

43. Frandsen, Peter

Author: Frandsen, Peter and Frandsen, Peter
Published: 2013

44. Polyethylene failure of metal—backed patellar components: 111 AGC total knees followedfor 7-22 months

Author: Andersen, Henrik N., primary, Ernst, Carsten, additional, and Frandsen, Peter A., additional
Published: 1991
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