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1. Continent-wide genomic analysis of the African buffalo (Syncerus caffer)

Author: Talenti, Andrea, Wilkinson, Toby, Cook, Elizabeth A., Hemmink, Johanneke D., Paxton, Edith, Mutinda, Matthew, Ngulu, Stephen D., Jayaraman, Siddharth, Bishop, Richard P., Obara, Isaiah, Hourlier, Thibaut, Garcia Giron, Carlos, Martin, Fergal J., Labuschagne, Michel, Atimnedi, Patrick, Nanteza, Anne, Keyyu, Julius D., Mramba, Furaha, Caron, Alexandre, Cornelis, Daniel, Chardonnet, Philippe, Fyumagwa, Robert, Lembo, Tiziana, Auty, Harriet K., Michaux, Johan, Smitz, Nathalie, Toye, Philip, Robert, Christelle, Prendergast, James G. D., and Morrison, Liam J.
Published: 2024
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2. 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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3. The evaluation of five serological assays in determining seroconversion to peste des petits ruminants virus in typical and atypical hosts

Author: Tully, Matthew, Batten, Carrie, Ashby, Martin, Mahapatra, Mana, Parekh, Krupali, Parida, Satya, Njeumi, Felix, Willett, Brian, Bataille, Arnaud, Libeau, Genevieve, Kwiatek, Olivier, Caron, Alexandre, Berguido, Francisco J., Lamien, Charles E., Cattoli, Giovanni, Misinzo, Gerald, Keyyu, Julius, Mdetele, Daniel, Gakuya, Francis, Bodjo, Sanne Charles, Taha, Fatima Abdelazeem, Elbashier, Husna Mohamed, Khalafalla, Abdelmalik Ibrahim, Osman, Abdinasir Y., and Kock, Richard
Published: 2023
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4. Sociocultural Factors Shaping Responses to Wildlife Crop-Raiding in Communities Adjacent to Protected Areas in Southern Tanzania

Author: Kimaro, Jerome, Bukombe, John, Leweri, Cecilia, Kakengi, Victor, Ntalwila, Janemary, Mwakatobe, Angela, Lowassa, Asanterabi, Kilimba, Neema, Marealle, Wilfred, Lobora, Alex, and Keyyu, Julius
Published: 2023
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5. Mathematical modelling Treponema infection in free-ranging Olive baboons (Papio anubis) in Tanzania

Author: Hawkins, Diamond, Kusi, Roland, Schwab, Solomaya, Chuma, Idrissa S., Keyyu, Julius D., Knauf, Sascha, Paciência, Filipa M.D., Zinner, Dietmar, Rychtář, Jan, and Taylor, Dewey
Published: 2022
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6. Predicting uptake of a malignant catarrhal fever vaccine by pastoralists in northern Tanzania: Opportunities for improving livelihoods and ecosystem health

Author: Decker, Catherine, Hanley, Nick, Czajkowski, Mikolaj, Morrison, Thomas A., Keyyu, Julius, Munishi, Linus, Lankester, Felix, and Cleaveland, Sarah
Published: 2021
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7. 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

8. 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

9. 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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10. Complex evolutionary history with extensive ancestral gene flow in an African primate radiation

Author: Jensen, Axel, primary, Swift, Frances, additional, de Vries, Dorien, additional, Beck, Robin, additional, Kuderna, Lukas F K, additional, Knauf, Sascha, additional, Chuma, Idrissa S, additional, Keyyu, Julius D, additional, Kitchener, Andrew C, additional, Farh, Kyle, additional, Rogers, Jeffrey, additional, Marques-Bonet, Tomas, additional, Detwiler, Kate M, additional, Roos, Christian, additional, and Guschanski, Katerina, additional
Published: 2023
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11. Continent-wide genomic analysis of the African buffalo (Syncerus caffer)

Author: Talenti, Andrea, primary, Wilkinson, Toby, additional, Cook, Elizabeth A., additional, Hemmink, Johanneke D., additional, Paxton, Edith, additional, Mutinda, Matthew, additional, Ngulu, Stephen D., additional, Jayaraman, Siddharth, additional, Bishop, Richard P., additional, Obara, Isaiah, additional, Hourlier, Thibaut, additional, Giron, Carlos Garcia, additional, Martin, Fergal J., additional, Labuschagne, Michel, additional, Atimnedi, Patrick, additional, Nanteza, Anne, additional, Keyyu, Julius D., additional, Mramba, Furaha, additional, Caron, Alexandre, additional, Cornelis, Daniel, additional, Chardonnet, Philippe, additional, Fyumagwa, Robert, additional, Lembo, Tiziana, additional, Auty, Harriet K., additional, Michaux, Johan, additional, Smitz, Nathalie, additional, Toye, Philip, additional, Robert, Christelle, additional, Prendergast, James G.D., additional, and Morrison, Liam J., additional
Published: 2023
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12. Identification of risk factors associated with carriage of resistant Escherichia coli in three culturally diverse ethnic groups in Tanzania: a biological and socioeconomic analysis

Author: Caudell, Mark A, Mair, Colette, Subbiah, Murugan, Matthews, Louise, Quinlan, Robert J, Quinlan, Marsha B, Zadoks, Ruth, Keyyu, Julius, and Call, Douglas R
Published: 2018
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13. The genomes of the yaws bacterium, Treponema pallidum subsp. pertenue, of nonhuman primate and human origin are not genomically distinct

Author: Janečková, Klára, primary, Roos, Christian, additional, Fedrová, Pavla, additional, Tom, Nikola, additional, Čejková, Darina, additional, Lueert, Simone, additional, Keyyu, Julius D., additional, Chuma, Idrissa S., additional, Knauf, Sascha, additional, and Šmajs, David, additional
Published: 2023
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14. Sero-prevalence and spatial distribution of Rift Valley fever infection among agro-pastoral and pastoral communities during Interepidemic period in the Serengeti ecosystem, northern Tanzania

Author: Abade Ahmed, Jabir Makame, Fyumagwa Robert, Keyyu Julius, and Matee Mecky
Subjects: Rift valley, Serengeti ecosystem, Inter-epidemic human, Tanzania, Infectious and parasitic diseases, RC109-216
Abstract: Abstract Background In the past two decades, Rift Valley Fever (RVF) outbreaks have been reported twice in Tanzania, with the most recent outbreak occurring in 2006/07. Given the ecology and climatic factors that support mosquito vectors in the Serengeti ecosystem, we hypothesized a continued transmission of RVF virus (RVFV) during interepidemic periods. This study was carried out to determine sero-prevalence, spatial distribution and factors associated with RVF in at-risk agro-pastoral and pastoral communities in the Serengeti Ecosystem in northern Tanzania. Methods A cross sectional study was carried out to establish the general exposure to RVFV by detecting anti–RVFV IgG and anti–RVFV IgM using ELISA techniques. The health facilities where human subjects were blood sampled concurrent with interviews included Bunda District Designated Hospital, Wasso DDH, Endulen hospital, Arash, Malambo, Olbabal, and Piyaya dispenaries (Ngorongoro district) and Nyerere DDH (Serengeti district) respectively. In addition, human subjects from Lamadi ward (Busega district) were recruited while receiving medical service at Bunda DDH. We conducted logistic regression to assess independent risk factor and mapped the hotspot areas for exposure to RVFV. Results A total of 751 subjects (males = 41.5%; females = 58.5%) with a median age of 35.5 years were enrolled at out-patient clinics. Of them, 34 (4.5, 95%CI 3.3–6.3%) tested positive for anti–RVFV IgG. Of the 34 that tested positive for anti–RVFV IgG, six (17.6%) tested positive for anti–RVFV IgM. Odds of exposure were higher among pastoral communities (aOR 2.9, 95% C.I: 1.21–6.89, p
Published: 2018
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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, 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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16. 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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17. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Author: Sørensen, Erik F., primary, Harris, R. Alan, additional, Zhang, Liye, additional, Raveendran, Muthuswamy, additional, Kuderna, Lukas F. K., additional, Walker, Jerilyn A., additional, Storer, Jessica M., additional, Kuhlwilm, Martin, additional, Fontsere, Claudia, additional, Seshadri, Lakshmi, additional, Bergey, Christina M., additional, Burrell, Andrew S., additional, Bergman, Juraj, additional, Phillips-Conroy, Jane E., additional, Shiferaw, Fekadu, additional, Chiou, Kenneth L., additional, Chuma, Idrissa S., additional, Keyyu, Julius D., additional, Fischer, Julia, additional, Gingras, Marie-Claude, additional, Salvi, Sejal, additional, Doddapaneni, Harshavardhan, additional, Schierup, Mikkel H., additional, Batzer, Mark A., additional, Jolly, Clifford J., additional, Knauf, Sascha, additional, Zinner, Dietmar, additional, Farh, Kyle K.-H., additional, Marques-Bonet, Tomas, additional, Munch, Kasper, additional, Roos, Christian, additional, and Rogers, Jeffrey, additional
Published: 2023
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18. 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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19. Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania

Author: Katale, Bugwesa Z., Mbelele, Peter M., Lema, Nsiande A., Campino, Susana, Mshana, Stephen E., Rweyemamu, Mark M., Phelan, Jody E., Keyyu, Julius D., Majigo, Mtebe, Mbugi, Erasto V., Dockrell, Hazel M., Clark, Taane G., Matee, Mecky I., and Mpagama, Stellah
Published: 2020
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20. Antimicrobial resistant enteric bacteria are widely distributed amongst people, animals and the environment in Tanzania

Author: Subbiah, Murugan, Caudell, Mark A., Mair, Colette, Davis, Margaret A., Matthews, Louise, Quinlan, Robert J., Quinlan, Marsha B., Lyimo, Beatus, Buza, Joram, Keyyu, Julius, and Call, Douglas R.
Published: 2020
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21. One Health approach in the prevention and control of mycobacterial infections in Tanzania: lessons learnt and future perspectives

Author: Katale, Bugwesa Z., Mbugi, Erasto V., Keyyu, Julius D., Fyumagwa, Robert D., Rweyemamu, Mark M., van Helden, Paul D., Dockrell, Hazel M., and Matee, Mecky I.
Published: 2019
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22. Flora Resources of Mikumi National Park (MINAPA): An Insight for Enhancing Strategic Management and Conservation of Protected Areas (PAs) in Tanzania.

Author: Bukombe, John, Kavana, Pius, Marealle, Wilfred, Nkwabi, Ally, Leweri, Cecilia, Makongoro, Rahabu, Kimaro, Jerome, Mwita, Machoke, Kija, Hamza, Okick, Raymond, Kohi, Edward, Keyyu, Julius, Mjingo, Eblate, Mangewa, Lazaro, Efraim, Joely, and Mbago, Frank
Subjects: VEGETATION surveys, TAXONOMY
Abstract: The flora within Protected Areas (PAs) plays a crucial role in providing essential resources for wildlife, including forage, shelter, breeding sites, and water. However, the current understanding of the floristic composition of Mikumi National Park (MINAPA) is limited, hindering the implementation of effective conservation and management strategies. This study aimed to update the plant species records for MINAPA based on the Angiosperm Phylogeny Group (APG) IV classification by analyzing the data from unpublished surveys conducted between the 1960s and 1990s, as well as a more recent survey in 2021. A total of 951 species records were compiled, representing 504 genera and 124 families. Among these, 35 species were listed in the International Union for Conservation of Nature (IUCN) red list with 15 (1.6%) classified as Vulnerable (VU), 7 (0.7%) as Near Threatened (NT), 10 (1.0%) as Endangered (EN), and 3 (0.3%) as Critically Endangered (CR). Additionally, 16 species were found to be endemic to Tanzania. The data from the 1960s-1990s surveys revealed 778 species distributed across 421 genera and 106 families with 12 (1.5%) listed in the IUCN red list. Notably, 173 species (18.2%) were newly recorded in 2021 and distributed across 148 genera and 58 families. Among these newly recorded species, 21 (2.2%) were listed in the IUCN red list and 13 were found to be endemic to Tanzania. This study significantly enhanced our understanding of the flora of MINAPA and emphasized the importance of conducting regular surveys to update the status of floral resources in PAs, particularly where reports are based on outdated taxonomic nomenclature. These findings will contribute to the advancement of scientific research and management techniques, particularly in the context of ongoing changes in climatic conditions. [ABSTRACT FROM AUTHOR]
Published: 2024
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23. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Author: Sørensen, Erik F., Harris, R. Alan, Zhang, Liye, Raveendran, Muthuswamy, Kuderna, Lukas F.K., Walker, Jerilyn A., Storer, Jessica M., Kuhlwilm, Martin, Fontsere, Claudia, Seshadri, Lakshmi, Bergey, Christina M., Burrell, Andrew S., Bergman, Juraj, Phillips-Conroy, Jane E., Shiferaw, Fekadu, Chiou, Kenneth L., Chuma, Idrissa S., Keyyu, Julius D., Fischer, Julia, Gingras, Marie Claude, Salvi, Sejal, Doddapaneni, Harshavardhan, Schierup, Mikkel H., Batzer, Mark A., Jolly, Clifford J., Knauf, Sascha, Zinner, Dietmar, Farh, Kyle K.H., Marques-Bonet, Tomas, Munch, Kasper, Roos, Christian, and Rogers, Jeffrey
Subjects: Article
Abstract: Baboons (genusPapio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.One-Sentence SummaryGenomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.
Published: 2023

24. The efficacy of alcelaphine herpesvirus-1 (AlHV-1) immunization with the adjuvants Emulsigen® and the monomeric TLR5 ligand FliC in zebu cattle against AlHV-1 malignant catarrhal fever induced by experimental virus challenge

Author: Lankester, Felix, Lugelo, Ahmed, Werling, Dirk, Mnyambwa, Nicholas, Keyyu, Julius, Kazwala, Rudovick, Grant, Dawn, Smith, Sarah, Parameswaran, Nevi, Cleaveland, Sarah, Russell, George, and Haig, David
Published: 2016
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25. Enhanced immunosurveillance for animal morbilliviruses using vesicular stomatitis virus (VSV) pseudotypes

Author: Logan, Nicola, Dundon, William G., Diallo, Adama, Baron, Michael D., James Nyarobi, M., Cleaveland, Sarah, Keyyu, Julius, Fyumagwa, Robert, Hosie, Margaret J., and Willett, Brian J.
Published: 2016
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26. Widespread Treponema pallidum Infection in Nonhuman Primates, Tanzania

Author: Chuma, Idrissa S., Batamuzi, Emmanuel K., Collins, D. Anthony, Fyumagwa, Robert D., Hallmaier-Wacker, Luisa K., Kazwala, Rudovick R., Keyyu, Julius D., Lejora, Inyasi A., Lipende, Iddi F., Luert, Simone, Paciencia, Filipa M.D., Piel, Alexander, Stewart, Fiona A., Zinner, Dietmar, Roos, Christian, and Knauf, Sascha
Subjects: Primates -- Health aspects, Medical research -- Health aspects, Infection -- Research -- Health aspects, Skin -- Health aspects, Antibodies -- Health aspects, Health
Abstract: The geographic distribution of infection with the bacterium Treponema pallidum in nonhuman primates (NHPs) in Africa has been reported to closely match the one seen in human yaws in Africa [...]
Published: 2018
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27. 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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28. 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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29. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation

Author: Jensen, Axel, Swift, Frances, de Vries, Dorien, Beck, Robin M. D., Kuderna, Lukas F. K., Knauf, Sascha, Chuma, Idrissa S., Keyyu, Julius D., Kitchener, Andrew C., Farh, Kyle, Rogers, Jeffrey, Marques-Bonet, Tomas, Detwiler, Kate M., Roos, Christian, Guschanski, Katerina, Jensen, Axel, Swift, Frances, de Vries, Dorien, Beck, Robin M. D., Kuderna, Lukas F. K., Knauf, Sascha, Chuma, Idrissa S., Keyyu, Julius D., Kitchener, Andrew C., Farh, Kyle, Rogers, Jeffrey, Marques-Bonet, Tomas, Detwiler, Kate M., Roos, Christian, and Guschanski, Katerina
Abstract: Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.
Published: 2023
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30. The genomes of the yaws bacterium, Treponema pallidum subsp. pertenue, of nonhuman primate and human origin are not genomically distinct

Author: Janečková, Klára, Roos, Christian, Fedrová, Pavla, Tom, Nikola, Čejková, Darina, Lueert, Simone, Keyyu, Julius D, Chuma, Idrissa S., Knauf, Sascha, Šmajs, David, Janečková, Klára, Roos, Christian, Fedrová, Pavla, Tom, Nikola, Čejková, Darina, Lueert, Simone, Keyyu, Julius D, Chuma, Idrissa S., Knauf, Sascha, and Šmajs, David
Abstract: BACKGROUND: Treponema pallidum subsp. pertenue (TPE) is the causative agent of human yaws. Yaws is currently reported in 13 endemic countries in Africa, southern Asia, and the Pacific region. During the mid-20th century, a first yaws eradication effort resulted in a global 95% drop in yaws prevalence. The lack of continued surveillance has led to the resurgence of yaws. The disease was believed to have no animal reservoirs, which supported the development of a currently ongoing second yaws eradication campaign. Concomitantly, genetic evidence started to show that TPE strains naturally infect nonhuman primates (NHPs) in sub-Saharan Africa. In our current study we tested hypothesis that NHP- and human-infecting TPE strains differ in the previously unknown parts of the genomes. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we determined complete (finished) genomes of ten TPE isolates that originated from NHPs and compared them to TPE whole-genome sequences from human yaws patients. We performed an in-depth analysis of TPE genomes to determine if any consistent genomic differences are present between TPE genomes of human and NHP origin. We were able to resolve previously undetermined TPE chromosomal regions (sequencing gaps) that prevented us from making a conclusion regarding the sequence identity of TPE genomes from NHPs and humans. The comparison among finished genome sequences revealed no consistent differences between human and NHP TPE genomes. CONCLUSION/SIGNIFICANCE: Our data show that NHPs are infected with strains that are not only similar to the strains infecting humans but are genomically indistinguishable from them. Although interspecies transmission in NHPs is a rare event and evidence for current spillover events is missing, the existence of the yaws bacterium in NHPs is demonstrated. While the low risk of spillover supports the current yaws treatment campaign, it is of importance to continue yaws surveillance in areas where NHPs are naturally infected wi
Published: 2023

31. 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

32. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Author: Fundación la Caixa, Vienna Science and Technology Fund, German Research Foundation, Novo Nordisk Foundation, Baylor College of Medicine, European Research Council, European Commission, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Sørensen, Erik F., Harris, R. Alan, Zhang, Liye, Raveendran, Muthuswamy, Kuderna, Lukas F. K., Walker, Jerilyn A., Storer, Jessica M., Kuhlwilm, Martin, Fontsere, Claudia, Seshadri, Lakshmi, Bergey, Christina M., Burrell, Andrew S., Bergman, Juraj, Phillips-Conroy, Jane E., Shiferaw, Fekadu, Chiou, Kenneth L., Chuma, Idrissa S., Keyyu, Julius D., Fischer, Julia, Gingras, Marie-Claude, Salvi, Sejal, Doddapaneni, Harshavardhan, Schierup, Mikkel Heide, Batzer, Mark A., Jolly, Clifford J., Knauf, Sascha, Zinner, Dietmar, Farh, Kyle Kai-How, Marqués-Bonet, Tomàs, Munch, Kasper, Roos, Christian, Rogers, Jeffrey, Fundación la Caixa, Vienna Science and Technology Fund, German Research Foundation, Novo Nordisk Foundation, Baylor College of Medicine, European Research Council, European Commission, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Sørensen, Erik F., Harris, R. Alan, Zhang, Liye, Raveendran, Muthuswamy, Kuderna, Lukas F. K., Walker, Jerilyn A., Storer, Jessica M., Kuhlwilm, Martin, Fontsere, Claudia, Seshadri, Lakshmi, Bergey, Christina M., Burrell, Andrew S., Bergman, Juraj, Phillips-Conroy, Jane E., Shiferaw, Fekadu, Chiou, Kenneth L., Chuma, Idrissa S., Keyyu, Julius D., Fischer, Julia, Gingras, Marie-Claude, Salvi, Sejal, Doddapaneni, Harshavardhan, Schierup, Mikkel Heide, Batzer, Mark A., Jolly, Clifford J., Knauf, Sascha, Zinner, Dietmar, Farh, Kyle Kai-How, Marqués-Bonet, Tomàs, Munch, Kasper, Roos, Christian, and Rogers, Jeffrey
Abstract: [INTRODUCTION] As a widespread but comparatively young clade of six parapatric species, the baboons (Papio sp.) exemplify a frequently observed pattern of mammalian diversity. In particular, they provide analogs for the population structure of the multibranched prehuman lineage that occupied a similar geographic range before the hegemony of “modern” humans, Homo sapiens. Despite phenotypic and genetic differences, interspecies hybridization has been described between baboons at several locations, and population relationships based on mitochondrial DNA (mtDNA) do not correspond with relationships based on phenotype. These previous studies captured the broad outlines of baboon population genetic structure and evolutionary history but necessarily used data that were limited in genomic and geographical coverage and therefore could not adequately document inter- and intrapopulation variation. In this study, we analyzed whole-genome sequences of 225 baboons representing all six species and 19 geographic sites, with 18 local populations represented by multiple individuals., [RATIONALE] Recent studies have identified several mammalian species groups in which genetically distinct lineages have hybridized to generate complex reticulate phylogenies. Baboons provide a valuable context for studying processes generating such population and phylogenetic complexity because extant parapatric species form hybrid zones in several regions of Africa, allowing for direct observation of ongoing introgression. Furthermore, prior studies of nuclear and mtDNA and phenotypic diversity have demonstrated gene flow among differentiated lineages but were unable to develop the detailed picture of process and history that is now possible using whole-genome sequences and modern computational methods. To address these questions, we designed a study that would provide a more fine-grained picture of recent and ancient genetic reticulation by comparing phenotypes and autosomal, X and Y chromosomal, and mtDNA sequences, along with polymorphic insertions of repetitive elements across multiple baboon populations., [RESULTS] Using deep whole-genome sequence data from 225 baboons representing multiple populations, we identified several previously unknown geographic sites of gene flow between genetically distinct populations. We report that yellow baboons (P. cynocephalus) from western Tanzania are the first nonhuman primate found to have received genetic input from three distinct lineages. We compared the ancestry shared among individuals, estimated separately from the X chromosome and autosomes, to distinguish shared ancestry due to ancestral population relationships from coancestry as a result of recent male-biased immigration and gene flow. This reveals directionality and sex bias of recent gene flow in several locations. Analyses of population differences within species quantified different degrees of interspecies introgression among populations with an essentially identical phenotype., [CONCLUSION] The population genetic structure and history of introgression among baboon lineages are even more complex than predicted from observed phenotypic diversity and prior studies of limited genetic data. Single populations can carry genetic contributions from more than two ancestral sources. Populations that appear homogeneous on the basis of observable phenotype can display different levels of interspecies introgression. The evolutionary dynamics and current structure of baboon population diversity indicate that other mammals displaying differentiated and geographically separate species may also have more-complex histories than anticipated. This may also be true for the morphologically defined hominin taxa from the past 4 million years.
Published: 2023

33. 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

34. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation

Author: Swedish National Infrastructure for Computing, Uppsala University, Swedish Research Council, Marqués-Bonet, Tomàs [0000-0002-5597-3075], Jensen, Axel, Swift, Frances, Vries, Dorien de, Beck, Robin M. D., Kuderna, Lukas F. K., Knauf, Sascha, Chuma, Idrissa S., Keyyu, Julius D., Kitchener, Andrew C., Farh, Kyle Kai-How, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Detwiler, Kate M., Roos, Christian, Guschanski, Katerina, Swedish National Infrastructure for Computing, Uppsala University, Swedish Research Council, Marqués-Bonet, Tomàs [0000-0002-5597-3075], Jensen, Axel, Swift, Frances, Vries, Dorien de, Beck, Robin M. D., Kuderna, Lukas F. K., Knauf, Sascha, Chuma, Idrissa S., Keyyu, Julius D., Kitchener, Andrew C., Farh, Kyle Kai-How, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Detwiler, Kate M., Roos, Christian, and Guschanski, Katerina
Abstract: Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.
Published: 2023

35. 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

36. Strain diversity of Treponema pallidum subsp. pertenue suggests rare interspecies transmission in African nonhuman primates

Author: Chuma, Idrissa S., Roos, Christian, Atickem, Anagaw, Bohm, Torsten, Anthony Collins, D., Grillová, Linda, Hallmaier-Wacker, Luisa K., Kazwala, Rudovick R., Keyyu, Julius D., Lüert, Simone, Maloueki, Ulrich, Oppelt, Jan, Petrželková, Klára J., Piel, Alexander, Stewart, Fiona A., Šmajs, David, and Knauf, Sascha
Published: 2019
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37. Optimization and evaluation of a non-invasive tool for peste des petits ruminants surveillance and control

Author: Bataille, Arnaud, Kwiatek, Olivier, Belfkhi, Salima, Mounier, Lucile, Parida, Satya, Mahapatra, Mana, Caron, Alexandre, Chubwa, Chobi Clement, Keyyu, Julius, Kock, Richard, Jones, Bryony A., and Libeau, Geneviève
Published: 2019
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38. Viability assessment of the Wami-Mbiki Game Reserve to Nyerere National Park wildlife corridor in southern Tanzania

Author: Bukombe, John, primary, Marealle, Wilfred, additional, Kimaro, Jerome, additional, Kija, Hamza, additional, Kavana, Pius, additional, Kakengi, Victor, additional, Nindi, Justice, additional, Keyyu, Julius, additional, Ntalwila, Janemary, additional, Kilimba, Neema, additional, Bwenge, Fidelis, additional, Nkwabi, Ally, additional, Lowassa, Asanterabi, additional, Sanare, John, additional, Mwita, Machoke, additional, Leweri, Cecilia, additional, Kohi, Edward, additional, Mangewa, Lazaro, additional, Juma, Ramadhani, additional, Okick, Raymond, additional, and Lobora, Alexander, additional
Published: 2022
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39. Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue

Author: Knauf, Sascha, Gogarten, Jan F., Schuenemann, Verena J., De Nys, Hélène M., Düx, Ariane, Strouhal, Michal, Mikalová, Lenka, Bos, Kirsten I., Armstrong, Roy, Batamuzi, Emmanuel K., Chuma, Idrissa S., Davoust, Bernard, Diatta, Georges, Fyumagwa, Robert D., Kazwala, Reuben R., Keyyu, Julius D., Lejora, Inyasi A. V., Levasseur, Anthony, Liu, Hsi, Mayhew, Michael A., Mediannikov, Oleg, Raoult, Didier, Wittig, Roman M., Roos, Christian, Leendertz, Fabian H., Šmajs, David, Nieselt, Kay, Krause, Johannes, and Calvignac-Spencer, Sébastien
Published: 2018
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40. Spillover of peste des petits ruminants virus from domestic to wild ruminants in the serengeti ecosystem, tanzania

Author: Mahapatra, Mana, Sayalel, Kuya, Muniraju, Murali, Eblate, Ernest, Fyumagwa, Robert, Shilinde, Ligge, Mdaki, Maulid, Keyyu, Julius, Panda, Satya, and Kock, Richard
Subjects: Genomics -- Research, Ecosystems -- Research, Goats -- Research -- Genetic aspects, Health
Abstract: Peste des petits ruminants (PPR) is caused by peste des petits ruminants virus (PPRV), a member of the genus Morbillivirus in the family Paramyxoviridae, and primarily affects sheep and goats. [...]
Published: 2015
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41. Mito-phylogenetic relationship of the new subspecies of gentle monkey <i>Cercopithecus mitis manyaraensis</i>, Butynski & De Jong, 2020

Author: Zinner, Dietmar, primary, Knauf, Sascha, additional, Chuma, Idrissa S., additional, Butynski, Thomas M., additional, De Jong, Yvonne A., additional, Keyyu, Julius D., additional, Kaitila, Rehema, additional, and Roos, Christian, additional
Published: 2022
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42. Mito-phylogenetic relationship of the new subspecies of gentle monkey Cercopithecus mitis manyaraensis, Butynski & De Jong, 2020

Author: Zinner, Dietmar, Knauf, Sascha, Chuma, Idrissa S., Butynski, Thomas M., Jong, Yvonne A., Keyyu, Julius D., Kaitila, Rehema, and Roos, Christian
Abstract: In 2020, a new subspecies was described in the Cercopithecus mitis complex, the Manyara monkey C. m. manyaraensis, Butynski & De Jong, 2020. The internal taxonomy of this species complex is still debated, and the phylogenetic relationships among the taxa are unclear. Here we provide the first mitochondrial sequence data for C. m. manyaraensis to determine its position within the mitochondrial phylogeny of C. mitis. This subspecies clusters within the youngest (internal divergences between 1.01 and 0.42 Ma) of three main taxonomic clades of C. mitis. Its sister lineages are C. m. boutourlinii (Ethiopia), C. m. albotorquatus (Kenya and Somalia), C. m. albogularis (Kenya and Tanzania), and C. m. monoides (Tanzania and Mozambique). In general, the phylogenetic tree of C. mitis based on mitochondrial sequence data indicates several paraphyletic relationships within the C. mitis complex. As in other African cercopithecines (e.g. Papio and Chlorocebus), these data are suitable for reconstructing historic biogeographical patterns, but they are only of limited value for delimitating taxa.
Published: 2022

43. 26. The Role of Research in Conservation and the Future of the Serengeti / Anthony R. E. Sinclair, Julius D. Keyyu, Simon A. R. Mduma, Mtango Mtahiko, Emily Kisamo, J. Grant C. Hopcraft, John M. Fryxell, Kristine L. Metzger, and Markus Borner

Author: Sinclair, Anthony R. E., primary, Keyyu, Julius D., additional, Mduma, Simon A. R., additional, Mtahiko, Mtango, additional, Kisamo, Emily, additional, Hopcraft, J. Grant C., additional, Fryxell, John M., additional, Metzger, Kristine L., additional, and Borner, Markus, additional
Published: 2015
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44. One Health: a concept led by Africa, with global benefits

Author: Kamani, Titus Mlengeya, Kazwala, Rudovick, Mfinanga, Sayoki, Haydon, Dan, Keyyu, Julius, Lankester, Felix, and Buza, Joram
Published: 2015
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45. Evaluating the Potential for the Environmentally Sustainable Control of Foot and Mouth Disease in Sub-Saharan Africa

Author: Ferguson, Kenneth J., Cleaveland, Sarah, Haydon, Daniel Thomas, Caron, Alexandre, Kock, Richard A., Lembo, Tiziana, Hopcraft, J. Grant C., Chardonnet, Bertrand, Nyariki, Thomas, Keyyu, Julius, Paton, David James, and Kivaria, Fredrick Mathias
Published: 2013
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46. Peste des Petits Ruminants Virus Infection at the Wildlife–Livestock Interface in the Greater Serengeti Ecosystem, 2015–2019

Author: Jones, Bryony A., primary, Mahapatra, Mana, additional, Mdetele, Daniel, additional, Keyyu, Julius, additional, Gakuya, Francis, additional, Eblate, Ernest, additional, Lekolool, Isaac, additional, Limo, Campaign, additional, Ndiwa, Josephine N., additional, Hongo, Peter, additional, Wanda, Justin S., additional, Shilinde, Ligge, additional, Mdaki, Maulid, additional, Benfield, Camilla, additional, Parekh, Krupali, additional, Mayora Neto, Martin, additional, Ndeereh, David, additional, Misinzo, Gerald, additional, Makange, Mariam R., additional, Caron, Alexandre, additional, Bataille, Arnaud, additional, Libeau, Geneviève, additional, Guendouz, Samia, additional, Swai, Emanuel S., additional, Nyasebwa, Obed, additional, Koyie, Stephen L., additional, Oyas, Harry, additional, Parida, Satya, additional, and Kock, Richard, additional
Published: 2021
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47. The Role of Research in Conservation and the Future of the Serengeti

Author: Sinclair, Anthony R. E., author, Keyyu, Julius D., author, Mduma, Simon A. R., author, Mtahiko, Mtango, author, Kisamo, Emily, author, Hopcraft, J. Grant C., author, Fryxell, John M., author, Metzger, Kristine L., author, and Borner, Markus, author
Published: 2015
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48. Peste des Petits Ruminants virus infection at the wildlife-livestock interface in the greater serengeti ecosystem, 2015-2019

Author: Jones, Bryony Anne, Mahapatra, Mana, Mdetele, Daniel, Keyyu, Julius, Gakuya, Francis, Eblate, Ernest, Lekolool, Isaac, Limo, Campaign, Ndiwa, Josephine N, Hongo, Peter, Wanda, Justin, S., Shilinde, Ligge, Mdaki, Maulid, Benfield, Camilla T.O., Parekh, Krupali, Neto, Martin Mayora, Ndeereh, David, Misinzo, Gerald, Makange, Mariam R., Caron, Alexandre, Bataille, Arnaud, Libeau, Geneviève, Guendouz, Samia, Swai, Emmanuel, Nyasebwa, Obed, Koyie, Stephen L., Oyas, Harry, Parida, Satya, Kock, Richard, Jones, Bryony Anne, Mahapatra, Mana, Mdetele, Daniel, Keyyu, Julius, Gakuya, Francis, Eblate, Ernest, Lekolool, Isaac, Limo, Campaign, Ndiwa, Josephine N, Hongo, Peter, Wanda, Justin, S., Shilinde, Ligge, Mdaki, Maulid, Benfield, Camilla T.O., Parekh, Krupali, Neto, Martin Mayora, Ndeereh, David, Misinzo, Gerald, Makange, Mariam R., Caron, Alexandre, Bataille, Arnaud, Libeau, Geneviève, Guendouz, Samia, Swai, Emmanuel, Nyasebwa, Obed, Koyie, Stephen L., Oyas, Harry, Parida, Satya, and Kock, Richard
Abstract: Peste des petits ruminants (PPR) is a viral disease of goats and sheep that occurs in Africa, the Middle East and Asia with a severe impact on livelihoods and livestock trade. Many wild artiodactyls are susceptible to PPR virus (PPRV) infection, and some outbreaks have threatened endangered wild populations. The role of wild species in PPRV epidemiology is unclear, which is a knowledge gap for the Global Strategy for the Control and Eradication of PPR. These studies aimed to investigate PPRV infection in wild artiodactyls in the Greater Serengeti and Amboseli ecosystems of Kenya and Tanzania. Out of 132 animals purposively sampled in 2015–2016, 19.7% were PPRV seropositive by ID Screen PPR competition enzyme-linked immunosorbent assay (cELISA; IDvet, France) from the following species: African buffalo, wildebeest, topi, kongoni, Grant's gazelle, impala, Thomson's gazelle, warthog and gerenuk, while waterbuck and lesser kudu were seronegative. In 2018–2019, a cross-sectional survey of randomly selected African buffalo and Grant's gazelle herds was conducted. The weighted estimate of PPRV seroprevalence was 12.0% out of 191 African buffalo and 1.1% out of 139 Grant's gazelles. All ocular and nasal swabs and faeces were negative by PPRV real-time reverse transcription-polymerase chain reaction (RT-qPCR). Investigations of a PPR-like disease in sheep and goats confirmed PPRV circulation in the area by rapid detection test and/or RT-qPCR. These results demonstrated serological evidence of PPRV infection in wild artiodactyl species at the wildlife–livestock interface in this ecosystem where PPRV is endemic in domestic small ruminants. Exposure to PPRV could be via spillover from infected small ruminants or from transmission between wild animals, while the relatively low seroprevalence suggests that sustained transmission is unlikely. Further studies of other major wild artiodactyls in this ecosystem are required, such as impala, Thomson's gazelle and wildebeest.
Published: 2021

49. Molecular detection of Coxiella burnetii infection in small mammals from Moshi Rural and Urban Districts, northern Tanzania

Author: Theonest, Ndyetabura O., primary, Carter, Ryan W., additional, Kasagama, Elizabeth, additional, Keyyu, Julius D., additional, Shirima, Gabriel M., additional, Tarimo, Rigobert, additional, Thomas, Kate M., additional, Wheelhouse, Nick, additional, Maro, Venance P., additional, Haydon, Daniel T., additional, Buza, Joram J., additional, Allan, Kathryn J., additional, and Halliday, Jo E.B., additional
Published: 2020
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50. Modified netting technique for capturing gazelles in Serengeti, Ngorongoro and Loliondo, Tanzania

Author: Mdetele, Daniel, primary, Misinzo, Gerald, additional, Komba, Erick, additional, Shemanche, Justin, additional, Eblate, Ernest, additional, Mdaki, Maulid, additional, Keyyu, Julius, additional, and Kock, Richard, additional
Published: 2020
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