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1. Identification of constrained sequence elements across 239 primate genomes

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

Author: Webb, Shasta E., Orkin, Joseph D., Williamson, Rachel E., and Melin, Amanda D.
Published: 2023
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3. Wild capuchin monkeys as a model system for investigating the social and ecological determinants of ageing.

Author: Campos, Fernando A., Wikberg, Eva C., Orkin, Joseph D., Park, Yeonjoo, Snyder-Mackler, Noah, Cheves Hernandez, Saul, Lopez Navarro, Ronald, Fedigan, Linda M., Gurven, Michael, Higham, James P., Jack, Katharine M., and Melin, Amanda D.
Subjects: ANIMAL models for aging, CAPUCHIN monkeys, GERONTOLOGY, BODY size, PRIMATES
Abstract: Studying biological ageing in animal models can circumvent some of the confounds exhibited by studies of human ageing. Ageing research in non-human primates has provided invaluable insights into human lifespan and healthspan. Yet data on patterns of ageing from wild primates remain relatively scarce, centred around a few populations of catarrhine species. Here, we introduce the white-faced capuchin, a long-lived platyrrhine primate, as a promising new model system for ageing research. Like humans, capuchins are highly social, omnivorous generalists, whose healthspan and lifespan relative to body size exceed that of other non-human primate model species. We review recent insights from capuchin ageing biology and outline our expanding, integrative research programme that combines metrics of the social and physical environments with physical, physiological and molecular hallmarks of ageing across the natural life courses of multiple longitudinally tracked individuals. By increasing the taxonomic breadth of well-studied primate ageing models, we generate new insights, increase the comparative value of existing datasets to geroscience and work towards the collective goal of developing accurate, non-invasive and reliable biomarkers with high potential for standardization across field sites and species, enhancing the translatability of primate studies. This article is part of the discussion meeting issue 'Understanding age and society using natural populations'. [ABSTRACT FROM AUTHOR]
Published: 2024
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4. 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

5. 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

6. Landscape and conservation genetics of western black crested gibbons (Nomascus concolor) in China.

Author: Orkin, Joseph D., He, Kai, Hu, Nai‐qing, Guan, Zhen‐hua, Huang, Bei, Yang, Chunyan, Fan, Peng‐fei, and Jiang, Xuelong
Subjects: *CONSERVATION genetics, *FOREST degradation, *GENETIC variation, *BROADLEAF forests, *MICROSATELLITE repeats, *INBREEDING
Abstract: Despite decades of field study, very little is known about the molecular ecology of gibbons, particularly as it relates to their ability to disperse across degraded and fragmentary landscapes. The critically endangered western black crested gibbon (Nomascus concolor) has been reduced to a small, fragmented population with about 1300 individuals. In the largest population genetic study of free‐ranging gibbons to date, we sampled 47 of these gibbons from 13 sites in China and generated 15 polymorphic autosomal microsatellite markers. We identify three population clusters of N. concolor in Yunnan centered in 1) the Wuliang and Ailao Mountains, 2) the Yongde Daxueshan Mountains, and 3) an isolated remnant near the border with Vietnam. Within the Wuliang Mountains, we identified four subclusters, three of which are bounded by high‐altitude rhododendron forest, and one that is isolated from the main population by ~2 km of degraded forest and pasture. Least‐cost path analysis and isolation by resistance modeling demonstrates that the population genetic distances among gibbons in Wuliangshan National Nature Reserve are significantly correlated with geographic paths that avoid use of high‐altitude rhododendron forest in favor of evergreen broadleaf forest. Although these gibbons have likely undergone reductions in heterozygosity from recent consanguineous mating, we suggest that their active avoidance of inbreeding on the population level maintains higher than expected levels of genetic diversity. This research provides new insights into how gibbons interact with heterogeneous environments and expands our understanding of their molecular ecology and conservation genetics. [ABSTRACT FROM AUTHOR]
Published: 2024
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7. Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

Author: Krueger, Johanna, primary, Fong Zazueta, Ricardo, additional, Alba, David M., additional, Aymerich, Xenia, additional, Beck, Robin M.D., additional, Cappellini, Enrico, additional, Carrillo Martin, Guillermo, additional, Cirilli, Omar, additional, Clark, Nathan, additional, Cornejo, Omar E., additional, Farh, Kyle, additional, Ferrandez-Peral, Luis, additional, Juan, David, additional, Kelley, Joanna L., additional, Kuderna, Lukas F. K., additional, Little, Jordan, additional, Orkin, Joseph D., additional, Paterson, Ryan S., additional, Pawar, Harvinder, additional, Marques-Bonet, Tomas, additional, and Lizano, Esther, additional
Published: 2024
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8. Fermentation and the Ethnobiology of Microbial Entanglement

Author: Flachs, Andrew and Orkin, Joseph D.
Published: 2019

9. Promise and limitations of 18S genetic screening of extracted fecal DNA from wild capuchins

Author: Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Alberta Innovates Health Solutions, Queen Elizabeth II Graduate Scholarships in Science and Technology (Canada), Alberta Children's Hospital Research Institute, O'Brien Centre Summer Studentships, National Science Foundation (US), Fundación la Caixa, European Commission, Orkin, Joseph D. [0000-0001-6922-2072], Pinto, Swellan Luciann, Carvalho Henriquez, Megan, Cheves Hernández, Saúl, Duytschaever, Gwen, Wit, Janneke, Avramenko, Russell William, Gilleard, John Stuart, Orkin, Joseph D., Melin, Amanda D., Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Alberta Innovates Health Solutions, Queen Elizabeth II Graduate Scholarships in Science and Technology (Canada), Alberta Children's Hospital Research Institute, O'Brien Centre Summer Studentships, National Science Foundation (US), Fundación la Caixa, European Commission, Orkin, Joseph D. [0000-0001-6922-2072], Pinto, Swellan Luciann, Carvalho Henriquez, Megan, Cheves Hernández, Saúl, Duytschaever, Gwen, Wit, Janneke, Avramenko, Russell William, Gilleard, John Stuart, Orkin, Joseph D., and Melin, Amanda D.
Abstract: Genomic screening of fecal DNA provides insight into diet, parasite infection dynamics, and other aspects of the ecology and pathogens of wild populations. Here, we amplify and sequence the V4/V5 regions of the eukaryotic 18S ribosomal RNA gene from fecal DNA of wild capuchin monkeys (Cebus imitator). We collected 94 fecal samples from 26 individuals, each sampled 1-4 times across a 19-month period and examined the eukaryotic diversity in 63 of these samples which had sufficient numbers and quality of reads during downstream analyses. We found a total of 234 distinct amplicon sequence variants (ASVs) classified as Eukaryotes in our samples. Of these, 66 were assigned to the phylum Nematoda. 64 ASVs are from taxa that possibly parasitize monkeys or their food items: 33 were assigned to lungworms (Superfamily Metastrongyloidae; genus Angiostrongylus), two to the genus Strongyloides, and one to the genus Austrostrongylus. The remaining 28 ASVs were assigned to nematodes that likely parasitize plants and/or invertebrates that the monkeys consume. Taken together with past dietary and coprological study of the same primate population, our results suggest that invertebrate consumption and parasitic infection, especially by lungworms, is common and widespread among this population of wild monkeys. We also discuss limitations of our approach, including the amplification of off-target ASVs, and make suggestions for future research. Overall, 18S screening shows promise for identifying various components of the capuchin gastrointestinal eukaryotic ecosystem, including parasitic helminths, and its utility will increase with the improvement of genetic databases.
Published: 2023

10. 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

11. Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques

Author: Janiak, Mareike C., Montague, Michael J., Villamil, Catalina I., Stock, Michala K., Trujillo, Amber E., DePasquale, Allegra N., Orkin, Joseph D., Bauman Surratt, Samuel E., Gonzalez, Olga, Platt, Michael L., Martínez, Melween I., Antón, Susan C., Dominguez-Bello, Maria Gloria, Melin, Amanda D., and Higham, James P.
Published: 2021
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12. On pickles: biological and sociocultural links between fermented foods and the human gut microbiome

Author: Flachs, Andrew and Orkin, Joseph D.
Published: 2021
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13. 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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14. Seasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest

Author: Orkin, Joseph D., Campos, Fernando A., Myers, Monica S., Cheves Hernandez, Saul E., Guadamuz, Adrián, and Melin, Amanda D.
Published: 2019
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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. 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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18. A global catalog of whole-genome diversity from 233 primate species

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

19. 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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20. 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

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

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

22. 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

23. Duplication and parallel evolution of the pancreatic ribonuclease gene (RNASE1) in folivorous non-colobine primates, the howler monkeys (Alouatta spp.)

Author: Janiak, Mareike C., Burrell, Andrew S., Orkin, Joseph D., and Disotell, Todd R.
Published: 2019
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24. Variation in predicted COVID-19 risk among lemurs and lorises

Author: Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Natural Environment Research Council (UK), Ministerio de Economía y Competitividad (España), Instituto de Salud Carlos III, European Commission, Generalitat de Catalunya, European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Obra Social la Caixa, Melin, Amanda D. [0000-0002-0612-2514], Orkin, Joseph D. [0000-0001-6922-2072], Janiak, Mareike C. [0000-0002-7759-2556], Kuderna, Lukas F. K. [0000-0002-9992-9295], Marrone, Frank [0000-0002-1735-0723], Arora, Paramjit S. [0000-0001-5315-401X], Higham, James P. [0000-0002-1133-2030], Melin, Amanda D., Orkin, Joseph D., Janiak, Mareike C., Valenzuela, Alejandro, Kuderna, Lukas F. K., Marrone, Frank, Ramangason, Hasinala, Horvath, Julie E., Roos, Christian, Kitchener, Andrew C., Khor, Chiea Chuen, Lim, Weng Khong, Lee, Jessica G. H., Tan, Patrick, Umapathy, Govindhaswamy, Raveendran, Muthuswamy, Harris, R. Alan, Gut, Ivo, Gut, Marta, Lizano, Esther, Nadler, Tilo, Zinner, Dietmar, Johnson, Steig E., Jarvis, Erich D., Fedrigo, Olivier, Wu, Dongdong, Zhang, Guojie, Farh, Kyle Kai-How, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Navarro, Arcadi, Juan, David, Arora, Paramjit S., Higham, James P., Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Natural Environment Research Council (UK), Ministerio de Economía y Competitividad (España), Instituto de Salud Carlos III, European Commission, Generalitat de Catalunya, European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Obra Social la Caixa, Melin, Amanda D. [0000-0002-0612-2514], Orkin, Joseph D. [0000-0001-6922-2072], Janiak, Mareike C. [0000-0002-7759-2556], Kuderna, Lukas F. K. [0000-0002-9992-9295], Marrone, Frank [0000-0002-1735-0723], Arora, Paramjit S. [0000-0001-5315-401X], Higham, James P. [0000-0002-1133-2030], Melin, Amanda D., Orkin, Joseph D., Janiak, Mareike C., Valenzuela, Alejandro, Kuderna, Lukas F. K., Marrone, Frank, Ramangason, Hasinala, Horvath, Julie E., Roos, Christian, Kitchener, Andrew C., Khor, Chiea Chuen, Lim, Weng Khong, Lee, Jessica G. H., Tan, Patrick, Umapathy, Govindhaswamy, Raveendran, Muthuswamy, Harris, R. Alan, Gut, Ivo, Gut, Marta, Lizano, Esther, Nadler, Tilo, Zinner, Dietmar, Johnson, Steig E., Jarvis, Erich D., Fedrigo, Olivier, Wu, Dongdong, Zhang, Guojie, Farh, Kyle Kai-How, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Navarro, Arcadi, Juan, David, Arora, Paramjit S., and Higham, James P.
Abstract: The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.
Published: 2021

25. Variation in predicted COVID-19 risk among lemurs and lorises

Author: Melin, Amanda D., Orkin, Joseph D., Janiak, Mareike C., Valenzuela, Alejandro, Kuderna, Lukas F. K., Marrone, Frank, Ramangason, Hasinala, Horvath, Julie E., Roos, Christian, Kitchener, Andrew C., Khor, Chiea Chuen, Lim, Weng Khong, Lee, Jessica G. H., Tan, Patrick, Umapathy, Govindhaswamy, Raveendran, Muthuswamy, Harris, R. Alan, Gut, Ivo, Gut, Marta, Lizano, Esther, Nadler, Tilo, Zinner, Dietmar, Johnson, Steig E., Jarvis, Erich D., Fedrigo, Olivier, Wu, Dongdong, Zhang, Guojie, Farh, Kyle Kai-How, Rogers, Jeffrey, Marqués-Bonet, Tomàs, Navarro, Arcadi, Juan, David, Arora, Paramjit S., Higham, James P., Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs, Natural Environment Research Council (UK), Ministerio de Economía y Competitividad (España), Instituto de Salud Carlos III, European Commission, Generalitat de Catalunya, European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Fundación 'la Caixa', Melin, Amanda D. [0000-0002-0612-2514], Orkin, Joseph D. [0000-0001-6922-2072], Janiak, Mareike C. [0000-0002-7759-2556], Kuderna, Lukas F. K. [0000-0002-9992-9295], Marrone, Frank [0000-0002-1735-0723], Arora, Paramjit S. [0000-0001-5315-401X], Higham, James P. [0000-0002-1133-2030], Melin, Amanda D., Orkin, Joseph D., Janiak, Mareike C., Kuderna, Lukas F. K., Marrone, Frank, Arora, Paramjit S., and Higham, James P.
Abstract: Versión editorial disponible en: http://hdl.handle.net/10261/239013, The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2., ADM is supported by the Natural Sciences and Engineering Research Council of Canada (NSERC Discovery Grant) and Canada Research Chairs Program. MCJ’s postdoctoral appointment is supported by funding from the Natural Environment Research Council (NERC NE/T000341/1). IG and MG acknowledge the support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III and the 2014–2020 Smart Growth Operating Program, to the EMBL partnership and cofinancing with the European Regional Development Fund (MINECO/FEDER, BIO2015-71792-P). We also acknowledge the support of the Centro de Excelencia Severo Ochoa, and the Generalitat de Catalunya through the Departament de Salut, Departament d’Empresa i Coneixement and the CERCA Programme. TMB is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 864203), BFU2017-86471-P (MINECO/FEDER, UE), “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M), Howard Hughes International Early Career, Obra Social "La Caixa" and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). PSA thanks the National Institutes of Health (R35GM130333) for financial support. E.L is supported by CGL2017- 82654-P (MINECO/FEDER,UE). EDJ and OF's contributions were supported by funds from Howard Hughes Medical Institute and the Rockefeller University. Chris Smith drew the images for Figure 1. The authors would like to thank the Veterinary and Zoology staff at Wildlife Reserves Singapore for their help in obtaining the tissue samples, as well as the Lee Kong Chian Natural History Museum for storage and provision of the tissue samples.
Published: 2021

26. Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics

Author: National Institutes of Health (US), Storer, Jessica M., Walker, Jerilyn A., Rockwell, Catherine E., Mores, Grayce, Beckstrom, Thomas O., Orkin, Joseph D., Melin, Amanda D., Phillips, Kimberley A., Roos, Christian, Batzer, Mark A., National Institutes of Health (US), Storer, Jessica M., Walker, Jerilyn A., Rockwell, Catherine E., Mores, Grayce, Beckstrom, Thomas O., Orkin, Joseph D., Melin, Amanda D., Phillips, Kimberley A., Roos, Christian, and Batzer, Mark A.
Abstract: Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships.
Published: 2022

27. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

Author: Fundación la Caixa, European Commission, European Research Council, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Generalitat de Catalunya, Palmada-Flores, Marc, Orkin, Joseph D., Haase, Bettina, Mountcastle, Jacquelyn, Bertelsen, Mads F., Fedrigo, Olivier, Kuderna, Lukas F. K., Jarvis, Erich D., Marqués-Bonet, Tomàs, Fundación la Caixa, European Commission, European Research Council, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Generalitat de Catalunya, Palmada-Flores, Marc, Orkin, Joseph D., Haase, Bettina, Mountcastle, Jacquelyn, Bertelsen, Mads F., Fedrigo, Olivier, Kuderna, Lukas F. K., Jarvis, Erich D., and Marqués-Bonet, Tomàs
Abstract: Background: The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship species and widespread publicity in the popular media. Unfortunately, a recent population decline has resulted in the census population decreasing to <2,500 individuals in the wild, and the species's classification as an endangered species by the IUCN. As is the case for most strepsirrhine primates, only a limited amount of genomic research has been conducted on L. catta, in part owing to the lack of genomic resources. Results: We generated a new high-quality reference genome assembly for L. catta (mLemCat1) that conforms to the standards of the Vertebrate Genomes Project. This new long-read assembly is composed of Pacific Biosciences continuous long reads (CLR data), Optical Mapping Bionano reads, Arima HiC data, and 10X linked reads. The contiguity and completeness of the assembly are extremely high, with scaffold and contig N50 values of 90.982 and 10.570 Mb, respectively. Additionally, when compared to other high-quality primate assemblies, L. catta has the lowest reported number of Alu elements, which results predominantly from a lack of AluS and AluY elements. Conclusions: mLemCat1 is an excellent genomic resource not only for the ring-tailed lemur community, but also for other members of the Lemuridae family, and is the first very long read assembly for a strepsirrhine.
Published: 2022

28. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

Author: Palmada-Flores, Marc, Orkin, Joseph D., Haase, Bettina, Mountcastle, Jacquelyn, Bertelsen, Mads F., Fedrigo, Olivier, Kuderna, Lukas F.K., Jarvis, Erich D., Marques-Bonet, Tomas, Palmada-Flores, Marc, Orkin, Joseph D., Haase, Bettina, Mountcastle, Jacquelyn, Bertelsen, Mads F., Fedrigo, Olivier, Kuderna, Lukas F.K., Jarvis, Erich D., and Marques-Bonet, Tomas
Abstract: Background: The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship species and widespread publicity in the popular media. Unfortunately, a recent population decline has resulted in the census population decreasing to <2,500 individuals in the wild, and the species's classification as an endangered species by the IUCN. As is the case for most strepsirrhine primates, only a limited amount of genomic research has been conducted on L. catta, in part owing to the lack of genomic resources. Results: We generated a new high-quality reference genome assembly for L. catta (mLemCat1) that conforms to the standards of the Vertebrate Genomes Project. This new long-read assembly is composed of Pacific Biosciences continuous long reads (CLR data), Optical Mapping Bionano reads, Arima HiC data, and 10X linked reads. The contiguity and completeness of the assembly are extremely high, with scaffold and contig N50 values of 90.982 and 10.570 Mb, respectively. Additionally, when compared to other high-quality primate assemblies, L. catta has the lowest reported number of Alu elements, which results predominantly from a lack of AluS and AluY elements. Conclusions: MLemCat1 is an excellent genomic resource not only for the ring-tailed lemur community, but also for other members of the Lemuridae family, and is the first very long read assembly for a strepsirrhine.
Published: 2022

29. Population and Conservation Status of Indochinese Gray Langurs (Trachypithecus crepusculus) in the Wuliang Mountains, Jingdong, Yunnan, China

Author: Ma, Chi, Luo, Zhonghua, Liu, Changming, Orkin, Joseph D., Xiao, Wen, and Fan, Pengfei
Published: 2015
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30. Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics

Author: Storer, Jessica M., primary, Walker, Jerilyn A., additional, Rockwell, Catherine E., additional, Mores, Grayce, additional, Beckstrom, Thomas O., additional, Orkin, Joseph D., additional, Melin, Amanda D., additional, Phillips, Kimberley A., additional, Roos, Christian, additional, and Batzer, Mark A., additional
Published: 2022
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31. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

Author: Palmada-Flores, Marc, primary, Orkin, Joseph D, additional, Haase, Bettina, additional, Mountcastle, Jacquelyn, additional, Bertelsen, Mads F, additional, Fedrigo, Olivier, additional, Kuderna, Lukas F K, additional, Jarvis, Erich D, additional, and Marques-Bonet, Tomas, additional
Published: 2022
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32. Activity budget and gut microbiota remain largely consistent across reproductive states in wild, female capuchin monkeys

Author: Webb, Shasta E., primary, Orkin, Joseph D., additional, Williamson, Rachel, additional, and Melin, Amanda D., additional
Published: 2021
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33. Additional file 2 of Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques

Author: Janiak, Mareike C., Montague, Michael J., Villamil, Catalina I., Stock, Michala K., Trujillo, Amber E., DePasquale, Allegra N., Orkin, Joseph D., Surratt, Samuel E. Bauman, Gonzalez, Olga, Platt, Michael L., Melween I. Martínez, Antón, Susan C., Dominguez-Bello, Maria Gloria, Melin, Amanda D., and Higham, James P.
Abstract: Additional file 1: Table S1. Pairwise adonis results – rectal. Table S2. Pairwise adonis results – oral. Table S3. Pairwise adonis results – penile. Table S4. Top ten genera in rectum, oral cavity, penis, and vagina. Table S5. Full results of DESeq2 analysis of differential expression between age groups. Table S6. Pairwise adonis results - predicted functional features in rectal community. Table S7. Pairwise adonis results - predicted functional features in oral community. Table S8. Pairwise adonis results - predicted functional features in penile community. Figure S1. Alpha-diversity (Shannon Index) of macaque (a) rectal, (b) oral, (c) penile, and (d) vaginal microbiomes across age groups. Figure S2. Alpha-diversity (Shannon Index) of the (a) rectal, (b) oral, and (c) genital microbiomes of males and females. Figure S3. Differences in alpha-diversity (Shannon Index) in the (a) rectal, (b) oral, (c) penile, and (d) vaginal microbiomes of macaques younger than 15 years or 15 years and older. Figure S4. Beta-diversity of genital samples by sex. Bray-Curtis dissimilarity ordinated with non metric multidimensional scaling (NMDS) shows clear separation of male and female genital samples. Figure S5. Differences in relative abundance of top ten genera (a) across all age groups in rectal and (b) oral communities, and between macaques ≥15 years old and
Published: 2021
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34. The Diversity of Primates: From Biomedicine to Conservation Genomics

Author: Orkin, Joseph D., Kuderna, Lukas F. K., Marqués-Bonet, Tomàs, Generalitat de Catalunya, Fundación 'la Caixa', European Commission, Ministerio de Economía y Competitividad (España), EMBO, European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), and Howard Hughes Medical Institute
Subjects: Primates, Whole-genome sequencing, Conservation, Noninvasive, Population genomics
Abstract: Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation. J.D.O. is supported by the Beatriu de Pinós postdoctoral program of the Government of Catalonia's Secretariat for Universities and Research of the Ministry of Economy and Knowledge. The project that gave rise to these results received the support of a fellowship from La Caixa Foundation (ID 100010434) and from the European Union's Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement 847648 to J.D.O. L.F.K.K. is supported by a Formación de Personal Investigador fellowship associated to BFU2014-55090-P (MINECO/FEDER, UE) and by a European Molecular Biology Organization short-term fellowship STF-8286. T.M.-B. is supported by funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement 864203); BFU2017-86471-P (MINECO/FEDER, UE); Unidad de Excelencia María de Maeztu, funded by the Agencia Estatal de Investigacíon (CEX2018-000792-M); Howard Hughes International Early Career Award; and Obra Social La Caixa and Secretaria d'Universitats i Recerca and CERCA Program del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). With funding from the Spanish government through the "Severo Ochoa Centre of Excellence" accreditation (CEX2018-000792-M).
Published: 2021

35. The Diversity of Primates: From Biomedicine to Conservation Genomics

Author: Generalitat de Catalunya, Fundación la Caixa, European Commission, Ministerio de Economía y Competitividad (España), EMBO, European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Orkin, Joseph D., Kuderna, Lukas F. K., Marqués-Bonet, Tomàs, Generalitat de Catalunya, Fundación la Caixa, European Commission, Ministerio de Economía y Competitividad (España), EMBO, European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Orkin, Joseph D., Kuderna, Lukas F. K., and Marqués-Bonet, Tomàs
Abstract: Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation.
Published: 2021

36. The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS

Author: Washington University in St. Louis, Canada Research Chairs, Natural Sciences and Engineering Research Council of Canada, Alberta Children's Hospital Research Institute, Generalitat de Catalunya, Japan Society for the Promotion of Science, Methuselah Foundation, Comisión Nacional de Investigación Científica y Tecnológica (Chile), Biotechnology and Biological Sciences Research Council (UK), European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Fundación la Caixa, Natural Environment Research Council (UK), Orkin, Joseph D., Montague, Michael J., Tejada-Martínez, Daniela, Manuel, Marc de, Campo, Javier del, Cheves Hernández, Saúl, Di Fiore, Anthony, Fontsere, Claudia, Hodgson, Jason A., Janiak, Mareike C., Kuderna, Lukas F. K., Lizano, Esther, Martín, María Pía, Niimura, Yoshihito, Perry, George H., Soto Valverde, Carmen, Tang, Jia, Warren, Wesley C., de Magalhães, João Pedro, Kawamura, Shoji, Marqués-Bonet, Tomàs, Krawetz, Roman, Melin, Amanda D., Washington University in St. Louis, Canada Research Chairs, Natural Sciences and Engineering Research Council of Canada, Alberta Children's Hospital Research Institute, Generalitat de Catalunya, Japan Society for the Promotion of Science, Methuselah Foundation, Comisión Nacional de Investigación Científica y Tecnológica (Chile), Biotechnology and Biological Sciences Research Council (UK), European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Fundación la Caixa, Natural Environment Research Council (UK), Orkin, Joseph D., Montague, Michael J., Tejada-Martínez, Daniela, Manuel, Marc de, Campo, Javier del, Cheves Hernández, Saúl, Di Fiore, Anthony, Fontsere, Claudia, Hodgson, Jason A., Janiak, Mareike C., Kuderna, Lukas F. K., Lizano, Esther, Martín, María Pía, Niimura, Yoshihito, Perry, George H., Soto Valverde, Carmen, Tang, Jia, Warren, Wesley C., de Magalhães, João Pedro, Kawamura, Shoji, Marqués-Bonet, Tomàs, Krawetz, Roman, and Melin, Amanda D.
Abstract: Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have among the largest relative brain size of any monkey and a lifespan that exceeds 50 y, despite their small (3 to 5 kg) body size. We assemble and annotate a de novo reference genome for Cebus imitator. Through high-depth sequencing of DNA derived from blood, various tissues, and feces via fluorescence-activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of noninvasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity.
Published: 2021

37. Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques

Author: Alberta Children's Hospital Research Institute, Natural Sciences and Engineering Research Council of Canada, Natural Environment Research Council (UK), New York University, Leakey Foundation, National Institutes of Health (US), Ford Foundation, Canadian Institute for Advanced Research, Janiak, Mareike C., Montague, Michael J., Villamil, Catalina I., Stock, Michala K., Trujillo, Amber E., DePasquale, Allegra N., Orkin, Joseph D., Bauman Surratt, Samuel E., González, Olga, Platt, Michael L., Martínez, Melween I., Antón, Susan C., Domínguez-Bello, María Gloria, Melin, Amanda D., Higham, James P., Alberta Children's Hospital Research Institute, Natural Sciences and Engineering Research Council of Canada, Natural Environment Research Council (UK), New York University, Leakey Foundation, National Institutes of Health (US), Ford Foundation, Canadian Institute for Advanced Research, Janiak, Mareike C., Montague, Michael J., Villamil, Catalina I., Stock, Michala K., Trujillo, Amber E., DePasquale, Allegra N., Orkin, Joseph D., Bauman Surratt, Samuel E., González, Olga, Platt, Michael L., Martínez, Melween I., Antón, Susan C., Domínguez-Bello, María Gloria, Melin, Amanda D., and Higham, James P.
Abstract: [Background] An individual’s microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interactions between age, health, and microbial changes in humans. Animal models present an excellent opportunity to study age- and sex-linked variation in the microbiome, but captivity is known to influence animal microbial abundance and composition, while studies of free-ranging animals are typically limited to studies of the fecal microbiome using samples collected non-invasively. Here, we analyze a large dataset of oral, rectal, and genital swabs collected from 105 free-ranging rhesus macaques (Macaca mulatta, aged 1 month-26 years), comprising one entire social group, from the island of Cayo Santiago, Puerto Rico. We sequenced 16S V4 rRNA amplicons for all samples., [Results] Infant gut microbial communities had significantly higher relative abundances of Bifidobacterium and Bacteroides and lower abundances of Ruminococcus, Fibrobacter, and Treponema compared to older age groups, consistent with a diet high in milk rather than solid foods. The genital microbiome varied widely between males and females in beta-diversity, taxonomic composition, and predicted functional profiles. Interestingly, only penile, but not vaginal, microbiomes exhibited distinct age-related changes in microbial beta-diversity, taxonomic composition, and predicted functions. Oral microbiome composition was associated with age, and was most distinctive between infants and other age classes., [Conclusions] Across all three body regions, with notable exceptions in the penile microbiome, while infants were distinctly different from other age groups, microbiomes of adults were relatively invariant, even in advanced age. While vaginal microbiomes were exceptionally stable, penile microbiomes were quite variable, especially at the onset of reproductive age. Relative invariance among adults, including elderly individuals, is contrary to findings in humans and mice. We discuss potential explanations for this observation, including that age-related microbiome variation seen in humans may be related to changes in diet and lifestyle.
Published: 2021

38. On pickles: biological and sociocultural links between fermented foods and the human gut microbiome

Author: Purdue University, Flachs, Andrew, Orkin, Joseph D., Purdue University, Flachs, Andrew, and Orkin, Joseph D.
Abstract: [Background] The composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa., [Methods] In this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews with eleven people and participated in a four-day craft fermentation workshop. We also collected 46 fermented food products and 46 stool samples from workshop participants eating those fermented foods., [Results] We identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 amplicon sequence variants (ASVs) shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes., [Conclusions] By combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.
Published: 2021

39. The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS.

Author: Orkin, Joseph D, Montague, Michael J, Tejada-Martinez, Daniela, de Manuel, Marc, Del Campo, Javier, Cheves Hernandez, Saul, Di Fiore, Anthony, Fontsere, Claudia, Hodgson, Jason A, Janiak, Mareike C, Kuderna, Lukas F K, Lizano, Esther, Martin, Maria Pia, Niimura, Yoshihito, Perry, George H, Valverde, Carmen Soto, Tang, Jia, Warren, Wesley C, de Magalhães, João Pedro, Kawamura, Shoji, Marquès-Bonet, Tomàs, Krawetz, Roman, Melin, Amanda D, Orkin, Joseph D, Montague, Michael J, Tejada-Martinez, Daniela, de Manuel, Marc, Del Campo, Javier, Cheves Hernandez, Saul, Di Fiore, Anthony, Fontsere, Claudia, Hodgson, Jason A, Janiak, Mareike C, Kuderna, Lukas F K, Lizano, Esther, Martin, Maria Pia, Niimura, Yoshihito, Perry, George H, Valverde, Carmen Soto, Tang, Jia, Warren, Wesley C, de Magalhães, João Pedro, Kawamura, Shoji, Marquès-Bonet, Tomàs, Krawetz, Roman, and Melin, Amanda D
Abstract: Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have among the largest relative brain size of any monkey and a lifespan that exceeds 50 y, despite their small (3 to 5 kg) body size. We assemble and annotate a de novo reference genome for Cebus imitator. Through high-depth sequencing of DNA derived from blood, various tissues, and feces via fluorescence-activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of noninvasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity.
Published: 2021

40. Variation in predicted COVID‐19 risk among lemurs and lorises

Author: Melin, Amanda D., primary, Orkin, Joseph D., additional, Janiak, Mareike C., additional, Valenzuela, Alejandro, additional, Kuderna, Lukas, additional, Marrone, Frank, additional, Ramangason, Hasinala, additional, Horvath, Julie E., additional, Roos, Christian, additional, Kitchener, Andrew C., additional, Khor, Chiea Chuen, additional, Lim, Weng Khong, additional, Lee, Jessica G. H., additional, Tan, Patrick, additional, Umapathy, Govindhaswamy, additional, Raveendran, Muthuswamy, additional, Alan Harris, R., additional, Gut, Ivo, additional, Gut, Marta, additional, Lizano, Esther, additional, Nadler, Tilo, additional, Zinner, Dietmar, additional, Le, Minh D., additional, Manu, Sivakumara, additional, Rabarivola, Clément J., additional, Zaramody, Alphonse, additional, Andriaholinirina, Nicole, additional, Johnson, Steig E., additional, Jarvis, Erich D., additional, Fedrigo, Olivier, additional, Wu, Dongdong, additional, Zhang, Guojie, additional, Farh, Kyle Kai‐How, additional, Rogers, Jeffrey, additional, Marques‐Bonet, Tomas, additional, Navarro, Arcadi, additional, Juan, David, additional, Arora, Paramjit S., additional, and Higham, James P., additional
Published: 2021
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41. Murine and related chapparvoviruses are nephro-tropic and produce novel accessory proteins in infected kidneys

Author: National Health and Medical Research Council (Australia), Cancer Institute NSW (Australia), Hillcrest Foundation, Alfred P. Sloan Foundation, National Institutes of Health (US), National Cancer Institute (US), Fundação de Amparo à Pesquisa do Estado de São Paulo, Natural Sciences and Engineering Research Council of Canada, Alberta Children's Hospital Research Institute, Generalitat de Catalunya, IDEXX BioAnalytics, Lee, Quintin, Padula, Matthew P., Pinello, Natalia, Williams, Simon H., O'Rourke, Matthew B., Fumagalli, Marcilio Jorge, Orkin, Joseph D., Song, Renhua, Shaban, Babak, Brenner, Ori, Pimanda, John E., Weninger, Wolfgang, de Souza, William Marciel, Melin, Amanda D., Wong, Justin J.-L., Crim, Marcus J., Monette, Sébastien, Roediger, Ben, Jolly, Christopher J., National Health and Medical Research Council (Australia), Cancer Institute NSW (Australia), Hillcrest Foundation, Alfred P. Sloan Foundation, National Institutes of Health (US), National Cancer Institute (US), Fundação de Amparo à Pesquisa do Estado de São Paulo, Natural Sciences and Engineering Research Council of Canada, Alberta Children's Hospital Research Institute, Generalitat de Catalunya, IDEXX BioAnalytics, Lee, Quintin, Padula, Matthew P., Pinello, Natalia, Williams, Simon H., O'Rourke, Matthew B., Fumagalli, Marcilio Jorge, Orkin, Joseph D., Song, Renhua, Shaban, Babak, Brenner, Ori, Pimanda, John E., Weninger, Wolfgang, de Souza, William Marciel, Melin, Amanda D., Wong, Justin J.-L., Crim, Marcus J., Monette, Sébastien, Roediger, Ben, and Jolly, Christopher J.
Abstract: [Abstract] Mouse kidney parvovirus (MKPV) is a member of the provisional genus Chapparvovirus that causes renal disease in immune-compromised mice, with a disease course reminiscent of polyomavirus-associated nephropathy in immune-suppressed kidney transplant patients. Here we map four major MKPV transcripts, created by alternative splicing, to a common initiator region, and use mass spectrometry to identify “p10” and “p15” as novel chapparvovirus accessory proteins produced in MKPV-infected kidneys. p15 and the splicing-dependent putative accessory protein NS2 are conserved in all near-complete amniote chapparvovirus genomes currently available (from mammals, birds and a reptile). In contrast, p10 may be encoded only by viruses with >60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that many mammal chapparvoviruses are likely to be nephrotropic., [Author summary] Parvoviruses are small, genetically simple single-strand DNA viruses that remain viable outside their hosts for very long periods of time. They cause disease in several domesticated species and in humans. Mouse kidney parvovirus (MKPV) is a causative agent of kidney failure in immune-compromised mice and is the only member of the provisional Chapparvovirus genus for which the complete genome including telomeres is known. Here, we show that MKPV propagates almost exclusively in the kidneys of mice infected naturally, wherein it produces novel accessory proteins whose coding regions are conserved in amniote-associated chapparvovirus sequences. We assemble a closely related complete viral genome present in DNA extracted from the kidney of a wild Cebus imitator monkey, and show that another related chapparvovirus is preferentially found in kidneys of the vampire bat Desmodus rotundus. We conclude that many mammal-hosted chapparvovirus are adapted to the kidney niche and may therefore cause disease following kidney stress in multiple species.
Published: 2020

42. The Diversity of Primates: From Biomedicine to Conservation Genomics

Author: Orkin, Joseph D., primary, Kuderna, Lukas F.K., additional, and Marques-Bonet, Tomas, additional
Published: 2021
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43. The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS

Author: Orkin, Joseph D., primary, Montague, Michael J., additional, Tejada-Martinez, Daniela, additional, de Manuel, Marc, additional, del Campo, Javier, additional, Cheves Hernandez, Saul, additional, Di Fiore, Anthony, additional, Fontsere, Claudia, additional, Hodgson, Jason A., additional, Janiak, Mareike C., additional, Kuderna, Lukas F. K., additional, Lizano, Esther, additional, Martin, Maria Pia, additional, Niimura, Yoshihito, additional, Perry, George H., additional, Valverde, Carmen Soto, additional, Tang, Jia, additional, Warren, Wesley C., additional, de Magalhães, João Pedro, additional, Kawamura, Shoji, additional, Marquès-Bonet, Tomàs, additional, Krawetz, Roman, additional, and Melin, Amanda D., additional
Published: 2021
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44. Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus / Sapajus Genomics.

Author: Storer, Jessica M., Walker, Jerilyn A., Rockwell, Catherine E., Mores, Grayce, Beckstrom, Thomas O., Orkin, Joseph D., Melin, Amanda D., Phillips, Kimberley A., Roos, Christian, and Batzer, Mark A.
Subjects: CAPUCHIN monkeys, GENOMICS, RETROTRANSPOSONS, MONKEYS, OLIGONUCLEOTIDES
Abstract: Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships. [ABSTRACT FROM AUTHOR]
Published: 2022
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45. Murine and related chapparvoviruses are nephro-tropic and produce novel accessory proteins in infected kidneys

Author: Lee, Quintin, primary, Padula, Matthew P., additional, Pinello, Natalia, additional, Williams, Simon H., additional, O'Rourke, Matthew B., additional, Fumagalli, Marcilio Jorge, additional, Orkin, Joseph D., additional, Song, Renhua, additional, Shaban, Babak, additional, Brenner, Ori, additional, Pimanda, John E., additional, Weninger, Wolfgang, additional, Souza, William Marciel de, additional, Melin, Amanda D., additional, Wong, Justin J.-L., additional, Crim, Marcus J., additional, Monette, Sébastien, additional, Roediger, Ben, additional, and Jolly, Christopher J., additional
Published: 2020
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46. Analysis of intraindividual and intraspecific variation in semicircular canal dimensions using high-resolution x-ray computed tomography

Author: Welker, Kelli L., Orkin, Joseph D., and Ryan, Timothy M.
Published: 2009
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47. Fermentation and the ethnobiology of microbial entanglement

Author: Generalitat de Catalunya, Ministerio de Economía y Competitividad (España), Flachs, Andrew, Orkin, Joseph D., Generalitat de Catalunya, Ministerio de Economía y Competitividad (España), Flachs, Andrew, and Orkin, Joseph D.
Abstract: Fermentation preserves and transforms foods through autochthonous or introduced microorganisms. Fermentation is of special interest to ethnobiologists because it relies on place‐ and practice‐based knowledge, local flora and microbial taxa, is sensitive to cultural and ecological conditions, and illuminates the interactions through which communities shape and are shaped by the world around them. In this short topical review, we discuss recent anthropological and ethnobiological research into fermentation, arguing that this topic deserves further attention during the current moment of microbial interest across social and natural sciences. We present a typology of scholarship on human ‐microbial relationships that delineates three intellectual camps in this literature: neo‐cultural ecology, microbiopolitics, and the environmental humanities. In light of biomedical and scientific attention to microbes-not only as threats but also as complex and beneficial actors in our lives-it is crucial to understand how socioecological practices including growing, preparing, and consuming fermented foods sustain microbial communities, heritage foodways, and human wellbeing.
Published: 2019

48. Unbiased whole genomes from mammalian feces using fluorescence-activated cell sorting

Author: Orkin, Joseph D., de Manuel, Marc, Krawetz, Roman, del Campo, Javier, Fontsere, Claudia, Kuderna, Lukas F. K., Lizano, Ester, Tang, Jia, Marques-Bonet, Tomas, and Melin, Amanda D.
Abstract: Non-invasive genomic research on free-ranging mammals typically relies on the use of fecal DNA. This requires the isolation and enrichment of endogenous DNA, given its small proportion compared to bacterial DNA. Current approaches for acquiring large-scale genomic data from feces rely on bait-and-capture techniques. While this technique has greatly improved our understanding of mammalian population genomics, it is limited by biases inherent to the capture process, including allele dropout, low mapping rates, PCR duplication artifacts, and structural biases. We report here a new method for generating whole mammalian genomes from feces using fluorescence-activated cell sorting (FACS). Instead of enriching endogenous DNA from extracted fecal DNA, we isolated mammalian cells directly from feces. We then built fragment libraries with low input material from commercially available kits, which we sequenced at high and low coverage. We validated this method on feces collected from primates stored in RNAlater for up to three years. We sequenced one fecal genome at high coverage (12X) and 15 additional fecal genomes at low coverage (0.1X - 4X). For comparative purposes, we also sequenced DNA from nine blood or tissue samples opportunistically collected from capuchin monkeys that died of natural causes or were treated in a local rehabilitation center. Across all fecal samples, we achieved median mapping and duplication rates of 82% and 6%, respectively. Our high-depth fecal genome did not differ in the distribution of coverage, heterozygosity, or GC content from those derived from blood or tissue origin. As a practical application of our new approach with low coverage fecal genomes, we were able to resolve the population genetic structure of capuchin monkeys from four sites in Costa Rica.
Published: 2018
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49. MKPV (aka MuCPV) and related chapparvoviruses are nephro-tropic and encode novel accessory proteins p15 and NS2

Author: Jolly, Christopher J., primary, Lee, Quintin, additional, Padula, Matthew P., additional, Pinello, Natalia, additional, Williams, Simon H., additional, O’Rourke, Matthew B., additional, Fumagalli, Marcilio Jorge, additional, Orkin, Joseph D., additional, Shaban, Babak, additional, Brenner, Ori, additional, Weninger, Wolfgang, additional, de Souza, William Marciel, additional, Melin, Amanda D., additional, Wong, Justin J.-L., additional, Crim, Marcus J., additional, Monette, Sébastien, additional, and Roediger, Ben, additional
Published: 2019
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50. Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage

Author: Storer, Jessica M, primary, Mierl, Jackson R, additional, Brantley, Sarah A, additional, Threeton, Breanna, additional, Sukharutski, Yahor, additional, Rewerts, Lydia C, additional, St. Romain, Corey P, additional, Foreman, Madeline M, additional, Baker, Jasmine N, additional, Walker, Jerilyn A, additional, Orkin, Joseph D, additional, Melin, Amanda D, additional, Phillips, Kimberley A, additional, Konkel, Miriam K, additional, and Batzer, Mark A, additional
Published: 2019
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