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2. The gut microbiome of exudivorous marmosets in the wild and captivity

Author

Malukiewicz, Joanna, Cartwright, Reed A., Dergam, Jorge A., Igayara, Claudia S., Kessler, Sharon E., Moreira, Silvia B., Nash, Leanne T., Nicola, Patricia A., Pereira, Luiz C. M., Pissinatti, Alcides, Ruiz-Miranda, Carlos R., Ozga, Andrew T., Quirino, Adriana A., Roos, Christian, Silva, Daniel L., Stone, Anne C., and Grativol, Adriana D.

Published
2022
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3. The era of reference genomes in conservation genomics

Author

Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlos, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Čiampor, Fedor, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Hoglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per, Pampoulie, Christophe, Ruiz-López, María José, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Goujie, Mazzoni, Camila J., Jarvis, Erich, Bálint, Miklós, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Berg, Paul R., Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe, Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Waterhouse, Robert M., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Höglund, Jacob, Palsbøll, Per J., Ruiz-López, María J., Zhang, Guojie, and Jarvis, Erich D.

Published
2022
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6. How genomics can help biodiversity conservation

Author

Theissinger, Kathrin, primary, Fernandes, Carlos, additional, Formenti, Giulio, additional, Bista, Iliana, additional, Berg, Paul R., additional, Bleidorn, Christoph, additional, Bombarely, Aureliano, additional, Crottini, Angelica, additional, Gallo, Guido R., additional, Godoy, José A., additional, Jentoft, Sissel, additional, Malukiewicz, Joanna, additional, Mouton, Alice, additional, Oomen, Rebekah A., additional, Paez, Sadye, additional, Palsbøll, Per J., additional, Pampoulie, Christophe, additional, Ruiz-López, María J., additional, Secomandi, Simona, additional, Svardal, Hannes, additional, Theofanopoulou, Constantina, additional, de Vries, Jan, additional, Waldvogel, Ann-Marie, additional, Zhang, Guojie, additional, Jarvis, Erich D., additional, Bálint, Miklós, additional, Ciofi, Claudio, additional, Waterhouse, Robert M., additional, Mazzoni, Camila J., additional, Höglund, Jacob, additional, Aghayan, Sargis A., additional, Alioto, Tyler S., additional, Almudi, Isabel, additional, Alvarez, Nadir, additional, Alves, Paulo C., additional, Amorim do Rosario, Isabel R., additional, Antunes, Agostinho, additional, Arribas, Paula, additional, Baldrian, Petr, additional, Bertorelle, Giorgio, additional, Böhne, Astrid, additional, Bonisoli-Alquati, Andrea, additional, Boštjančić, Ljudevit L., additional, Boussau, Bastien, additional, Breton, Catherine M., additional, Buzan, Elena, additional, Campos, Paula F., additional, Carreras, Carlos, additional, Castro, L. FIlipe C., additional, Chueca, Luis J., additional, Čiampor, Fedor, additional, Conti, Elena, additional, Cook-Deegan, Robert, additional, Croll, Daniel, additional, Cunha, Mónica V., additional, Delsuc, Frédéric, additional, Dennis, Alice B., additional, Dimitrov, Dimitar, additional, Faria, Rui, additional, Favre, Adrien, additional, Fedrigo, Olivier D., additional, Fernández, Rosa, additional, Ficetola, Gentile Francesco, additional, Flot, Jean-François, additional, Gabaldón, Toni, additional, Agius, Dolores R., additional, Giani, Alice M., additional, Gilbert, M. Thomas P., additional, Grebenc, Tine, additional, Guschanski, Katerina, additional, Guyot, Romain, additional, Hausdorf, Bernhard, additional, Hawlitschek, Oliver, additional, Heintzman, Peter D., additional, Heinze, Berthold, additional, Hiller, Michael, additional, Husemann, Martin, additional, Iannucci, Alessio, additional, Irisarri, Iker, additional, Jakobsen, Kjetill S., additional, Klinga, Peter, additional, Kloch, Agnieszka, additional, Kratochwil, Claudius F., additional, Kusche, Henrik, additional, Layton, Kara K.S., additional, Leonard, Jennifer A., additional, Lerat, Emmanuelle, additional, Liti, Gianni, additional, Manousaki, Tereza, additional, Marques-Bonet, Tomas, additional, Matos-Maraví, Pável, additional, Matschiner, Michael, additional, Maumus, Florian, additional, Mc Cartney, Ann M., additional, Meiri, Shai, additional, Melo-Ferreira, José, additional, Mengual, Ximo, additional, Monaghan, Michael T., additional, Montagna, Matteo, additional, Mysłajek, Robert W., additional, Neiber, Marco T., additional, Nicolas, Violaine, additional, Novo, Marta, additional, Ozretić, Petar, additional, Palero, Ferran, additional, Pârvulescu, Lucian, additional, Pascual, Marta, additional, Paulo, Octávio S., additional, Pavlek, Martina, additional, Pegueroles, Cinta, additional, Pellissier, Loïc, additional, Pesole, Graziano, additional, Primmer, Craig R., additional, Riesgo, Ana, additional, Rüber, Lukas, additional, Rubolini, Diego, additional, Salvi, Daniele, additional, Seehausen, Ole, additional, Seidel, Matthias, additional, Studer, Bruno, additional, Theodoridis, Spyros, additional, Thines, Marco, additional, Urban, Lara, additional, Vasemägi, Anti, additional, Vella, Adriana, additional, Vella, Noel, additional, Vernes, Sonja C., additional, Vernesi, Cristiano, additional, Vieites, David R., additional, Wheat, Christopher W., additional, Wörheide, Gert, additional, Wurm, Yannick, additional, and Zammit, Gabrielle, additional

Published
2023
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8. Pelage Variation and Morphometrics of Closely RelatedCallithrixMarmoset Species and Their Hybrids

Author

Malukiewicz, Joanna, primary, Warren, Kerryn, additional, Boere, Vanner, additional, Bandeira, Illaira LC, additional, Curi, Nelson HA, additional, das Dores, Fabio T, additional, Fitorra, Lilian S, additional, Furuya, Haroldo R, additional, Igayara, Claudia S, additional, Milanelo, Liliane, additional, Moreira, Silvia B, additional, Molina, Camila V, additional, Nardi, Marcello S, additional, Nicola, Patricia A, additional, Passamani, Marcello, additional, Pedro, Valeria S, additional, Pereira, Luiz CM, additional, Petri, Bruno, additional, Pissinatti, Alcides, additional, Quirino, Adriana Alves, additional, Rogers, Jeffrey, additional, Ruiz-Miranda, Carlos R, additional, Silva, Daniel L, additional, Silva, Ita O, additional, Silva, Monique OM, additional, Summa, Juliana L, additional, Zwarg, Ticiana, additional, and Ackermann, Rebecca R, additional

Published
2023
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9. How genomics can help biodiversity conservation

Author

Theissinger, Kathrin, Fernandes, Carlos, Formenti, Giulio, Bista, Iliana, Berg, Paul R., Bleidorn, Christoph, Bombarely, Aureliano, Crottini, Angelica, Gallo, Guido R., Godoy, José A., Jentoft, Sissel, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per J., Pampoulie, Christophe, Ruiz-López, María J., Secomandi, Simona, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Jarvis, Erich D., Bálint, Miklós, Ciofi, Claudio, Waterhouse, Robert M., Mazzoni, Camila J., and Höglund, Jacob

Subjects
Genetics
Published
2023

10. Comparison of Mitogenomic and Mitochondrial Markers for the Phylogenetic and Evolutionary Study of Marmosets, with special focus on captive Callithrix jacchus

Author

Fonseca, João L.G., primary, del Rosario, Ricardo C. H., additional, de Oliveira, Maria Adélia Borstelmann, additional, Feng, Guoping, additional, Igayara, Claudia S., additional, McCarroll, Steven A., additional, Nicola, Patricia A., additional, Pereira, Luiz C. M., additional, Rogers, Jeffery, additional, Roos, Christian, additional, and Malukiewicz, Joanna, additional

Published
2022
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11. Bifidobacteria Define Gut Microbiome Profiles of Golden Lion Tamarin (Leontopithecus rosalia) and Marmoset (Callithrix sp.) Metagenomic Shotgun Pools

Author

Malukiewicz, Joanna, primary, D'arc, Mirela, additional, Dias, Ceclia A., additional, Cartwright, Reed A., additional, Grativol, Adriana D., additional, Moreira, Silvia Bahadian, additional, Souza, Antonizete R, additional, Tavares, Maria Clotilde Henriques, additional, Pissinatti, Alcides, additional, Ruiz-Miranda, Carlos R., additional, and Santos, André F. A., additional

Published
2022
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14. Additional file 1 of Mitogenomic phylogeny of Callithrix with special focus on human transferred taxa

Author

Malukiewicz, Joanna, Cartwright, Reed A., Curi, Nelson H. A., Dergam, Jorge A., Igayara, Claudia S., Moreira, Silvia B., Molina, Camila V., Nicola, Patricia A., Noll, Angela, Passamani, Marcello, Luiz C. M. Pereira, Pissinatti, Alcides, Ruiz-Miranda, Carlos R., Silva, Daniel L., Stone, Anne C., Zinner, Dietmar, and Roos, Christian

Abstract

Additional file 1: Table S1. Metadata for newly collected samples as well as primate mitogenome sequences obtained from GenBank. The ‘Sample’ column gives ID of each new sampled individual or the species for sequences obtained from previous studies. The ‘Accession’ column gives GenBank accession numbers for each sequence, the ‘Assembly Method This Study’ column states the manner in which new Callithrix mitogenomes were sequenced and assembled (S=Sanger; N=NOVOPlasty2.6.4). The ‘Phenotype’ column indicates whether the sampled individual possessed a pure species or hybrid phenotype, and capital letters in parentheses next to C. penicillata x C. geoffroyi category are specific phenotype classifications following Figure 5 in Fuzessy et al. (2014). The ‘mtDNA Genome Lineage’ column indicates phylogenetic classification of the mitogenome of the sampled individual. The ‘Sampling Location’ column indicates where each individual was sampled. Nearest cities are located for individuals sampled from the wild, and facilities are indicated for individuals sampled in captivity. The Guarulhos Municipal Zoo is located in Guarulhos, São Paulo, Brazil; CRC (Callitrichid Research Center) is located in Omaha, Nebraska, US; NEPRC (New England Primate Research Center, no longer in operation) was located in Southborough, Massachusetts, US; CPRJ (Centro de Primatologia do Rio de Janeiro) is located in Guapimirim, Rio de Janeiro, Brazil; CEMAFAUNA (Centro de Conservação e Manejo de Fauna da Caatinga) is located in Petrolina, Pernambuco. Abbreviations for Brazilian states in the ‘Sampling Location’ column are as follows: Espírito Santo (ES), Minas Gerais (MG), Rio de Janeiro (RJ), São Paulo (SP). DF is the Brazilian Federal District. (NA=No data Available). Table S2. Each cell lists individuals that possess the same mtDNA haplotypes. Table S3. Organization of the C. aurita mitogenome based on 16,471 sequenced bases of individual BJT065 (Accession number MT041703). Table S4. Divergence times for Callithrix species and select nodes (MRCA = Most recent common ancestor; values in brackets = 95% highest posterior density). Node names follow major node designations shown in Figure S3 as capital letters. Table S5. BMM posterior probabilities for Fig. 4 nodes. Location abbreviations follow Fig. 4. Table S6. Summary of record numbers for collected samples that have been entered into the Brazilian CGEN SISGEN sample database (ES=Espírito Santo, MG=Minas Gerais, PE= Pernambuco, RJ=Rio de Janeiro, SP=São Paulo).

Published
2021
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15. Genomic Skimming and Nanopore Sequencing Uncover Cryptic Hybridization in One of World’s Most Threatened Primates

Author

Malukiewicz, Joanna, primary, Cartwright, Reed A, additional, Dergam, Jorge A, additional, Igayara, Claudia S, additional, Nicola, Patricia A, additional, Pereira, Luiz MC, additional, Ruiz-Miranda, Carlos R, additional, Stone, Anne C, additional, Silva, Daniel L, additional, de Fátima Rodrigues da Silva, Fernanda, additional, Varsani, Arvind, additional, Walter, Lutz, additional, Wilson, Melissa A, additional, Zinner, Dietmar, additional, and Roos, Christian, additional

Published
2021
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17. An Introduction to the Callithrix Genus and Overview of Recent Advances in Marmoset Research

Author

Malukiewicz, Joanna, primary, Boere, Vanner, additional, Borstelmann de Oliveira, Maria Adelia, additional, D’Arc, Mirela, additional, Viviane Amorim Ferreira, Jessica, additional, French, Jeffery, additional, Houman, Genevieve, additional, Almeida Igayara de Souza, Claudia, additional, Jerusalinsky, Leandro, additional, Rodrigues de Melo, Fabiano, additional, Mafra Valença-Montenegro, Mônica, additional, Bahadian Moreira, Silvia, additional, de Oliveira e Silva, Ita, additional, Santos Pacheco, Felipe, additional, Rogers, Jeff, additional, Pissinatti, Alcides, additional, del Rosario, Ricardo, additional, Ross, Corinna, additional, R. Ruiz-Miranda, Carlos, additional, C.M. Pereira, Luiz, additional, Schiel, Nicola, additional, de Fátima Rodrigues da Silva, Fernanda, additional, Souto, Antonio, additional, Šlipogor, Vedrana, additional, and Tardif, Suzette, additional

Published
2021
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18. An Introduction to the Callithrix Genus and Overview of Recent Advances in Marmoset Research

Author

Malukiewicz, Joanna, primary, Boere, Vanner, additional, Borstelmann de Oliveira, Maria Adelia, additional, D’Arc, Mirela, additional, Viviane Amorim Ferreira, Jessica, additional, French, Jeffery, additional, Houman, Genevieve, additional, Almeida Igayara de Souza, Claudia, additional, Jerusalinsky, Leandro, additional, Rodrigues de Melo, Fabiano, additional, Mafra Valença-Montenegro, Mônica, additional, Bahadian Moreira, Silvia, additional, de Oliveira e Silva, Ita, additional, Santos Pacheco, Felipe, additional, Rogers, Jeff, additional, Pissinatti, Alcides, additional, del Rosario, Ricardo, additional, Ross, Corinna, additional, R. Ruiz-Miranda, Carlos, additional, C.M. Pereira, Luiz, additional, Schiel, Nicola, additional, de Fátima Rodrigues da Silva, Fernanda, additional, Souto, Antonio, additional, Šlipogor, Vedrana, additional, and Tardif, Suzette, additional

Published
2020
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19. Mitogenomic Phylogeny of Callithrix with Special Focus on Human Transferred Taxa

Author

Malukiewicz, Joanna, primary, Cartwright, Reed A., additional, Curi, Nelson H.A., additional, Dergam, Jorge A., additional, Igayara, Claudia S., additional, Moreira, Silvia B., additional, Molina, Camila V., additional, Nicola, Patricia A., additional, Noll, Angela, additional, Passamani, Marcello, additional, Pereira, Luiz C.M., additional, Pissinatti, Alcides, additional, Ruiz-Miranda, Carlos R., additional, Silva, Daniel L., additional, Stone, Anne C., additional, Zinner, Dietmar, additional, and Roos, Christian, additional

Published
2020
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20. An Introduction to theCallithrixGenus and Overview of Recent Advances in Marmoset Research

Author

Malukiewicz, Joanna, primary, Boere, Vanner, additional, de Oliveira, Maria Adélia Borstelmann, additional, D’arc, Mirela, additional, Ferreira, Jéssica V A, additional, French, Jeffrey, additional, Housman, Genevieve, additional, de Souza, Claudia Igayara, additional, Jerusalinsky, Leandro, additional, R de Melo, Fabiano, additional, M Valença-Montenegro, Mônica, additional, Moreira, Silvia Bahadian, additional, de Oliveira e Silva, Ita, additional, Pacheco, Felipe Santos, additional, Rogers, Jeffrey, additional, Pissinatti, Alcides, additional, del Rosario, Ricardo C H, additional, Ross, Corinna, additional, Ruiz-Miranda, Carlos R, additional, Pereira, Luiz C M, additional, Schiel, Nicola, additional, de Fátima Rodrigues da Silva, Fernanda, additional, Souto, Antonio, additional, Šlipogor, Vedrana, additional, and Tardif, Suzette, additional

Published
2020
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21. The Effects of Host Taxon, Hybridization, and Environment on the Gut Microbiome of Callithrix Marmosets

Author

Malukiewicz, Joanna, Cartwright, Reed A., Dergam, Jorge A., Igayara, Claudia S., Kessler, Sharon, Moreira, Silvia B., Nash, Leanne T., Nicola, Patricia A., Pereira, Luiz C.M., Pissinati, Alcides, Ruiz-Miranda, Carlos R., Ozga, Andrew T., Roos, Christian, Silva, Daniel L., Stone, Anne C., and Grativol, Adriana D.

Subjects
digestive system
Abstract

Microbiome studies show that host taxon, diet, and environment influence gut bacteria. However, these factors are rarely studied in animal hybrids and exudivores (which nutritionally exploit indigestible oligosaccharides). To investigate the effects of host taxon, hybridization, and environment on gut microbiota, we conducted 16S V4 ribosomal sequencing of the gut microbiome of marmosets ( Callithrix ), non-human primate (NHP) specialist exudivores that also hybridize. We sampled 59 wild, translocated, and captive pure and hybrid Callithrix , including endangered C. aurita . Gut microbiome diversity differed significantly between hybrids and non-hybrids, but host environment had the strongest overall effect on the gut microbiome. Captive marmosets showed relatively reduced gut microbiome diversity. Wild Callithrix had the highest relative abundance of Bifidobacterium , which process host-indigestible carbohydrates, while captive marmosets had the highest relative abundance of Enterobacteriaceae, a family containing several pathogenic bacteria. The wild marmoset gut microbiome was enriched predictively for carbohydrate metabolism functions, while that of captive marmosets was enriched for nucleotide and amino acid metabolism function. Our findings show that carbohydrate metabolism is integral to the composition and function of the wild exudivore gut microbiome. Further, captivity perturbs the exudivore gut microbiome, raising implications for captive host health and endangered exudivore conservation.

Published
2019
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22. The Gut Microbiome of Exudivorous Marmosets in the Wild and Captivity

Author

Malukiewicz, Joanna, primary, Cartwright, Reed A., additional, Dergam, Jorge A., additional, Igayara, Claudia S., additional, Kessler, Sharon, additional, Moreira, Silvia B., additional, Nash, Leanne T., additional, Nicola, Patricia A., additional, Pereira, Luiz C.M., additional, Pissinatti, Alcides, additional, Ruiz-Miranda, Carlos R., additional, Ozga, Andrew T., additional, Quirino, Adriana A., additional, Roos, Christian, additional, Silva, Daniel L., additional, Stone, Anne C., additional, and Grativol, Adriana D., additional

Published
2019
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23. Hybridization in human evolution: Insights from other organisms

Author

Ackermann, Rebecca R., primary, Arnold, Michael L., additional, Baiz, Marcella D., additional, Cahill, James A., additional, Cortés‐Ortiz, Liliana, additional, Evans, Ben J., additional, Grant, B. Rosemary, additional, Grant, Peter R., additional, Hallgrimsson, Benedikt, additional, Humphreys, Robyn A., additional, Jolly, Clifford J., additional, Malukiewicz, Joanna, additional, Percival, Christopher J., additional, Ritzman, Terrence B., additional, Roos, Christian, additional, Roseman, Charles C., additional, Schroeder, Lauren, additional, Smith, Fred H., additional, Warren, Kerryn A., additional, Wayne, Robert K., additional, and Zinner, Dietmar, additional

Published
2019
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25. Introduction to the Callithrix Genus and Overview of Recent Advances in Marmoset Research.

Author

Malukiewicz, Joanna, Boere, Vanner, Oliveira, Maria Adélia Borstelmann de, D'arc, Mirela, Ferreira, Jéssica V A, French, Jeffrey, Housman, Genevieve, Souza, Claudia Igayara de, Jerusalinsky, Leandro, Melo, Fabiano R de, Valença-Montenegro, Mônica M, Moreira, Silvia Bahadian, Silva, Ita de Oliveira e, Pacheco, Felipe Santos, Rogers, Jeffrey, Pissinatti, Alcides, Rosario, Ricardo C H del, Ross, Corinna, Ruiz-Miranda, Carlos R, and Pereira, Luiz C M

Published
2020
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26. Hybridization in human evolution: insights from other organisms

Author

Ackermann, Rebecca Rogers, primary, Arnold, Michael, additional, Baiz, Marcella, additional, Cahill, James A, additional, Cortés-Ortiz, Liliana, additional, Evans, Ben J, additional, Grant, B Rosemary, additional, Grant, Peter R, additional, Hallgrimsson, Benedikt, additional, Humphreys, Robyn, additional, Jolly, Clifford J, additional, Malukiewicz, Joanna, additional, Percival, Christopher J, additional, Ritzman, Terrence, additional, Roos, Christian, additional, Roseman, Charles C, additional, Schroeder, Lauren, additional, Smith, Fred H, additional, Warren, Kerryn, additional, Wayne, Robert, additional, and Zinner, Dietmar, additional

Published
2018
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27. Callithrix aurita: a marmoset species on its way to extinction in the Brazilian Atlantic Forest

Author

De Carvalho, Rodrigo Salles, primary, Bergallo, Helena Godoy, additional, Cronemberger, Cecilia, additional, Guimarães-Luiz, Thaís, additional, Igayara-Souza, Claudia Almeida, additional, Jerusalinsky, Leandro, additional, Knogge, Christoph, additional, Lacerda, Wagner Rafael, additional, Malukiewicz, Joanna, additional, De Melo, Fabiano Rodrigues, additional, Moreira, Silvia Bahadian, additional, Pereira, Daniel Gomes, additional, Pissinatti, Alcides, additional, Port-Carvalho, Marcio, additional, Ruiz-Miranda, Carlos R., additional, and Wormell, Dominic, additional

Published
2018
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29. An Introduction to the CallithrixGenus and Overview of Recent Advances in Marmoset Research

Author

Malukiewicz, Joanna, Boere, Vanner, de Oliveira, Maria Adélia Borstelmann, D’arc, Mirela, Ferreira, Jéssica V A, French, Jeffrey, Housman, Genevieve, de Souza, Claudia Igayara, Jerusalinsky, Leandro, R de Melo, Fabiano, M Valença-Montenegro, Mônica, Moreira, Silvia Bahadian, de Oliveira e Silva, Ita, Pacheco, Felipe Santos, Rogers, Jeffrey, Pissinatti, Alcides, del Rosario, Ricardo C H, Ross, Corinna, Ruiz-Miranda, Carlos R, Pereira, Luiz C M, Schiel, Nicola, de Fátima Rodrigues da Silva, Fernanda, Souto, Antonio, Šlipogor, Vedrana, and Tardif, Suzette

Abstract

We provide here a current overview of marmoset (Callithrix) evolution, hybridization, species biology, basic/biomedical research, and conservation initiatives. Composed of 2 subgroups, the auritagroup (C auritaand C flaviceps) and the jacchusgroup (C geoffroyi, C jacchus, C kuhlii, and C penicillata), this relatively young primate radiation is endemic to the Brazilian Cerrado, Caatinga, and Atlantic Forest biomes. Significant impacts on Callithrixwithin these biomes resulting from anthropogenic activity include (1) population declines, particularly for the auritagroup; (2) widespread geographic displacement, biological invasions, and range expansions of C jacchusand C penicillata; (3) anthropogenic hybridization; and (4) epizootic Yellow Fever and Zika viral outbreaks. A number of Brazilian legal and conservation initiatives are now in place to protect the threatened auritagroup and increase research about them. Due to their small size and rapid life history, marmosets are prized biomedical models. As a result, there are increasingly sophisticated genomic Callithrixresources available and burgeoning marmoset functional, immuno-, and epigenomic research. In both the laboratory and the wild, marmosets have given us insight into cognition, social group dynamics, human disease, and pregnancy. Callithrix jacchusand C penicillataare emerging neotropical primate models for arbovirus disease, including Dengue and Zika. Wild marmoset populations are helping us understand sylvatic transmission and human spillover of Zika and Yellow Fever viruses. All of these factors are positioning marmosets as preeminent models to facilitate understanding of facets of evolution, hybridization, conservation, human disease, and emerging infectious diseases.

Published
2020
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33. A Survey of Wild and Introduced Marmosets (Callithrix: Callitrichidae) in the Southern and Eastern Portions of the State of Minas Gerais, Brazil.

Author

de Fátima Rodrigues Silva, Fernanda, Malukiewicz, Joanna, Silva, Leanes Cruz, Carvalho, Rodrigo Salles, Ruiz-Miranda, Carlos Ramon, da Silva Coelho, Flávio Augusto, de Paula Figueira, Milene, Boere, Vanner, and de Oliveira Silva, Ita

Subjects
*MARMOSETS, *CEBIDAE, *MONKEYS, *BIODIVERSITY, *SPECIES
Abstract

An understanding of current Callithrix distributions is important for species management and conservation in the wild because of widespread deforestation and the introduction, and spread, of marmosets outside their natural ranges. Here we report on a survey of the natural and introduced Callithrix distributions in five mesoregions of the southeastern Brazilian state of Minas Gerais: Metropolitana de Belo Horizonte, Sul/Sudoeste de Minas, Zona da Mata, Campo das Vertentes and Vale do Rio Doce. Our study was based on on- and off-line literature searches, e-mail questionnaires, photographic records, and field observations. The collected data were superimposed on geopolitical and vegetation maps and compared to the historical records available in mammal collections from national museums and the currently recognized natural ranges of Callithrix species. Callithrix geoffroyi and C. penicillata were widely distributed in our study area, particularly in regions and biomes where they do not occur naturally. Callithrix penicillata has apparently expanded its range into the Atlantic Forest from its native Cerrado in Central Brazil. Although not native to Minas Gerais, C. jacchus was reported at several locations in our study area. These three species were reported even in the areas of natural occurrence of C. aurita and C. flaviceps. We detected the presence of five species of Callithrix (C. aurita, C. flaviceps, C. geoffroyi, C. penicillata, and C. jacchus) in some locations of the Zona da Mata. Marmoset groups are present in some urban areas, in close contact with human populations. Marmosets are found in artificial sympatry due to the introduction of species outside their native areas of distribution. Such introductions, together with the destruction of native marmoset habitats, are a threat due to ongoing hybridization. [ABSTRACT FROM AUTHOR]

Published
2018

35. Application of PE-RADSeq to the study of genomic diversity and divergence of two Brazilian marmoset species ( Callithrix jacchus and C. penicillata).

Author

Malukiewicz, Joanna, Guschanski, Katerina, Grativol, Adriana D., Oliveira, Maria Adélia B., Ruiz‐Miranda, Carlos R., and Stone, Anne C.

Subjects
*MARMOSETS, *CALLITHRIX, *GENOMICS, *BIODIVERSITY, *GENETIC speciation
Abstract

Callithrix jacchus and C. penicillata are among the smallest anthropoid primates, are highly specialized tree gougers, and largely occupy Brazil's most extreme, semi-arid biomes. However, the underlying genomic factors that underpin the evolution of these species and their unique traits are under-investigated. Additionally, exotic populations of these two species are widely established throughout Brazil and hybridize with threatened native congers. Thus, both genomic and conservation factors call for a better understanding of C. jacchus and C. penicillata evolution. Here, we applied PE-RADseq to characterize genomic variation in these two species, using six C. jacchus and seven C. penicillata individuals. We identified an average of 7,463 and 5,180 SNPs/individual in C. penicillata and C. jacchus, respectively, and also found 1,395 variable sites that were represented in both species. C. penicillata showed overall higher levels of genetic diversity than C. jacchus at the variable sites present in both species. Additionally, among these variable sites, 106 showed relative interspecific divergence levels that were significantly higher than the genome-wide average. We further compared relative and absolute divergence for C. penicillata and C. jacchus between RAD loci associated with the 106 significantly diverged variable sites and all other RAD loci present in both species. The former RAD loci set showed significantly elevated relative and absolute divergence measures in comparison to the latter set. This convergence suggests that C. jacchus and C. penicillata may have diverged under a scenario of gene flow under secondary contact. Here, we demonstrate that RADseq is an efficient method to simultaneously discover and genotype a large number of markers and validate the utility of RADseq for examining Callithrix evolution. [ABSTRACT FROM AUTHOR]

Published
2017
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36. Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes.

Author

Malukiewicz, Joanna, Hepp, Crystal M., Guschanski, Katerina, and Stone, Anne C.

Subjects
*CALLITHRIX, *PHYLOGENY, *MARMOSETS, *MITOCHONDRIAL DNA
Abstract

Objectives Two subgroups make up the marmoset genus Callithrix. The ' aurita' group is composed of two species, whereas evolutionary relationships among the four species of the ' jacchus' group remain unclear. To uncover these relationships, we first sequenced mitochondrial genomes for C. kuhlii and C. penicillata to complement data available for congeners. We then constructed a phylogenetic tree based on mtDNA heavy chain protein coding genes from several primates to untangle species relationships and estimate divergence times of the jacchus group. Materials and Methods MtDNA genomes of C. kuhlii and C. penicillata were Sanger sequenced. These Callithrix mitogenomes were combined with other publically available primate mtDNA genomes. Phylogenies were produced using maximum likelihood and Bayesian inference. Finally, divergence times within the jacchus group of marmosets were estimated with Bayesian inference. Results In our phylogenetic tree, C. geoffroyi was the sister to all other jacchus group species, followed by C. kuhlii, while C. jacchus and C. penicillata diverged most recently. Bayesian inference showed that C. jacchus and C. penicillata diverged approximately 0.70 MYA and that the jacchus group radiated approximately 1.30 MYA. Discussion Callithrix nuclear and mtDNA phylogenies frequently result in polytomies and paraphyly. Here, we present a well-supported phylogenetic tree based on mitochondrial genome sequences, which facilitates the understanding of the divergence of the jacchus marmosets. Our results demonstrate how mitochondrial genomes can enrich Callithrix phylogenetic studies by alleviating some of the difficulties faced by previous mtDNA studies and allow formulation of hypotheses to test further under larger genomic-scale analyses. [ABSTRACT FROM AUTHOR]

Published
2017
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37. Hybridization effects and genetic diversity of the common and black‐tufted marmoset (Callithrix jacchus and Callithrix penicillata) mitochondrial control region

Author

Malukiewicz, Joanna, primary, Boere, Vanner, additional, Fuzessy, Lisieux F., additional, Grativol, Adriana D., additional, French, Jeffrey A., additional, Silva, Ita de Oliveira e, additional, Pereira, Luiz C.M., additional, Ruiz‐Miranda, Carlos R., additional, Valença, Yuri M., additional, and Stone, Anne C., additional

Published
2014
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38. Hybridization effects and genetic diversity of the common and black-tufted marmoset ( C allithrix jacchus and C allithrix penicillata) mitochondrial control region.

Author

Malukiewicz, Joanna, Boere, Vanner, Fuzessy, Lisieux F., Grativol, Adriana D., French, Jeffrey A., Silva, Ita de Oliveira e, Pereira, Luiz C.M., Ruiz‐Miranda, Carlos R., Valença, Yuri M., and Stone, Anne C.

Subjects
*SPECIES hybridization, *MARMOSETS, *PRIMATE genetics, *ANIMAL populations, *PHYLOGENY, *BIODIVERSITY
Abstract

ABSTRACT Hybridization is continually documented in primates, but effects of natural and anthropogenic hybridization on biodiversity are still unclear and differentiating between these contexts remains challenging in regards to primate evolution and conservation. Here, we examine hybridization effects on the mitochondrial DNA (mtDNA) control region of Callithrix marmosets, which provide a unique glimpse into interspecific mating under distinct anthropogenic and natural conditions. DNA was sampled from 40 marmosets along a 50-km transect from a previously uncharacterized hybrid zone in NE Brazil between the ranges of Callithrix jacchus and Callithrix penicillata. DNA was also collected from 46 marmosets along a 30-km transect in a hybrid zone in Rio de Janeiro state, Brazil, where exotic marmosets appeared in the 1980s. Combining Callithrix DNA sampled inside and outside of these hybrid zones, phylogenetic and network analyses show C. jacchus and C. penicillata being parental species to sampled hybrids. We expand limited Callithrix population genetics work by describing mtDNA diversity and demographic history of these parental species. We show ancient population expansion in C. jacchus and historically constant population size in C. penicillata, with the latter being more genetically diverse than the former. The natural hybrid zone contained higher genetic diversity relative to the anthropogenic zone. While our data suggest hybrid swarm formation within the anthropogenic zone due to removed physical reproductive barriers, this pattern is not seen in the natural hybrid zone. These results suggest different genetic dynamics within natural and anthropogenic hybridization contexts that carry important implications for primate evolution and conservation. Am J Phys Anthropol 155:522-536, 2014. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Published
2014
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39. Regulatory element copy number differences shape primate expression profiles.

Author

lskow, Rebecca C., Gokcumen, Omer, Abyzov, Alexej, Malukiewicz, Joanna, Qihui Zhu, Sukumar, Ann T., Pai, Athma A., Mills, Ryan E., Habegger, Lukas, Cusanovich, Darren A., Rubel, Meagan A., Perry, George H., Gerstein, Mark, Stone, Anne C., Gilad, Yoav, and Charles Lee

Subjects
GENETIC regulation, GENE expression, ANIMAL species, GENETIC code, DEVELOPMENTAL biology, PHENOTYPES
Abstract

Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across three primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral "copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs that were processed pseudogenes and some of which were expressed. Furthermore, there were copy number-different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA. [ABSTRACT FROM AUTHOR]

Published
2012
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40. The era of reference genomes in conservation genomics

Author

Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, José A. Godoy, Jacob Höglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklós Bálint, Fedor Čiampor, Jacob Hoglund, Per Palsbøll, María José Ruiz-López, Goujie Zhang, Erich Jarvis, Sargis A. Aghayan, Tyler S. Alioto, Isabel Almudi, Nadir Alvarez, Paulo C. Alves, Isabel R. Amorim, Agostinho Antunes, Paula Arribas, Petr Baldrian, Paul R. Berg, Giorgio Bertorelle, Astrid Böhne, Andrea Bonisoli-Alquati, Ljudevit L. Boštjančić, Bastien Boussau, Catherine M. Breton, Elena Buzan, Paula F. Campos, Carlos Carreras, L. FIlipe Castro, Luis J. Chueca, Elena Conti, Robert Cook-Deegan, Daniel Croll, Mónica V. Cunha, Frédéric Delsuc, Alice B. Dennis, Dimitar Dimitrov, Rui Faria, Adrien Favre, Olivier D. Fedrigo, Rosa Fernández, Gentile Francesco Ficetola, Jean-François Flot, Toni Gabaldón, Dolores R. Galea Agius, Guido R. Gallo, Alice M. Giani, M. Thomas P. Gilbert, Tine Grebenc, Katerina Guschanski, Romain Guyot, Bernhard Hausdorf, Oliver Hawlitschek, Peter D. Heintzman, Berthold Heinze, Michael Hiller, Martin Husemann, Alessio Iannucci, Iker Irisarri, Kjetill S. Jakobsen, Sissel Jentoft, Peter Klinga, Agnieszka Kloch, Claudius F. Kratochwil, Henrik Kusche, Kara K.S. Layton, Jennifer A. Leonard, Emmanuelle Lerat, Gianni Liti, Tereza Manousaki, Tomas Marques-Bonet, Pável Matos-Maraví, Michael Matschiner, Florian Maumus, Ann M. Mc Cartney, Shai Meiri, José Melo-Ferreira, Ximo Mengual, Michael T. Monaghan, Matteo Montagna, Robert W. Mysłajek, Marco T. Neiber, Violaine Nicolas, Marta Novo, Petar Ozretić, Ferran Palero, Lucian Pârvulescu, Marta Pascual, Octávio S. Paulo, Martina Pavlek, Cinta Pegueroles, Loïc Pellissier, Graziano Pesole, Craig R. Primmer, Ana Riesgo, Lukas Rüber, Diego Rubolini, Daniele Salvi, Ole Seehausen, Matthias Seidel, Simona Secomandi, Bruno Studer, Spyros Theodoridis, Marco Thines, Lara Urban, Anti Vasemägi, Adriana Vella, Noel Vella, Sonja C. Vernes, Cristiano Vernesi, David R. Vieites, Robert M. Waterhouse, Christopher W. Wheat, Gert Wörheide, Yannick Wurm, Gabrielle Zammit, Repositório da Universidade de Lisboa, Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlo, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Höglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per J., Pampoulie, Christophe, Ruiz-López, María J., Svardal, Hanne, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Mazzoni, Camila J., Jarvis, Erich D., Bálint, Mikló, Čiampor, Fedor, Hoglund, Jacob, Palsbøll, Per, José Ruiz-López, María, Zhang, Goujie, Jarvis, Erich, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., R Amorim, Isabel, Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, R Berg, Paul, Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, L Boštjančić, Ljudevit, Boussau, Bastien, M Breton, Catherine, Buzan, Elena, F Campos, Paula, Carreras, Carlo, FIlipe Castro, L., Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, V Cunha, Mónica, Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Francesco Ficetola, Gentile, Flot, Jean-Françoi, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Thomas P Gilbert, M., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, D Heintzman, Peter, Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, S Jakobsen, Kjetill, Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, F Kratochwil, Claudiu, Kusche, Henrik, KS Layton, Kara, A Leonard, Jennifer, Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Toma, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Robertwmysłajek, T Neiber, Marco, Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loc, Pesole, Graziano, R Primmer, Craig, Riesgo, Ana, Rüber, Luka, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthia, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyro, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, C Vernes, Sonja, Vernesi, Cristiano, R Vieites, David, M Waterhouse, Robert, W Wheat, Christopher, Wörheide, Gert, Wurm, Yannick, Zammit., and Gabrielle, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Barcelona Supercomputing Center, European Reference Genome Atlas (ERGA) Consortium, University of St Andrews. School of Biology, University of St Andrews. St Andrews Bioinformatics Unit, Palsbøll lab, Marine Biology, University of Zurich, and Bálint, Miklós

Subjects
QH301 Biology, 580 Plants (Botany), Genetics -- Research, Evolutionsbiologi, biodiversity conservation, conservation genetics, ERGA, European Reference Genome Atlas, Conservation genetics, Biodiversity conservation, Animal genome mapping, udc:630*1, Genome, GE, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDE.BE.BIOD]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.biod, Biodiversity [MeSH], Genomics [MeSH], Ecology, Evolution, Behavior and Systematics, Genome [MeSH], 3rd-DAS, Genomics, Biodiversity, referenčni genomi, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDE.BE.BEC]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.bec, Chemistry, 10121 Department of Systematic and Evolutionary Botany, genomika, GE Environmental Sciences, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], biodiverziteta, Settore BIO/18 - GENETICA, education, QH426 Genetics, QH301, VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470, [SDE.BE.EVO]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.evo, Genetics, genomi, 10211 Zurich-Basel Plant Science Center, Genomes, Genetik, Biology, QH426, Evolutionary Biology, Ambientale, Ecología, Genética, 1105 Ecology, Evolution, Behavior and Systematics, Wildlife conservation, 570 Life sciences, biology, Human medicine, Animal genetics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genètica
Abstract

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Trends in Ecology & Evolution, 37 (3), ISSN:0169-5347, ISSN:1872-8383

Published
2022

41. Complete sequencing of ape genomes.

Author

Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Anez GM, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O'Neill RJ, Koren S, Makova KD, Phillippy AM, and Eichler EE

Abstract

We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives., Competing Interests: COMPETING INTERESTS E.E.E. is a scientific advisory board (SAB) member of Variant Bio, Inc. C.T.W. is a co-founder/CSO of Clareo Biosciences, Inc. W.L. is a co-founder/CIO of Clareo Biosciences, Inc. The other authors declare no competing interests.

Published
2024
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42. An Introduction to the Callithrix Genus and Overview of Recent Advances in Marmoset Research.

Author

Malukiewicz J, Boere V, de Oliveira MAB, D'arc M, Ferreira JVA, French J, Housman G, de Souza CI, Jerusalinsky L, R de Melo F, M Valença-Montenegro M, Moreira SB, de Oliveira E Silva I, Pacheco FS, Rogers J, Pissinatti A, Del Rosario RCH, Ross C, Ruiz-Miranda CR, Pereira LCM, Schiel N, de Fátima Rodrigues da Silva F, Souto A, Šlipogor V, and Tardif S

Subjects
Animals, Brazil, Callithrix genetics, Genomics, Hybridization, Genetic, Yellow Fever, Zika Virus, Zika Virus Infection
Abstract

We provide here a current overview of marmoset (Callithrix) evolution, hybridization, species biology, basic/biomedical research, and conservation initiatives. Composed of 2 subgroups, the aurita group (C aurita and C flaviceps) and the jacchus group (C geoffroyi, C jacchus, C kuhlii, and C penicillata), this relatively young primate radiation is endemic to the Brazilian Cerrado, Caatinga, and Atlantic Forest biomes. Significant impacts on Callithrix within these biomes resulting from anthropogenic activity include (1) population declines, particularly for the aurita group; (2) widespread geographic displacement, biological invasions, and range expansions of C jacchus and C penicillata; (3) anthropogenic hybridization; and (4) epizootic Yellow Fever and Zika viral outbreaks. A number of Brazilian legal and conservation initiatives are now in place to protect the threatened aurita group and increase research about them. Due to their small size and rapid life history, marmosets are prized biomedical models. As a result, there are increasingly sophisticated genomic Callithrix resources available and burgeoning marmoset functional, immuno-, and epigenomic research. In both the laboratory and the wild, marmosets have given us insight into cognition, social group dynamics, human disease, and pregnancy. Callithrix jacchus and C penicillata are emerging neotropical primate models for arbovirus disease, including Dengue and Zika. Wild marmoset populations are helping us understand sylvatic transmission and human spillover of Zika and Yellow Fever viruses. All of these factors are positioning marmosets as preeminent models to facilitate understanding of facets of evolution, hybridization, conservation, human disease, and emerging infectious diseases., (© The Author(s) 2021. Published by Oxford University Press on behalf of the National Academies of Sciences, Engineering, and Medicine 2021. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Published
2020
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