30 results on '"Fiddaman, Steven R."'
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2. Genomic insights into the secondary aquatic transition of penguins
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Cole, Theresa L., Zhou, Chengran, Fang, Miaoquan, Pan, Hailin, Ksepka, Daniel T., Fiddaman, Steven R., Emerling, Christopher A., Thomas, Daniel B., Bi, Xupeng, Fang, Qi, Ellegaard, Martin R., Feng, Shaohong, Smith, Adrian L., Heath, Tracy A., Tennyson, Alan J. D., Borboroglu, Pablo García, Wood, Jamie R., Hadden, Peter W., Grosser, Stefanie, Bost, Charles-André, Cherel, Yves, Mattern, Thomas, Hart, Tom, Sinding, Mikkel-Holger S., Shepherd, Lara D., Phillips, Richard A., Quillfeldt, Petra, Masello, Juan F., Bouzat, Juan L., Ryan, Peter G., Thompson, David R., Ellenberg, Ursula, Dann, Peter, Miller, Gary, Dee Boersma, P., Zhao, Ruoping, Gilbert, M. Thomas P., Yang, Huanming, Zhang, De-Xing, and Zhang, Guojie
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- 2022
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3. Pattern recognition receptors
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Smith, Adrian L., primary and Fiddaman, Steven R., additional
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- 2022
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4. List of contributors
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Adelman, James S., primary, Ardia, Daniel R., additional, Astill, Jake, additional, Balic, Adam, additional, Barrow, Paul, additional, Beal, Richard, additional, Bean, Andrew G.D., additional, Bortoluzzi, Cristiano, additional, Dalgaard, Tina Sørensen, additional, Davison, Fred, additional, de Wit, J.J. (Sjaak), additional, Dekkers, Jack C.M., additional, Doran, Timothy, additional, Dunon, Dominique, additional, Erf, Gisela F., additional, Fiddaman, Steven R., additional, Gautron, Joel, additional, Göbel, Thomas W., additional, Guabiraba, Rodrigo, additional, Guyot, Nicolas, additional, Härtle, Sonja, additional, Hincke, Maxwell, additional, Jaffredo, Thierry, additional, Kaspers, Bernd, additional, Kaufman, Jim, additional, Kogut, Michael H., additional, Lamont, Susan J., additional, Lowenthal, John W., additional, Magor, Katharine E., additional, Montiel, Enrique, additional, Nagy, Nándor, additional, Nair, Venugopal, additional, Oláh, Imre, additional, Powers, Claire, additional, Ratcliffe, Michael J.H., additional, Rebel, Johanna M.J., additional, Réhault-Godbert, Sophie, additional, Robin, Catherine, additional, Schat, Karel A., additional, Schultz, Ursula, additional, Schusser, Benjamin, additional, Sharif, Shayan, additional, Skinner, Michael A., additional, Smith, Adrian L., additional, Sutton, Kate, additional, Veldhuizen, Edwin J.A., additional, Vervelde, Lonneke, additional, Vinkler, Michal, additional, Wigley, Paul, additional, Wolc, Anna, additional, Wood, R. Darren, additional, Yvernogeau, Laurent, additional, and Zhou, Huaijun, additional
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- 2022
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5. Receding ice drove parallel expansions in Southern Ocean penguins
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Cole, Theresa L., Dutoit, Ludovic, Dussex, Nicolas, Hart, Tom, Alexander, Alana, Younger, Jane L., Clucas, Gemma V., Frugone, María José, Cherel, Yves, Cuthbert, Richard, Ellenberg, Ursula, Fiddaman, Steven R., Hiscock, Johanna, Houston, David, Jouventin, Pierre, Mattern, Thomas, Miller, Gary, Miskelly, Colin, Nolan, Paul, Polito, Michael J., Quillfeldt, Petra, Ryan, Peter G., Smith, Adrian, Tennyson, Alan J. D., Thompsona, David, Wieneckeb, Barbara, Viannac, Juliana A., and Waters, Jonathan M.
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- 2019
6. Correction to: Repertoire analysis of γδ T cells in the chicken enables functional annotation of the genomic region revealing highly variable pan-tissue TCR gamma V gene usage as well as identifying public and private repertoires
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Dixon, Robert, Preston, Stephen G., Dascalu, Stefan, Flammer, Patrik G., Fiddaman, Steven R., McLoughlin, Kirstie, Boyd, Amy, Volf, Jiri, Rychlik, Ivan, Bonsall, Michael B., Kaspers, Bernd, and Smith, Adrian L.
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- 2021
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7. Repertoire analysis of γδ T cells in the chicken enables functional annotation of the genomic region revealing highly variable pan-tissue TCR gamma V gene usage as well as identifying public and private repertoires
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Dixon, Robert, Preston, Stephen G., Dascalu, Stefan, Flammer, Patrik G., Fiddaman, Steven R., McLoughlin, Kirstie, Boyd, Amy, Volf, Jiri, Rychlik, Ivan, Bonsall, Michael B., Kaspers, Bernd, and Smith, Adrian L.
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- 2021
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8. Understanding the evolution of immune genes in jawed vertebrates
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Vinkler, Michal, Fiddaman, Steven R., Tesický, Martin, O'Connor, Emily A., Savage, Anna E., Lenz, Tobias L., Smith, Adrian L., Kaufman, Jim, Bolnick, Daniel I., Davies, Charli S., Dedic, Neira, Flies, Andrew S., Gomez Samblas, M. Mercedes, Henschen, Amberleigh E., Novák, Karel, Palomar, Gemma, Raven, Nynke, Samaké, Kalifa, Slade, Joel, Kuttiyarthu Veetil, Nithya, Voukali, Eleni, Höglund, Jacob, Richardson, David S., Westerdahl, Helena, Vinkler, Michal, Fiddaman, Steven R., Tesický, Martin, O'Connor, Emily A., Savage, Anna E., Lenz, Tobias L., Smith, Adrian L., Kaufman, Jim, Bolnick, Daniel I., Davies, Charli S., Dedic, Neira, Flies, Andrew S., Gomez Samblas, M. Mercedes, Henschen, Amberleigh E., Novák, Karel, Palomar, Gemma, Raven, Nynke, Samaké, Kalifa, Slade, Joel, Kuttiyarthu Veetil, Nithya, Voukali, Eleni, Höglund, Jacob, Richardson, David S., and Westerdahl, Helena
- Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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- 2023
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9. Ancient chicken remains reveal the origins of virulence in Marek’s disease virus
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Fiddaman, Steven R., Dimopoulos, Evangelos A., Lebrasseur, Ophélie, du Plessis, Louis, Vrancken, Bram, Charlton, Sophy, Haruda, Ashleigh F., Tabbada, Kristina, Flammer, Patrik G., Dascalu, Stefan, Marković, Nemanja, Li, Hannah, Franklin, Gabrielle, Symmons, Robert, Baron, Henriette, Daróczi-Szabó, László, Shaymuratova, Dilyara N., Askeyev, Igor V., Putelat, Olivier, Sana, Maria, Davoudi, Hossein, Fathi, Homa, Mucheshi, Amir Saed, Vahdati, Ali Akbar, Zhang, Liangren, Foster, Alison, Sykes, Naomi, Baumberg, Gabrielle Cass, Bulatović, Jelena, Askeyev, Arthur O., Askeyev, Oleg V., Mashkour, Marjan, Pybus, Oliver G., Nair, Venugopal, Larson, Greger, Smith, Adrian L., Frantz, Laurent A. F., Fiddaman, Steven R., Dimopoulos, Evangelos A., Lebrasseur, Ophélie, du Plessis, Louis, Vrancken, Bram, Charlton, Sophy, Haruda, Ashleigh F., Tabbada, Kristina, Flammer, Patrik G., Dascalu, Stefan, Marković, Nemanja, Li, Hannah, Franklin, Gabrielle, Symmons, Robert, Baron, Henriette, Daróczi-Szabó, László, Shaymuratova, Dilyara N., Askeyev, Igor V., Putelat, Olivier, Sana, Maria, Davoudi, Hossein, Fathi, Homa, Mucheshi, Amir Saed, Vahdati, Ali Akbar, Zhang, Liangren, Foster, Alison, Sykes, Naomi, Baumberg, Gabrielle Cass, Bulatović, Jelena, Askeyev, Arthur O., Askeyev, Oleg V., Mashkour, Marjan, Pybus, Oliver G., Nair, Venugopal, Larson, Greger, Smith, Adrian L., and Frantz, Laurent A. F.
- Abstract
The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek’s disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.
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- 2023
10. Fourth Report on Chicken Genes and Chromosomes 2022
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Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, Zhou, Huaijun, Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, and Zhou, Huaijun
- Abstract
Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens
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- 2023
11. Understanding the evolution of immune genes in jawed vertebrates
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Vinkler, Michal, primary, Fiddaman, Steven R., additional, Těšický, Martin, additional, O'Connor, Emily A., additional, Savage, Anna E., additional, Lenz, Tobias L., additional, Smith, Adrian L., additional, Kaufman, Jim, additional, Bolnick, Daniel I., additional, Davies, Charli S., additional, Dedić, Neira, additional, Flies, Andrew S., additional, Samblás, M. Mercedes Gómez, additional, Henschen, Amberleigh E., additional, Novák, Karel, additional, Palomar, Gemma, additional, Raven, Nynke, additional, Samaké, Kalifa, additional, Slade, Joel, additional, Veetil, Nithya Kuttiyarthu, additional, Voukali, Eleni, additional, Höglund, Jacob, additional, Richardson, David S., additional, and Westerdahl, Helena, additional
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- 2023
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12. Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens
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Fiddaman, Steven R, Klopp, Christophe, Charles, Mathieu, Bardou, Philippe, Lebrasseur, Ophélie, Derks, Martijn F. L., Schauer, Jens, Reimer, Christian, Geibel, Johannes, Gheyas, Almas, Smith, Adrian L., Schnabel, Robert, Cerezo, Maria Luisa Martin, Nishibori, Masahide, Godinez, Cyrill John P., Layos, John King N., Alfieri, James M., Blackmon, Heath, Athrey, Giridhar N., Larson, Greger, Ng’ang’a, Ismael, Muir, William, Lange, Margaret, Wright, Dominic, Cheng, Hans H, Simianer, Henner, Weigend, Steffen, Warren, Wesley, Crooijmans, Richard P. M. A., Hanotte, Olivier, Smith, Jacqueline, Tixier-Boichard, Michele, and Frantz, Laurent Af
- Abstract
On October 25-26, 2019, a satellite meeting devoted to the preparation of a Chicken Genome Diversity Consortium was organised after the 11th European Symposium of Poultry Genetics in Prague. Researchers involved in chicken genomics from Europe, Africa and China, discussed the objectives of such a consortium with some presenting their data. However, the technical aspects of how to share and jointly analyse the data were not finalized, nor was the funding model for the cost of data storage and computation. In 2021, an opportunity arose with the call for projects of the SuperMUC computing cluster of the Leibniz-Rechenzentrum in Germany. A new consortium of scientists re-launched the discussion to establish a project with the aim to explore how the high-throughput genomics age can be harnessed to answer evolutionary questions surrounding the chicken. The FARMGENOMIC project (23826) was accepted for funding in autumn 2021, gathering around 20 members from 10 institutions in Europe, North America, and Africa. This newly formed Chicken Genomic Diversity consortium brings together members from a variety of disciplines, including genomics, palaeogenetics, animal breeding, immunology, organismal biology, evolutionary biology, and archaeology. Central to the consortium are the concepts of inclusivity and openness – all data are to be made available to all members of the consortium, and later distributed to the wider community, and collaborations between groups are fostered and actively encouraged. It is hoped this state-of-the-art resource, curated in-house by bioinformaticians, will enable the community to answer previously intractable questions in chicken evolution.
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- 2023
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13. Fourth Report on Chicken Genes and Chromosomes 2022
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Smith, Jacqueline, primary, Alfieri, James M., additional, Anthony, Nick, additional, Arensburger, Peter, additional, Athrey, Giridhar N., additional, Balacco, Jennifer, additional, Balic, Adam, additional, Bardou, Philippe, additional, Barela, Paul, additional, Bigot, Yves, additional, Blackmon, Heath, additional, Borodin, Pavel M., additional, Carroll, Rachel, additional, Casono, Meya C., additional, Charles, Mathieu, additional, Cheng, Hans, additional, Chiodi, Maddie, additional, Cigan, Lacey, additional, Coghill, Lyndon M., additional, Crooijmans, Richard, additional, Das, Neelabja, additional, Davey, Sean, additional, Davidian, Asya, additional, Degalez, Fabien, additional, Dekkers, Jack M., additional, Derks, Martijn, additional, Diack, Abigail B., additional, Djikeng, Appolinaire, additional, Drechsler, Yvonne, additional, Dyomin, Alexander, additional, Fedrigo, Olivier, additional, Fiddaman, Steven R., additional, Formenti, Giulio, additional, Frantz, Laurent A.F., additional, Fulton, Janet E., additional, Gaginskaya, Elena, additional, Galkina, Svetlana, additional, Gallardo, Rodrigo A., additional, Geibel, Johannes, additional, Gheyas, Almas, additional, Godinez, Cyrill John P., additional, Goodell, Ashton, additional, Graves, Jennifer A. M., additional, Griffin, Daren K., additional, Haase, Bettina, additional, Han, Jian-Lin, additional, Hanotte, Olivier, additional, Henderson, Lindsay J., additional, Hou, Zhuo-Cheng, additional, Howe, Kerstin, additional, Huynh, Lan, additional, Ilatsia, Evans, additional, Jarvis, Erich, additional, Johnson, Sarah M., additional, Kaufman, Jim, additional, Kelly, Terra, additional, Kemp, Steve, additional, Kern, Colin, additional, Keroack, Jacob H., additional, Klopp, Christophe, additional, Lagarrigue, Sandrine, additional, Lamont, Susan J., additional, Lange, Margaret, additional, Lanke, Anika, additional, Larkin, Denis M., additional, Larson, Greger, additional, Layos, John King N., additional, Lebrasseur, Ophélie, additional, Malinovskaya, Lyubov P., additional, Martin, Rebecca J., additional, Martin Cerezo, Maria Luisa, additional, Mason, Andrew S., additional, McCarthy, Fiona M., additional, McGrew, Michael J., additional, Mountcastle, Jacquelyn, additional, Muhonja, Christine Kamidi, additional, Muir, William, additional, Muret, Kévin, additional, Murphy, Terence, additional, Ng’ang’a, Ismael, additional, Nishibori, Masahide, additional, O’Connor, Rebecca E., additional, Ogugo, Moses, additional, Okimoto, Ron, additional, Ouko, Ochieng, additional, Patel, Hardip R., additional, Perini, Francesco, additional, Pigozzi, María Ines, additional, Potter, Krista C., additional, Price, Peter D., additional, Reimer, Christian, additional, Rice, Edward S., additional, Rocos, Nicolas, additional, Rogers, Thea F., additional, Saelao, Perot, additional, Schauer, Jens, additional, Schnabel, Robert, additional, Schneider, Valerie, additional, Simianer, Henner, additional, Smith, Adrian, additional, Stevens, Mark P., additional, Stiers, Kyle, additional, Tiambo, Christian Keambou, additional, Tixier-Boichard, Michele, additional, Torgasheva, Anna A., additional, Tracey, Alan, additional, Tregaskes, Clive A., additional, Vervelde, Lonneke, additional, Wang, Ying, additional, Warren, Wesley C., additional, Waters, Paul D., additional, Webb, David, additional, Weigend, Steffen, additional, Wolc, Anna, additional, Wright, Alison E., additional, Wright, Dominic, additional, Wu, Zhou, additional, Yamagata, Masahito, additional, Yang, Chentao, additional, Yin, Zhong-Tao, additional, Young, Michelle C., additional, Zhang, Guojie, additional, Zhao, Bingru, additional, and Zhou, Huaijun, additional
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- 2023
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14. RNA-seq raw reads of chicken hypothalamus and breast muscle
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Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, Zhou, Huaijun, Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, and Zhou, Huaijun
- Abstract
The objective of the study was to identify genes, gene networks, and signaling pathways associated with heat stress under Newcastle disease virus (NDV infection in the hypothalamus and the breast muscle of chickens by transcriptome profiling, using two highly genetically distinct inbred chicken lines (Leghorn and Fayoumi).
- Published
- 2022
15. Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors
- Author
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Fiddaman, Steven R., Vinkler, Michal, Spiro, Simon G., Levy, Hila, Emerling, Christopher A., Boyd, Amy C., Dimopoulos, Evangelos A., Vianna, Juliana A., Cole, Theresa L., Pan, Hailin, Fang, Miaoquan, Zhang, Guojie, Hart, Tom, Frantz, Laurent A. F., Smith, Adrian L., Fiddaman, Steven R., Vinkler, Michal, Spiro, Simon G., Levy, Hila, Emerling, Christopher A., Boyd, Amy C., Dimopoulos, Evangelos A., Vianna, Juliana A., Cole, Theresa L., Pan, Hailin, Fang, Miaoquan, Zhang, Guojie, Hart, Tom, Frantz, Laurent A. F., and Smith, Adrian L.
- Abstract
Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations.
- Published
- 2022
16. Chapter 8.6 - Pattern recognition receptors
- Author
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Smith, Adrian L. and Fiddaman, Steven R.
- Published
- 2022
- Full Text
- View/download PDF
17. Comparison of CpG- and UpA-mediated restriction of RNA virus replication in mammalian and avian cells and investigation of potential ZAP-mediated shaping of host transcriptome compositions
- Author
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Odon, Valerie, primary, Fiddaman, Steven R., additional, Smith, Adrian L., additional, and Simmonds, Peter, additional
- Published
- 2022
- Full Text
- View/download PDF
18. Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors
- Author
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Fiddaman, Steven R, primary, Vinkler, Michal, additional, Spiro, Simon G, additional, Levy, Hila, additional, Emerling, Christopher A, additional, Boyd, Amy C, additional, Dimopoulos, Evangelos A, additional, Vianna, Juliana A, additional, Cole, Theresa L, additional, Pan, Hailin, additional, Fang, Miaoquan, additional, Zhang, Guojie, additional, Hart, Tom, additional, Frantz, Laurent A F, additional, and Smith, Adrian L, additional
- Published
- 2021
- Full Text
- View/download PDF
19. Additional file 2 of Repertoire analysis of ���� T cells in the chicken enables functional annotation of the genomic region revealing highly variable pan-tissue TCR gamma V gene usage as well as identifying public and private repertoires
- Author
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Dixon, Robert, Preston, Stephen G., Dascalu, Stefan, Flammer, Patrik G., Fiddaman, Steven R., McLoughlin, Kirstie, Boyd, Amy, Volf, Jiri, Rychlik, Ivan, Bonsall, Michael B., Kaspers, Bernd, and Smith, Adrian L.
- Abstract
Additional file 2: Supplementary Fig. 1. - Levels of Publicity in each TRGV Gene in PA12 White Leghorn Chickens. Supplementary Fig. 2. - Rarefaction Plots generated using iNEXT. Supplementary Fig. 3. - Variation in the Patterns of TRGV Gamma Diversity in Tissues of PA12 White Leghorn Chickens. Supplementary Fig. 4. - Diversity of TRGV Genes in different Tissues
- Published
- 2021
- Full Text
- View/download PDF
20. Additional file 1 of Repertoire analysis of ���� T cells in the chicken enables functional annotation of the genomic region revealing highly variable pan-tissue TCR gamma V gene usage as well as identifying public and private repertoires
- Author
-
Dixon, Robert, Preston, Stephen G., Dascalu, Stefan, Flammer, Patrik G., Fiddaman, Steven R., McLoughlin, Kirstie, Boyd, Amy, Volf, Jiri, Rychlik, Ivan, Bonsall, Michael B., Kaspers, Bernd, and Smith, Adrian L.
- Abstract
Additional file 1. Primers Used in this Study
- Published
- 2021
- Full Text
- View/download PDF
21. Identification of Circovirus Genome in a Chinstrap Penguin (Pygoscelis antarcticus) and Adélie Penguin (Pygoscelis adeliae) on the Antarctic Peninsula
- Author
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Levy, Hila, primary, Fiddaman, Steven R., additional, Djurhuus, Anni, additional, Black, Caitlin E., additional, Kraberger, Simona, additional, Smith, Adrian L., additional, Hart, Tom, additional, and Varsani, Arvind, additional
- Published
- 2020
- Full Text
- View/download PDF
22. Evidence of pathogen-induced immunogenetic selection across the large geographic range of a wild seabird
- Author
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Levy, Hila, Fiddaman, Steven R., Vianna, Juliana A., Noll, Daly, Clucas, Gemma V., Sidhu, Jasmine K.H., Polito, Michael J., Bost, Charles A., Phillips, Richard, Crofts, Sarah, Miller, Gary D., Pistorius, Pierre, Bonnadonna, Francesco, Le Bohec, Céline, Barbosa, Andrés A., Trathan, Phil, Rey, Andrea Raya, Frantz, Laurent A.F., Hart, Tom, Smith, Adrian L., Levy, Hila, Fiddaman, Steven R., Vianna, Juliana A., Noll, Daly, Clucas, Gemma V., Sidhu, Jasmine K.H., Polito, Michael J., Bost, Charles A., Phillips, Richard, Crofts, Sarah, Miller, Gary D., Pistorius, Pierre, Bonnadonna, Francesco, Le Bohec, Céline, Barbosa, Andrés A., Trathan, Phil, Rey, Andrea Raya, Frantz, Laurent A.F., Hart, Tom, and Smith, Adrian L.
- Abstract
Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depends on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes - the Toll-like receptors (TLRs) - across the range of the Gentoo. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected co-segregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo as a sentinel species in some of the world’s most rapidly changing environments.
- Published
- 2020
23. Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird
- Author
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Biotechnology and Biological Sciences Research Council (UK), Ministerio de Ciencia e Innovación (España), Levy, Hila, Fiddaman, Steven R., Vianna, Juliana A., Noll, Daly, Clucas, Gemma V., Sidhu, Jasmine K. H., Polito, Michael J., Bost, Charles A., Phillips, Richard A., Crofts, Sarah, Miller, Gary D., Pistorius, Pierre, Bonnadonna, Francesco, Le Bohec, Céline, Barbosa, Andrés, Trathan, Philip N., Raya Rey, Andrea, Frantz, Laurent A. F., Hart, Tom, Smith, Adrian L., Biotechnology and Biological Sciences Research Council (UK), Ministerio de Ciencia e Innovación (España), Levy, Hila, Fiddaman, Steven R., Vianna, Juliana A., Noll, Daly, Clucas, Gemma V., Sidhu, Jasmine K. H., Polito, Michael J., Bost, Charles A., Phillips, Richard A., Crofts, Sarah, Miller, Gary D., Pistorius, Pierre, Bonnadonna, Francesco, Le Bohec, Céline, Barbosa, Andrés, Trathan, Philip N., Raya Rey, Andrea, Frantz, Laurent A. F., Hart, Tom, and Smith, Adrian L.
- Abstract
Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes-the Toll-like receptors (TLRs)-across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected cosegregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo penguin as a sentinel species in some of the world's most rapidly changing environments.
- Published
- 2020
24. Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors.
- Author
-
Fiddaman, Steven R, Vinkler, Michal, Spiro, Simon G, Levy, Hila, Emerling, Christopher A, Boyd, Amy C, Dimopoulos, Evangelos A, Vianna, Juliana A, Cole, Theresa L, Pan, Hailin, Fang, Miaoquan, Zhang, Guojie, Hart, Tom, Frantz, Laurent A F, and Smith, Adrian L
- Subjects
IMMUNOGENETICS ,PSEUDOGENES ,WILDLIFE diseases ,IMMUNOLOGY ,HAPLOTYPES - Abstract
Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B , TLR4 , and TLR5. Intriguingly, TLR15 , which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp. but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus , which is responsible for significant mortality in wild and captive bird populations. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
25. Correction to: High-coverage genomes to elucidate the evolution of penguins
- Author
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Pan, Hailin, primary, Cole, Theresa L, primary, Bi, Xupeng, primary, Fang, Miaoquan, primary, Zhou, Chengran, primary, Yang, Zhengtao, primary, Ksepka, Daniel T, primary, Hart, Tom, primary, Bouzat, Juan L, primary, Argilla, Lisa S, primary, Bertelsen, Mads F, primary, Boersma, P Dee, primary, Bost, Charles-Andre, primary, Cherel, Yves, primary, Dann, Peter, primary, Fiddaman, Steven R, primary, Howard, Pauline, primary, Labuschagne, Kim, primary, Mattern, Thomas, primary, Miller, Gary, primary, Parker, Patricia, primary, Phillips, Richard A, primary, Quillfeldt, Petra, primary, Ryan, Peter G, primary, Taylor, Helen, primary, Thompson, David R, primary, Young, Melanie J, primary, Ellegaard, Martin R, primary, Gilbert, M Thomas P, primary, Sinding, Mikkel-Holger S, primary, Pacheco, George, primary, Shepherd, Lara D, primary, Tennyson, Alan J D, primary, Grosser, Stefanie, primary, Kay, Emily, primary, Nupen, Lisa J, primary, Ellenberg, Ursula, primary, Houston, David M, primary, Reeve, Andrew Hart, primary, Johnson, Kathryn, primary, Masello, Juan F, primary, Stracke, Thomas, primary, McKinlay, Bruce, primary, Garc´ıa Borboroglu, Pablo, primary, Zhang, De-Xing, primary, and Zhang, Guojie, primary
- Published
- 2020
- Full Text
- View/download PDF
26. Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird
- Author
-
Levy, Hila, primary, Fiddaman, Steven R, primary, Vianna, Juliana A, primary, Noll, Daly, primary, Clucas, Gemma V, primary, Sidhu, Jasmine K H, primary, Polito, Michael J, primary, Bost, Charles A, primary, Phillips, Richard A, primary, Crofts, Sarah, primary, Miller, Gary D, primary, Pistorius, Pierre, primary, Bonnadonna, Francesco, primary, Le Bohec, Céline, primary, Barbosa, Andrés, primary, Trathan, Phil, primary, Raya Rey, Andrea, primary, Frantz, Laurent A F, primary, Hart, Tom, primary, and Smith, Adrian L, primary
- Published
- 2020
- Full Text
- View/download PDF
27. High-coverage genomes to elucidate the evolution of penguins
- Author
-
Pan, Hailin, primary, Cole, Theresa L, primary, Bi, Xupeng, primary, Fang, Miaoquan, primary, Zhou, Chengran, primary, Yang, Zhengtao, primary, Ksepka, Daniel T, primary, Hart, Tom, primary, Bouzat, Juan L, primary, Argilla, Lisa S, primary, Bertelsen, Mads F, primary, Boersma, P Dee, primary, Bost, Charles-André, primary, Cherel, Yves, primary, Dann, Peter, primary, Fiddaman, Steven R, primary, Howard, Pauline, primary, Labuschagne, Kim, primary, Mattern, Thomas, primary, Miller, Gary, primary, Parker, Patricia, primary, Phillips, Richard A, primary, Quillfeldt, Petra, primary, Ryan, Peter G, primary, Taylor, Helen, primary, Thompson, David R, primary, Young, Melanie J, primary, Ellegaard, Martin R, primary, Gilbert, M Thomas P, primary, Sinding, Mikkel-Holger S, primary, Pacheco, George, primary, Shepherd, Lara D, primary, Tennyson, Alan J D, primary, Grosser, Stefanie, primary, Kay, Emily, primary, Nupen, Lisa J, primary, Ellenberg, Ursula, primary, Houston, David M, primary, Reeve, Andrew Hart, primary, Johnson, Kathryn, primary, Masello, Juan F, primary, Stracke, Thomas, primary, McKinlay, Bruce, primary, Borboroglu, Pablo García, primary, Zhang, De-Xing, primary, and Zhang, Guojie, primary
- Published
- 2019
- Full Text
- View/download PDF
28. High-coverage genomes to elucidate the evolution of penguins
- Author
-
Pan, Hailin, Cole, Theresa L., Bi, Xupeng, Fang, Miaoquan, Zhou, Chengran, Yang, Zhengtao, Hart, Tom, Bouzat, Juan L., Argilla, Lisa S., Bertelsen, Mads F., Boersma, P. Dee, Bost, Charles-André, Cherel, Yves, Dann, Peter, Fiddaman, Steven R., Howard, Pauline, Labuschagne, Kim, Mattern, Thomas, Miller, Gary, Parker, Patricia, Phillips, Richard A., Quillfeldt, Petra, Ryan, Peter G., Taylor, Helen, Thompson, David R., Young, Melanie J., Ellegaard, Martin R., Gilbert, M. Thomas P., Mikkel-Holger, S. Sinding, Pacheco, George, Shepherd, Lara D., Tennyson, Alan J.D., Grosser, Stefanie, Kay, Emily, Nupen, Lisa j., Ellenberg, Ursula, Houston, David M., Reeve, Andrew Hart, Johnson, Kathryn, Masello, Juan F., Stracke, Thomas, McKinlay, Bruce, Zhang, De Xing, Zhang, Guojie, Pan, Hailin, Cole, Theresa L., Bi, Xupeng, Fang, Miaoquan, Zhou, Chengran, Yang, Zhengtao, Hart, Tom, Bouzat, Juan L., Argilla, Lisa S., Bertelsen, Mads F., Boersma, P. Dee, Bost, Charles-André, Cherel, Yves, Dann, Peter, Fiddaman, Steven R., Howard, Pauline, Labuschagne, Kim, Mattern, Thomas, Miller, Gary, Parker, Patricia, Phillips, Richard A., Quillfeldt, Petra, Ryan, Peter G., Taylor, Helen, Thompson, David R., Young, Melanie J., Ellegaard, Martin R., Gilbert, M. Thomas P., Mikkel-Holger, S. Sinding, Pacheco, George, Shepherd, Lara D., Tennyson, Alan J.D., Grosser, Stefanie, Kay, Emily, Nupen, Lisa j., Ellenberg, Ursula, Houston, David M., Reeve, Andrew Hart, Johnson, Kathryn, Masello, Juan F., Stracke, Thomas, McKinlay, Bruce, Zhang, De Xing, and Zhang, Guojie
- Abstract
Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes.
- Published
- 2019
29. Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation
- Author
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Cole, Theresa L., Ksepka, Daniel T., Mitchell, Kieren J, Tennyson, Alan J. D., Thomas, Daniel B., Pan, Hailin, Zhang, Guojie, Rawlence, Nicolas J., Wood, Jamie R., Bover, Pere, Bouzat, Juan L., Cooper, Alan, Fiddaman, Steven R., Hart, Tom, Miller, Gary, Ryan, Peter G., Shepherd, Lara D., Wilmshurst, Janet M., Waters, Jonathan M., Cole, Theresa L., Ksepka, Daniel T., Mitchell, Kieren J, Tennyson, Alan J. D., Thomas, Daniel B., Pan, Hailin, Zhang, Guojie, Rawlence, Nicolas J., Wood, Jamie R., Bover, Pere, Bouzat, Juan L., Cooper, Alan, Fiddaman, Steven R., Hart, Tom, Miller, Gary, Ryan, Peter G., Shepherd, Lara D., Wilmshurst, Janet M., and Waters, Jonathan M.
- Abstract
The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa diverged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins. Our analysis also reveals two new recently extinct island-endemic penguin taxa from New Zealand's Chatham Islands: Eudyptes warhami sp. nov. and a dwarf subspecies of the yellow-eyed penguin, Megadyptes antipodes richdalei ssp. nov. Eudyptes warhami diverged from the Antipodes Islands erect-crested penguin between 1.1 and 2.5 Ma, shortly after the emergence of the Chatham Islands (∼3 Ma). This new finding of recently evolved taxa on this young archipelago provides further evidence that the radiation of penguins over the last 5 Ma has been linked to island emergence. Mitogenomic analyses of all penguin species, and the discovery of two new extinct penguin taxa, highlight the importance of island formation in the diversification of penguins, as well as the extent to which anthropogenic extinctions have affected island-endemic taxa across the Southern Hemisphere's isolated archipelagos.
- Published
- 2019
30. Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation
- Author
-
Cole, Theresa L, primary, Ksepka, Daniel T, primary, Mitchell, Kieren J, primary, Tennyson, Alan J D, primary, Thomas, Daniel B, primary, Pan, Hailin, primary, Zhang, Guojie, primary, Rawlence, Nicolas J, primary, Wood, Jamie R, primary, Bover, Pere, primary, Bouzat, Juan L, primary, Cooper, Alan, primary, Fiddaman, Steven R, primary, Hart, Tom, primary, Miller, Gary, primary, Ryan, Peter G, primary, Shepherd, Lara D, primary, Wilmshurst, Janet M, primary, and Waters, Jonathan M, primary
- Published
- 2019
- Full Text
- View/download PDF
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