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Browsing by Author "Antunes, Agostinho"

Browsing by Author "Antunes, Agostinho"

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  • Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments 
    Borges, Rui; Johnson, Warren E.; O'Brien, Stephen J.; Gomes, Cidalia; Heesy, Christopher P.; Antunes, Agostinho (2018)
    Background: Based on evolutionary patterns of the vertebrate eye, Walls (1942) hypothesized that early placental mammals evolved primarily in nocturnal habitats. However, not only Eutheria, but all mammals show photic ...
  • Avian binocularity and adaptation to nocturnal environments: genomic insights from a highly-derived visual phenotype 
    Borges, Rui; Fonseca, João; Gomes, Cidália; Johnson, Warren E.; O'brien, Stephen J.; Zhang, Guojie; Gilbert, M. T.; Jarvis, Erich D.; Antunes, Agostinho (2019)
    Typical avian eyes are phenotypically engineered for photopic vision (daylight). In contrast, the highly-derived eyes of the barn owl (Tyto alba) are adapted for scotopic vision (dim light). The dramatic modifications ...
  • Bone-associated gene evolution and the origin of flight in birds 
    Machado, João Paulo; Johnson, Warren E.; Gilbert, M. T.; Zhang, Guojie; Jarvis, Erich D.; O'Brien, Stephen J.; Antunes, Agostinho (2016)
    Background Bones have been subjected to considerable selective pressure throughout vertebrate evolution, such as occurred during the adaptations associated with the development of powered flight. Powered flight evolved ...
  • A collective statement in support of saving pangolins 
    Choo, Siew Woh; Chong, Ju Lian; Gaubert, Philippe; Hughes, Alice Catherine; O'Brien, Stephen; Chaber, Anne-Lise; Antunes, Agostinho; Platto, Sara; Sun, Nick Ching-Min; Yu, Li; Koepfli, Klaus-Peter; Suwal, Tulshi Laxmi; Thakur, Mukesh; Ntie, Stephan; Panjang, Elisa; Kumaran, Jayaraj Vijaya; Mahmood, Tariq; Heighton, Sean P.; Dorji, Dago; Gonedele, Bi Sery; Nelson, Bryan Raveen; Djagoun, Chabi A. M. S.; Loh, Ing Hoe; Kaspal, Prativa; Pauklin, Siim; Michelena, Toby; Zhu, Hongxiang; Lipovich, Leonard; Tian, Xuechen; Deng, Siwei; Mason, Christopher E.; Hu, Jingyang; White, Robert; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Tze King; Wong, Kum Thong; Paterson, Steve; Chen, Ming; Zhang, Yixin; Othman, Rofina Yasmin; Brown, Larry C.; Shen, Bairong; Shui, Guanghou; Ang, Mia Yang; Zhao, Yunqi; Li, Yongming; Zhang, Bo; Chong, Cheng Tung; Meng, Yu; Wong, Aloysius; Su, Jianzhong; Omar, Hasmahzaiti; Shen, Hua; Tan, Choo Hock; Xu, Hongyu; Paterson, Ian C.; Wang, Minyan; Chan, Chee-Kai; Zhang, Siyuan; Dutta, Avirup; Tee, Tay Sun; Juvigny-Khenafou, Noel P. D.; Mutha, Naresh V. R.; Aziz, Muhamad Afiq (2022)
  • Comparative genomics reveals insights into avian genome evolution and adaptation 
    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; Fonseca, Rute R. da; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N.; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth P.; Warren, Wesley; Wilson, Richard K.; Li, Shengbin; Ray, David A.; Green, Richard E.; O'Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. T.; Wang, Jun; Ye, Chen; Liang, Shaoguang; Yan, Zengli; Zepeda, M. L.; Campos, Paula F.; Velazquez, Amhed Missael Vargas; Samaniego, José Alfredo; Avila-Arcos, Mar; Martin, Michael D.; Barnett, Ross; Ribeiro, Angela M.; Mello, Claudio V.; Lovell, Peter V.; Almeida, Daniela; Maldonado, Emanuel; Pereira, Joana; Sunagar, Kartik; Philip, Siby; Dominguez-Bello, Maria; Bunce, Michael; Lambert, David; Brumfield, Robb T.; Sheldon, Frederick H.; Holmes, Edward C.; Gardner, Paul P.; Steeves, Tammy E.; Stadler, Peter F.; Burge, Sarah W.; Lyons, Eric; Smith, Jacqueline; McCarthy, Fiona; Pitel, Frederique; Rhoads, Douglas; Froman, David P. (2014)
    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant ...
  • The complete phylogeny of pangolins: scaling up resources for the molecular tracing of the most trafficked mammals on Earth 
    Gaubert, Philippe; Antunes, Agostinho; Meng, Hao; Miao, Lin; Peigné, Stéphane; Justy, Fabienne; Njiokou, Flobert; Dufour, Sylvain; Danquah, Emmanuel; Alahakoon, Jayanthi; Verheyen, Erik; Stanley, William T.; O'Brien, Stephen J.; Johnson, Warren E.; Luo, Shu-Jin (2018)
    Pangolins, considered the most-trafficked mammals on Earth, are rapidly heading to extinction. Eight extant species of these African and Asian scale-bodied anteaters are commonly recognized, but their evolutionary relationships ...
  • Evolutionary genomics and adaptive evolution of the hedgehog gene family (<I>S</I>hh, <I>Ihh </I>and <I>Dhh</I>) in vertebrates 
    Pereira, Joana; Johnson, Warren E.; O'Brien, Stephen J.; Jarvis, Erich D.; Zhang, Guojie; Gilbert, M. T.; Vasconcelos, Vitor; Antunes, Agostinho (2014)
    The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems ...
  • The evolutionary history of extinct and living lions 
    de Manuel, Marc; Barnett, Ross; Sandoval-Velasco, Marcela; Yamaguchi, Nobuyuki; Vieira, Filipe Garrett; Mendoza, M. Lisandra Zepeda; Liu, Shiping; Martin, Michael D.; Sinding, Mikkel-Holger S.; Mak, Sarah S. T.; Caroe, Christian; Liu, Shanlin; Guo, Chunxue; Zheng, Jiao; Zazula, Grant; Baryshnikov, Gennady; Eizirik, Eduardo; Koepfli, Klaus-Peter; Johnson, Warren E.; Antunes, Agostinho; Sicheritz-Ponten, Thomas; Gopalakrishnan, Shyam; Larson, Greger; Yang, Huanming; O'Brien, Stephen J.; Hansen, Anders J.; Zhang, Guojie; Marques-Bonet, Tomas; Gilbert, M. Thomas P. (2020)
    Lions are one of the world&#39;s most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. ...
  • Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds 
    Borges, Rui; Khan, Imran; Johnson, Warren E.; Gilbert, M. T.; Zhang, Guojie; Jarvis, Erich D.; O'Brien, Stephen J.; Antunes, Agostinho (2015)
    The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary ...
  • Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, <I>Homotherium latidens</I> 
    Barnett, Ross; Westbury, Michael V.; Sandoval-Velasco, Marcela; Vieira, Filipe Garrett; Jeon, Sungwon; Zazula, Grant; Martin, Michael D.; Ho, Simon Y. W.; Mather, Niklas; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmin; de Manuel, Marc; Zepeda-Mendoza, M. Lisandra; Antunes, Agostinho; Baez, Aldo Carmona; De Cahsan, Binia; Larson, Greger; O'Brien, Stephen J.; Eizirik, Eduardo; Johnson, Warren E.; Koepfli, Klaus-Peter; Wilting, Andreas; Fickel, Jorns; Dalen, Love; Lorenzen, Eline D.; Marques-Bonet, Tomas; Hansen, Anders J.; Zhang, Guojie; Bhak, Jong; Yamaguchi, Nobuyuki; Gilbert, M. Thomas P. (2020)
    Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine ...
  • Genomic legacy of the African cheetah, Acinonyx jubatus 
    Dobrynin, Pavel; Liu, Shiping; Tamazian, Gaik; Xiong, Zijun; Yurchenko, Andrey A.; Krasheninnikova, Ksenia; Kliver, Sergey; Schmidt-Küntzel, Anne; Koepfli, Klaus-Peter; Johnson, Warren E.; Kuderna, Lukas F. K.; García-Pérez, Raquel; Manuel, Marc de; Godinez, Ricardo; Komissarov, Aleksey; Makunin, Alexey; Brukhin, Vladimir; Qiu, Weilin; Zhou, Long; Li, Fang; Yi, Jian; Driscoll, Carlos; Antunes, Agostinho; Oleksyk, Taras K.; Eizirik, Eduardo; Perelman, Polina; Roelke, Melody; Wildt, David E.; Diekhans, Mark; Marques-Bonet, Tomas; Marker, Laurie; Bhak, Jong; Wang, Jun; Zhang, Guojie; O'Brien, Stephen J. (2015)
    BACKGROUND: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. RESULTS: Here the genome sequence of wild-born African cheetahs ...
  • Genomic Signatures of Divergent Ecological Strategies in a Recent Radiation of Neotropical Wild Cats 
    Ramirez, Jorge L.; Lescroart, Jonas; Figueiro, Henrique, V.; Torres-Florez, Juan Pablo; Villela, Priscilla M. S.; Coutinho, Luiz L.; Freitas, Patricia D.; Johnson, Warren E.; Antunes, Agostinho; Galetti, Pedro M.; Eizirik, Eduardo (2022)
    Ecological differentiation among diverging species is an important component of the evolutionary process and can be investigated in rapid and recent radiations. Here, we use whole genome sequences of five species from the ...
  • De <I>novo</I> sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin 
    Mohamed Yusoff, Aini; Tan, Tze King; Hari, Ranjeev; Koepfli, Klaus-Peter; Wee, Wei Yee; Antunes, Agostinho; Sitam, Frankie Thomas; Rovie-Ryan, Jeffrine; Karuppannan, Kayal Vizi; Wong, Guat Jah; Lipovich, Leonard; Warren, Wesley C.; O'Brien, Stephen J.; Choo, Siew Woh (2016)
    Pangolins are scale-covered mammals, containing eight endangered species. Maintaining pangolins in captivity is a significant challenge, in part because little is known about their genetics. Here we provide the first ...
  • Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments 
    Khan, Imran; Maldonado, Emanuel; Vasconcelos, Vitor; O'Brien, Stephen J.; Johnson, Warren E.; Antunes, Agostinho (2014)
    Background: Adaptation of mammals to terrestrial life was facilitated by the unique vertebrate trait of body hair, which occurs in a range of morphological patterns. Keratin associated proteins (KRTAPs), the major structural ...
  • Olfactory receptor subgenomes linked with broad ecological adaptations in Sauropsida 
    Khan, Imran; Yang, Zhikai; Maldonado, Emanuel; Li, Cai; Zhang, Guojie; Gilbert, M. T.; Jarvis, Erich D.; O'Brien, Stephen J.; Johnson, Warren E.; Antunes, Agostinho (2015)
    Olfactory receptors (ORs) govern a prime sensory function. Extant birds have distinct olfactory abilities, but the molecular mechanisms underlining diversification and specialization remain mostly unknown. We explored OR ...
  • Pangolin genomes and the evolution of mammalian scales and immunity 
    Choo, Siew Woh; Rayko, Mike; Tan, Tze King; Hari, Ranjeev; Komissarov, Aleksey; Wee, Wei Yee; Yurchenko, Andrey A.; Kliver, Sergey; Tamazian, Gaik; Antunes, Agostinho; Wilson, Richard K.; Warren, Wesley C.; Koepfli, Klaus-Peter; Minx, Patrick; Krasheninnikova, Ksenia; Kotze, Antoinette; Dalton, Desire L.; Vermaak, Elaine; Paterson, Ian C.; Dobrynin, Pavel; Sitam, Frankie Thomas; Rovie-Ryan, Jeffrine; Johnson, Warren E.; Yusoff, Aini Mohamed; Luo, Shu-Jin; Karuppannan, Kayal Vizi; Fang, Gang; Zheng, Deyou; Gerstein, Mark B.; Lipovich, Leonard; O'Brien, Stephen J.; Wong, Guat Jah (2016)
    Pangolins, unique mammals with scales over most of their body, no teeth, poor vision, and an acute olfactory system, comprise the only placental order (Pholidota) without a whole-genome map. To investigate pangolin biology ...
  • Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns 
    Machado, João Paulo; Philip, Siby; Maldonado, Emanuel; O'Brien, Stephen J.; Johnson, Warren E.; Antunes, Agostinho (2016)
    A diverse group of genes are involved in the tooth development of mammals. Several studies, focused mainly on mice and rats, have provided a detailed depiction of the processes coordinating tooth formation and shape. Here ...
  • Response to Comment by Faurby, Werdelin and Svenning 
    O'Brien, Stephen J.; Koepfli, Klaus Peter; Eizirik, Eduardo; Johnson, Warren E.; Driscoll, Carlos; Antunes, Agostinho; Schmidt-Kuntzel, Anne; Marker, Laurie; Dobrynin, Pavel (2016)
  • Sympatric Asian Felid Phylogeography Reveals A Major Indochinese-Sundaic Divergence 
    Luo, Shu-Jin; Zhang, Yue; Johnson, Warren E.; Miao, Lin; Martelli, Paolo; Antunes, Agostinho; Smith, James L. D.; O'Brien, Stephen J. (2014)
    The dynamic geological and climatological history of Southeast Asia has spawned a complex array of ecosystems and 12 of the 37 cat species, making it the most felid-rich region in the world. To examine evolutionary histories ...
  • The Vertebrate TLR Supergene Family Evolved Dynamically by Gene Gain/Loss and Positive Selection Revealing a Host-Pathogen Arms Race in Birds 
    Khan, Imran; Maldonado, Emanuel; Silva, Liliana; Almeida, Daniela; Johnson, Warren E.; O'Brien, Stephen J.; Zhang, Guojie; Jarvis, Erich D.; Gilbert, M. Thomas P.; Antunes, Agostinho (2019)
    The vertebrate toll-like receptor (TLRs) supergene family is a first-line immune defense against viral and non-viral pathogens. Here, comparative evolutionary-genomics of 79 vertebrate species (8 mammals, 48 birds, 11 ...

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