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Browsing by Author "O'Brien, Stephen J."

Browsing by Author "O'Brien, Stephen J."

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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 ...
  • Analysis of demographic and genetic trends for developing a captive breeding masterplan for the giant panda 
    Ballou, Jonathan D.; Miller, P. S.; Xie, Z.; Wei, R.; Zhang, H.; Zhang, A.; Huang, S.; Sun, S.; David, V.; O'Brien, Stephen J.; Traylor-Holzer, K.; Seal, Ulysses S.; Wildt, David E. (Cambridge University Press, 2006)
  • Author Correction: Puma genomes from North and South America provide insights into the genomic consequences of inbreeding 
    Saremi, Nedda F.; Supple, Megan A.; Byrne, Ashley; Cahill, James A.; Coutinho, Luiz Lehmann; Dalén, Love; Figueiró, Henrique V.; Johnson, Warren E.; Milne, Heather J.; O'Brien, Stephen J.; O'Connell, Brendan; Onorato, David P.; Riley, Seth P. D.; Sikich, Jeff A.; Stahler, Daniel R.; Villela, Priscilla Marqui Schmidt; Vollmers, Christopher; Wayne, Robert K.; Eizirik, Eduardo; Corbett-Detig, Russell; Green, Richard E.; Wilmers, Christopher C.; Shapiro, Beth (2019)
    An amendment to this paper has been published and can be accessed via a link at the top of the paper.
  • Author Correction: Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours 
    Kukekova, Anna V.; Johnson, Jennifer L.; Xiang, Xueyan; Feng, Shaohong; Liu, Shiping; Rando, Halie M.; Kharlamova, Anastasiya V.; Herbeck, Yury; Serdyukova, Natalya A.; Xiong, Zijun; Beklemischeva, Violetta; Koepfli, Klaus-Peter; Gulevich, Rimma G.; Vladimirova, Anastasiya V.; Hekman, Jessica P.; Perelman, Polina L.; Graphodatsky, Aleksander S.; O'Brien, Stephen J.; Wang, Xu; Clark, Andrew G.; Acland, Gregory M.; Trut, Lyudmila N.; Zhang, Guojie (2018)
    In the version of this Article originally published, there were some errors in the affiliations: Stephen J. O'Brien's affiliations were incorrectly listed as 8,9; they should have been 7,9. Affiliation 3 was incorrectly ...
  • 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 ...
  • Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences 
    Tamazian, Gaik; Dobrynin, Pavel; Krasheninnikova, Ksenia; Komissarov, Aleksey; Koepfli, Klaus-Peter; O'Brien, Stephen J. (2016)
    BackgroundAs the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study. Since de novo chromosome assemblies are confounded by repeat-mediated artifacts, ...
  • Comparative Chromosome Mapping of Musk Ox and the X Chromosome among Some Bovidae Species 
    Proskuryakova, Anastasia A.; Kulemzina, Anastasia, I.; Perelman, Polina L.; Yudkin, Dmitry, V.; Lemskaya, Natalya A.; Okhlopkov, Innokentii M.; Kirillin, Egor, V.; Farre, Marta; Larkin, Denis M.; Roelke-Parker, Melody E.; O'Brien, Stephen J.; Bush, Mitchell; Graphodatsky, Alexander S. (2019)
    Bovidae, the largest family in Pecora infraorder, are characterized by a striking variability in diploid number of chromosomes between species and among individuals within a species. The bovid X chromosome is also remarkably ...
  • 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 ...
  • Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation 
    Schmidt-Küntzel, Anne; Dalton, Desiré L.; Menotti-Raymond, Marilyn; Fabiano, Ezequiel; Charruau, Pauline; Johnson, Warren E.; Sommer, Simone; Marker, Laurie; Kotzé, Antoinette; O'Brien, Stephen J. (Elsevier, 2018)
  • Continued decline in genetic diversity among wild cheetahs (Acinonyx jubatus) without further loss of semen quality 
    Terrell, Kimberly A.; Crosier, Adrienne E.; Wildt, David E.; O'Brien, Stephen J.; Anthony, Nicola M.; Marker, Laurie; Johnson, Warren E. (2016)
    As a well-studied felid with limited genetic diversity, the cheetah (Acinonyx jubatus) has shaped much of the scientific debate surrounding inbreeding depression. The species survived a population bottleneck ~ 12,000 years ...
  • Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi 
    Tamazian, Gaik; Dobrynin, Pavel; Zhuk, Anna; Zhernakova, Daria, V.; Perelman, Polina L.; Serdyukova, Natalia A.; Graphodatsky, Alexander S.; Komissarov, Aleksey; Kliver, Sergei; Cherkasov, Nikolay; Scott, Alan F.; Mohr, David W.; Koepfli, Klaus-Peter; O'Brien, Stephen J.; Krasheninnikova, Ksenia (2021)
    The Puma lineage within the family Felidae consists of 3 species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of 2 species from the lineage were previously reported: the cheetah ...
  • The Dynamic Proliferation of CanSINEs Mirrors the Complex Evolution of Feliforms 
    Walters-Conte, Kathryn; Le Johnson, Diana; Johnson, Warren E.; O'Brien, Stephen J.; Pecon-Slattery, Jill (2014)
    Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. Of these, SINEs unique to the order ...
  • Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks 
    Farré, Marta; Kim, Jaebum; Proskuryakova, Anastasia A.; Zhang, Yang; Kulemzina, Anastasia I.; Li, Qiye; Zhou, Yang; Xiong, Yingqi; Johnson, Jennifer L.; Perelman, Polina; Johnson, Warren E.; Warren, Wesley C.; Kukekova, Anna V.; Zhang, Guojie; O'Brien, Stephen J.; Ryder, Oliver A.; Graphodatsky, Alexander S.; Ma, Jian; Lewin, Harris A.; Larkin, Denis M. (2019)
    The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution ...
  • 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. ...
  • GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data 
    Noskova, Ekaterina; Ulyantsev, Vladimir; Koepfli, Klaus-Peter; O'Brien, Stephen J.; Dobrynin, Pavel (2020)
    BACKGROUND: The demographic history of any population is imprinted in the genomes of the individuals that make up the population. One of the most popular and convenient representations of genetic information is the allele ...
  • 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 ...
  • Genetic Monitors of Zoo Populations: Morphological and Electrophoretic Assays 
    Wayne, Robert K.; Forman, Lisa; Newman, A. K.; Simonson, J. M.; O'Brien, Stephen J. (1986)
  • Genetic Restoration of the Florida Panther 
    Johnson, Warren E.; Onorato, David P.; Roelke, Melody E.; Land, E. Darrell; Cunningham, Mark; Belden, Robert C.; McBride, Roy; Jansen, Deborah; Lotz, Mark; Shindle, David; Howard, JoGayle; Wildt, David E.; Penfold, Linda M.; Hostetler, Jeffrey A.; Oli, Madan K.; O'Brien, Stephen J. (2010)
    The rediscovery of remnant Florida panthers (Puma concolor coryi) in southern Florida swamplands prompted a program to protect and stabilize the population. In 1995, conservation managers translocated eight female pumas ...

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