Now showing items 1-17 of 17

    • A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis. 

      Ribeiro, Ângela M; Zepeda-Mendoza, M Lisandra; Bertelsen, Mads F; Kristensen, Annemarie T; Jarvis, Erich D; Gilbert, M Thomas P; da Fonseca, Rute R (BMC Evol Biol, 2015-06-30)
      BACKGROUND: Hemostasis is a defense mechanism that enhances an organism's survival by minimizing blood loss upon vascular injury. In vertebrates, hemostasis has been evolving with the cardio-vascular and hemodynamic systems ...
    • Avian genomes. A flock of genomes. Introduction. 

      Zhang, Guojie; Jarvis, Erich D; Gilbert, M Thomas P (Science, 2014-12-12)
    • Avianbase: a community resource for bird genomics. 

      Eöry, Lél; Gilbert, M Thomas P; Li, Cai; Li, Bo; Archibald, Alan; Aken, Bronwen L; Zhang, Guojie; ... (10 authors) (Genome Biol, 2015-01-29)
      Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore ...
    • Comparative genomic data of the Avian Phylogenomics Project. 

      Zhang, Guojie; Li, Bo; Li, Cai; Gilbert, M Thomas P; Jarvis, Erich D; Wang, Jun; Wang, Jun; ... (8 authors) (2014)
      BACKGROUND: The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the ...
    • Comparative genomics reveals insights into avian genome evolution and adaptation. 

      Alfaro-Núñez, A; Alström, P; An, N; Antunes, A; Avian Genome Consortium; Bertelsen, MF; Borges, R; ... (106 authors) (Science, 2014-12-12)
      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 clades. ...
    • Complex evolutionary trajectories of sex chromosomes across bird taxa. 

      Zhou, Qi; Zhang, Jilin; Bachtrog, Doris; An, Na; Huang, Quanfei; Jarvis, Erich D; Gilbert, M Thomas P; ... (8 authors) (Science, 2014-12-12)
      Sex-specific chromosomes, like the W of most female birds and the Y of male mammals, usually have lost most genes owing to a lack of recombination. We analyze newly available genomes of 17 bird species representing the avian ...
    • Convergent transcriptional specializations in the brains of humans and song-learning birds. 

      Pfenning, Andreas R; Hara, Erina; Whitney, Osceola; Rivas, Miriam V; Wang, Rui; Roulhac, Petra L; Howard, Jason T; ... (25 authors) (Science, 2014-12-12)
      Song-learning birds and humans share independently evolved similarities in brain pathways for vocal learning that are essential for song and speech and are not found in most other species. Comparisons of brain transcriptomes ...
    • Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles. 

      Greenwold, Matthew J; Bao, Weier; Jarvis, Erich D; Hu, Haofu; Li, Cai; Gilbert, M Thomas P; Zhang, Guojie; ... (8 authors) (BMC Evol Biol, 2014-12-12)
      BACKGROUND: Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We ...
    • Evidence for a single loss of mineralized teeth in the common avian ancestor. 

      Meredith, Robert W; Zhang, Guojie; Gilbert, M Thomas P; Jarvis, Erich D; Springer, Mark S (Science, 2014-12-12)
      Edentulism, the absence of teeth, has evolved convergently among vertebrates, including birds, turtles, and several lineages of mammals. Instead of teeth, modern birds (Neornithes) use a horny beak (rhamphotheca) and a muscular ...
    • Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates. 

      Pereira, Joana; Johnson, Warren E; O'Brien, Stephen J; Jarvis, Erich D; Zhang, Guojie; Gilbert, M Thomas P; Vasconcelos, Vitor; ... (8 authors) (PLoS One, 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 ...
    • Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. 

      Borges, Rui; Borges, Rui; Khan, Imran; Johnson, Warren E; Gilbert, M Thomas P; Zhang, Guojie; Jarvis, Erich D; ... (9 authors) (BMC Genomics, 2015-10-06)
      BACKGROUND: 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 ...
    • Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species 

      Li, Shengbin; Li, Bo; Cheng, Cheng; Xiong, Zijun; Liu, Qingbo; Lai, Jianghua; Carey, Hannah V; ... (33 authors) (GENOME BIOLOGY, 2014)
      BACKGROUND: Nearly one-quarter of all avian species is either threatened or nearly threatened. Of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. One of the previously most ...
    • Low frequency of paleoviral infiltration across the avian phylogeny. 

      Cui, Jie; Zhao, Wei; Huang, Zhiyong; Jarvis, Erich D; Gilbert, M Thomas P; Walker, Peter J; Holmes, Edward C; ... (8 authors) (Genome Biol, 2014)
      BACKGROUND: Mammalian genomes commonly harbor endogenous viral elements. Due to a lack of comparable genome-scale sequence data, far less is known about endogenous viral elements in avian species, even though their small ...
    • Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida. 

      Khan, Imran; Yang, Zhikai; Maldonado, Emanuel; Li, Cai; Zhang, Guojie; Gilbert, M Thomas P; Jarvis, Erich D; ... (10 authors) (Mol Biol Evol, 2015-11)
      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 ...
    • Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds". 

      Cracraft, Joel; Houde, Peter; Ho, Simon YW; Mindell, David P; Fjeldså, Jon; Lindow, Bent; Edwards, Scott V; ... (14 authors) (Science, 2015-09-25)
      Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, ...
    • Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. 

      Li, Cai; Zhang, Yong; Li, Jianwen; Kong, Lesheng; Hu, Haofu; Pan, Hailin; Xu, Luohao; ... (41 authors) (Gigascience, 2014)
      BACKGROUND: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have ...
    • Whole-genome analyses resolve early branches in the tree of life of modern birds. 

      Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon YW; ... (106 authors) (Science, 2014-12-12)
      To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered ...