Journal Articles

  • [Special Issue Research Article] Core and region-enriched networks of behaviorally regulated genes and the singing genome
    [Dec 2014]

    Songbirds represent an important model organism for elucidating molecular mechanisms that link genes with complex behaviors, in part because they have discrete vocal learning circuits that have parallels with those that mediate human speech. We found that ~10% of the genes in the avian genome were regulated by singing, and we found a striking regional diversity of both basal and singing-induced programs in the four key song nuclei of the zebra finch, a vocal learning songbird. The region-enriched patterns were a result of distinct combinations of region-enriched transcription factors (TFs), their binding motifs, and presinging acetylation of histone 3 at lysine 27 (H3K27ac) enhancer activity in the regulatory regions of the associated genes. RNA interference manipulations validated the role of the calcium-response transcription factor (CaRF) in regulating genes preferentially expressed in specific song nuclei in response to singing. Thus, differential combinatorial binding of a small group of activity-regulated TFs and predefined epigenetic enhancer activity influences the anatomical diversity of behaviorally regulated gene networks. Authors: Osceola Whitney, Andreas R. Pfenning, Jason T. Howard, Charles A Blatti, Fang Liu, James M. Ward, Rui Wang, Jean-Nicoles Audet, Manolis Kellis, Sayan Mukherjee, Saurabh Sinha, Alexander J. Hartemink, Anne E. West, Erich D. Jarvis
    Categories: Journal Articles
  • [Special Issue Research Article] Convergent transcriptional specializations in the brains of humans and song-learning birds
    [Dec 2014]

    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 of song-learning birds and humans relative to vocal nonlearners identified convergent gene expression specializations in specific song and speech brain regions of avian vocal learners and humans. The strongest shared profiles relate bird motor and striatal song-learning nuclei, respectively, with human laryngeal motor cortex and parts of the striatum that control speech production and learning. Most of the associated genes function in motor control and brain connectivity. Thus, convergent behavior and neural connectivity for a complex trait are associated with convergent specialized expression of multiple genes. Authors: Andreas R. Pfenning, Erina Hara, Osceola Whitney, Miriam V. Rivas, Rui Wang, Petra L. Roulhac, Jason T. Howard, Morgan Wirthlin, Peter V. Lovell, Ganeshkumar Ganapathy, Jacquelyn Mouncastle, M. Arthur Moseley, J. Will Thompson, Erik J. Soderblom, Atsushi Iriki, Masaki Kato, M. Thomas P. Gilbert, Guojie Zhang, Trygve Bakken, Angie Bongaarts, Amy Bernard, Ed Lein, Claudio V. Mello, Alexander J. Hartemink, Erich D. Jarvis
    Categories: Journal Articles
  • [Special Issue Research Article] Complex evolutionary trajectories of sex chromosomes across bird taxa
    [Dec 2014]

    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 phylogenetic range, and find that more than half of them do not have as fully degenerated W chromosomes as that of chicken. We show that avian sex chromosomes harbor tremendous diversity among species in their composition of pseudoautosomal regions and degree of Z/W differentiation. Punctuated events of shared or lineage-specific recombination suppression have produced a gradient of “evolutionary strata” along the Z chromosome, which initiates from the putative avian sex-determining gene DMRT1 and ends at the pseudoautosomal region. W-linked genes are subject to ongoing functional decay after recombination was suppressed, and the tempo of degeneration slows down in older strata. Overall, we unveil a complex history of avian sex chromosome evolution. Authors: Qi Zhou, Jilin Zhang, Doris Bachtrog, Na An, Quanfei Huang, Erich D. Jarvis, M. Thomas P. Gilbert, Guojie Zhang
    Categories: Journal Articles
  • [Special Issue Research Article] Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
    [Dec 2014]

    To provide context for the diversification of archosaurs—the group that includes crocodilians, dinosaurs, and birds—we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. Authors: Richard E. Green, Edward L. Braun, Joel Armstrong, Dent Earl, Ngan Nguyen, Glenn Hickey, Michael W. Vandewege, John A. St. John, Salvador Capella-Gutiérrez, Todd A. Castoe, Colin Kern, Matthew K. Fujita, Juan C. Opazo, Jerzy Jurka, Kenji K. Kojima, Juan Caballero, Robert M. Hubley, Arian F. Smit, Roy N. Platt, Christine A. Lavoie, Meganathan P. Ramakodi, John W. Finger, Alexander Suh, Sally R. Isberg, Lee Miles, Amanda Y. Chong, Weerachai Jaratlerdsiri, Jaime Gongora, Christopher Moran, Andrés Iriarte, John McCormack, Shane C. Burgess, Scott V. Edwards, Eric Lyons, Christina Williams, Matthew Breen, Jason T. Howard, Cathy R. Gresham, Daniel G. Peterson, Jürgen Schmitz, David D. Pollock, David Haussler, Eric W. Triplett, Guojie Zhang, Naoki Irie, Erich D. Jarvis, Christopher A. Brochu, Carl J. Schmidt, Fiona M. McCarthy, Brant C. Faircloth, Federico G. Hoffmann, Travis C. Glenn, Toni Gabaldón, Benedict Paten, David A. Ray
    Categories: Journal Articles
  • [Special Issue Research Article] Evidence for a single loss of mineralized teeth in the common avian ancestor
    [Dec 2014]

    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 gizzard to acquire and process food. We performed comparative genomic analyses representing lineages of nearly all extant bird orders and recovered shared, inactivating mutations within genes expressed in both the enamel and dentin of teeth of other vertebrate species, indicating that the common ancestor of modern birds lacked mineralized teeth. We estimate that tooth loss, or at least the loss of enamel caps that provide the outer layer of mineralized teeth, occurred about 116 million years ago. Authors: Robert W. Meredith, Guojie Zhang, M. Thomas P. Gilbert, Erich D. Jarvis, Mark S. Springer
    Categories: Journal Articles
  • [Special Issue Review] An integrative approach to understanding bird origins
    [Dec 2014]

    Recent discoveries of spectacular dinosaur fossils overwhelmingly support the hypothesis that birds are descended from maniraptoran theropod dinosaurs, and furthermore, demonstrate that distinctive bird characteristics such as feathers, flight, endothermic physiology, unique strategies for reproduction and growth, and a novel pulmonary system originated among Mesozoic terrestrial dinosaurs. The transition from ground-living to flight-capable theropod dinosaurs now probably represents one of the best-documented major evolutionary transitions in life history. Recent studies in developmental biology and other disciplines provide additional insights into how bird characteristics originated and evolved. The iconic features of extant birds for the most part evolved in a gradual and stepwise fashion throughout archosaur evolution. However, new data also highlight occasional bursts of morphological novelty at certain stages particularly close to the origin of birds and an unavoidable complex, mosaic evolutionary distribution of major bird characteristics on the theropod tree. Research into bird origins provides a premier example of how paleontological and neontological data can interact to reveal the complexity of major innovations, to answer key evolutionary questions, and to lead to new research directions. A better understanding of bird origins requires multifaceted and integrative approaches, yet fossils necessarily provide the final test of any evolutionary model. Authors: Xing Xu, Zhonghe Zhou, Robert Dudley, Susan Mackem, Cheng-Ming Chuong, Gregory M. Erickson, David J. Varricchio
    Categories: Journal Articles
  • [Special Issue Research Article] Statistical binning enables an accurate coalescent-based estimation of the avian tree
    [Dec 2014]

    Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce the accuracy of concatenation-based estimations of species trees. Although coalescent-based species tree estimation methods can have good accuracy in the presence of ILS, they are sensitive to gene tree estimation error. We propose a pipeline that uses bootstrapping to evaluate whether two genes are likely to have the same tree, then it groups genes into sets using a graph-theoretic optimization and estimates a tree on each subset using concatenation, and finally produces an estimated species tree from these trees using the preferred coalescent-based method. Statistical binning improves the accuracy of MP-EST, a popular coalescent-based method, and we use it to produce the first genome-scale coalescent-based avian tree of life. Authors: Siavash Mirarab, Md. Shamsuzzoha Bayzid, Bastien Boussau, Tandy Warnow
    Categories: Journal Articles
  • [Editorial] Zero infection
    [Dec 2014]

    Last month, United Nations (UN) Secretary-General Ban Ki-moon, World Bank Group President Jim Yong Kim, and World Health Organization (WHO) Director-General Margaret Chan held a press conference after the UN Chief Executive Board's meeting to assess the global response to the Ebola epidemic. The secretary-general's message was clear: “Our end game is not near.” To eliminate infection from the human population by mid-2015, as Ban Ki-moon hopes, the world must intensify its fight against this virus, but we should also recognize that we need better ways to combat international health hazards of all kinds. Authors: Mark Woolhouse, Patrick Drury, Christopher Dye
    Categories: Journal Articles
  • [In Brief] This Week's Section
    [Dec 2014]

    A roundup of weekly science policy and related news.
    Categories: Journal Articles
  • [In Depth] Bird genomes give new perches to old friends
    [Dec 2014]

    Comparing genomes clarifies family relations and pinpoints genes for song learning. Author: Elizabeth Pennisi
    Categories: Journal Articles
  • [In Depth] The genetics of resistant malaria
    [Dec 2014]

    Studies confirm changes in suspected gene confer resistance to artemisinin. Author: Gretchen Vogel
    Categories: Journal Articles
  • [In Depth] The trouble with tritium
    [Dec 2014]

    Japan searches for a way to cleanse contaminated water from the damaged Fukushima plant. Author: Dennis Normile
    Categories: Journal Articles
  • [In Depth] From hell on Earth, life's building blocks
    [Dec 2014]

    Simulated meteorite impact forges RNA components. Author: Sid Perkins
    Categories: Journal Articles
  • [In Depth] E.U. to let wary members ban genetically modified crops
    [Dec 2014]

    Revived proposal allows countries to reject varieties even if scientific assessments say they're safe. Author: Tania Rabesandratana
    Categories: Journal Articles
  • [Feature] Back from the Dead
    [Dec 2014]

    The once-moribund idea that volcanism helped kill off the dinosaurs gains new credibility. Author: Richard Stone
    Categories: Journal Articles
  • [Feature] Live Wire
    [Dec 2014]

    Do cells use electricity to repair DNA? Jacqueline Barton aims to find out. Author: Robert F. Service
    Categories: Journal Articles
  • [Perspective] Scratching the surface of martian habitability
    [Dec 2014]

    Are the right chemical ingredients enough to make a habitable planet? Author: Pamela G. Conrad
    Categories: Journal Articles
  • [Perspective] Expanding the breadth of an HIV-1 vaccine
    [Dec 2014]

    Immunogens are designed to elicit the production of highly coveted broadly neutralizing antibodies that protect against HIV-1 [Also see Report by McGuire et al.] Authors: Gilad Ofek, Ron Diskin
    Categories: Journal Articles
  • [Perspective] Cancer by super-enhancer
    [Dec 2014]

    Tiny changes in our genomes can enhance oncogene expression and contribute to tumorigenesis [Also see Report by Mansour et al.] Authors: Anna Vähärautio, Jussi Taipale
    Categories: Journal Articles
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