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  • *Evolution, Molecular  (17)
  • *Climate Change  (11)
  • American Association for the Advancement of Science (AAAS)  (28)
  • American Physical Society
  • 2020-2024
  • 2010-2014  (28)
  • 1980-1984
  • 1945-1949
  • 2014  (28)
  • 1949
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  • 2020-2024
  • 2010-2014  (28)
  • 1980-1984
  • 1945-1949
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  • 1
    Publication Date: 2014-12-17
    Description: 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. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390078/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390078/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Guojie -- Li, Cai -- Li, Qiye -- Li, Bo -- Larkin, Denis M -- Lee, Chul -- Storz, Jay F -- Antunes, Agostinho -- Greenwold, Matthew J -- Meredith, Robert W -- Odeen, 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 -- da Fonseca, Rute R -- Alfaro-Nunez, Alonzo -- Schubert, Mikkel -- Orlando, Ludovic -- Mourier, Tobias -- Howard, Jason T -- Ganapathy, Ganeshkumar -- Pfenning, Andreas -- Whitney, Osceola -- Rivas, Miriam V -- Hara, Erina -- Smith, Julia -- Farre, Marta -- Narayan, Jitendra -- Slavov, Gancho -- Romanov, Michael N -- Borges, Rui -- Machado, Joao Paulo -- Khan, Imran -- Springer, Mark S -- Gatesy, John -- Hoffmann, Federico G -- Opazo, Juan C -- Hastad, 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 -- 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 -- Alstrom, Per -- Fjeldsa, Jon -- Mindell, David P -- Edwards, Scott V -- Braun, Edward L -- Rahbek, Carsten -- Burt, David W -- Houde, Peter -- Zhang, Yong -- Yang, Huanming -- Wang, Jian -- Avian Genome Consortium -- Jarvis, Erich D -- Gilbert, M Thomas P -- Wang, Jun -- DP1 OD000448/OD/NIH HHS/ -- DP1OD000448/OD/NIH HHS/ -- R01 HL087216/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. ; Royal Veterinary College, University of London, London, UK. ; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. ; School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA. ; Centro de Investigacion en Ciencias del Mar y Limnologia (CIMAR)/Centro Interdisciplinar de Investigacao Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Departamento de Biologia, Faculdade de Ciencias, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal. ; Department of Biological Sciences, University of South Carolina, Columbia, SC, USA. ; Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA. ; Department of Animal Ecology, Uppsala University, Norbyvagen 18D, S-752 36 Uppsala, Sweden. ; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia. Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore. ; Department of Integrative Biology University of California, Berkeley, CA 94720, USA. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. College of Life Sciences, Wuhan University, Wuhan 430072, China. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. BGI Education Center,University of Chinese Academy of Sciences,Shenzhen, 518083, China. ; Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA. ; Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK. ; School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK. ; Centro de Investigacion en Ciencias del Mar y Limnologia (CIMAR)/Centro Interdisciplinar de Investigacao Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Instituto de Ciencias Biomedicas Abel Salazar (ICBAS), Universidade do Porto, Portugal. ; Department of Biology, University of California Riverside, Riverside, CA 92521, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. ; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile. ; Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Post Office Box 7011, S-750 07, Uppsala, Sweden. ; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea. ; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. ; Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. ; State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China. ; State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China. College of Animal Science and Technology, China Agricultural University, Beijing 100094, China. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK. Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 China. ; International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK. ; Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark. ; Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA. Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA. ; The Genome Institute at Washington University, St. Louis, MO 63108, USA. ; College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China. ; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. ; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia. Nova Southeastern University Oceanographic Center 8000 N Ocean Drive, Dania, FL 33004, USA. ; Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA. ; Genetics Division, San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA. ; Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Post Office Box 37012, Washington, DC 20013-7012, USA. Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. ; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China. Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-750 07 Uppsala, Sweden. ; Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. ; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA. ; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA. ; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. ; Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Imperial College London, Grand Challenges in Ecosystems and the Environment Initiative, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK. ; Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The Roslin Institute Building, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK. ; Department of Biology, New Mexico State University, Box 30001 MSC 3AF, Las Cruces, NM 88003, USA. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. ; Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Department of Medicine, University of Hong Kong, Hong Kong. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504712" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; Biodiversity ; *Biological Evolution ; Birds/classification/*genetics/physiology ; Conserved Sequence ; Diet ; *Evolution, Molecular ; Female ; Flight, Animal ; Genes ; Genetic Variation ; *Genome ; Genomics ; Male ; Molecular Sequence Annotation ; Phylogeny ; Reproduction/genetics ; Selection, Genetic ; Sequence Analysis, DNA ; Synteny ; Vision, Ocular/genetics ; Vocalization, Animal
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-12-17
    Description: 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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Richard E -- Braun, Edward L -- Armstrong, Joel -- Earl, Dent -- Nguyen, Ngan -- Hickey, Glenn -- Vandewege, Michael W -- St John, John A -- Capella-Gutierrez, Salvador -- Castoe, Todd A -- Kern, Colin -- Fujita, Matthew K -- Opazo, Juan C -- Jurka, Jerzy -- Kojima, Kenji K -- Caballero, Juan -- Hubley, Robert M -- Smit, Arian F -- Platt, Roy N -- Lavoie, Christine A -- Ramakodi, Meganathan P -- Finger, John W Jr -- Suh, Alexander -- Isberg, Sally R -- Miles, Lee -- Chong, Amanda Y -- Jaratlerdsiri, Weerachai -- Gongora, Jaime -- Moran, Christopher -- Iriarte, Andres -- McCormack, John -- Burgess, Shane C -- Edwards, Scott V -- Lyons, Eric -- Williams, Christina -- Breen, Matthew -- Howard, Jason T -- Gresham, Cathy R -- Peterson, Daniel G -- Schmitz, Jurgen -- Pollock, David D -- Haussler, David -- Triplett, Eric W -- Zhang, Guojie -- Irie, Naoki -- Jarvis, Erich D -- Brochu, Christopher A -- Schmidt, Carl J -- McCarthy, Fiona M -- Faircloth, Brant C -- Hoffmann, Federico G -- Glenn, Travis C -- Gabaldon, Toni -- Paten, Benedict -- Ray, David A -- 1U41HG006992-2/HG/NHGRI NIH HHS/ -- 1U41HG007234-01/HG/NHGRI NIH HHS/ -- 5U01HG004695/HG/NHGRI NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- U41 HG006992/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449. Epub 2014 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ed@soe.ucsc.edu david.a.ray@ttu.edu. ; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. ; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. ; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain. ; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA. Department of Biology, University of Texas, Arlington, TX 76019, USA. ; Department of Computer and Information Sciences, University of Delaware, Newark, DE 19717, USA. ; Department of Biology, University of Texas, Arlington, TX 76019, USA. ; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile. ; Genetic Information Research Institute, Mountain View, CA 94043, USA. ; Institute for Systems Biology, Seattle, WA 98109, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. ; Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA. ; Institute of Experimental Pathology (ZMBE), University of Munster, D-48149 Munster, Germany. Department of Evolutionary Biology (EBC), Uppsala University, SE-752 36 Uppsala, Sweden. ; Porosus Pty. Ltd., Palmerston, NT 0831, Australia. Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia. Centre for Crocodile Research, Noonamah, NT 0837, Australia. ; Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia. ; Departamento de Desarrollo Biotecnologico, Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Montevideo, Uruguay. ; Moore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, USA. ; College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85721, USA. ; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. ; School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA. ; Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA. ; Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA. ; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. ; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA. ; Institute of Experimental Pathology (ZMBE), University of Munster, D-48149 Munster, Germany. ; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA. ; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. Howard Hughes Medical Institute, Bethesda, MD 20814, USA. ; Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA. ; China National GeneBank, BGI-Shenzhen, Shenzhen, China. Center for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. ; Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan. ; Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA. ; Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USA. ; School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA. ; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90019, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avancats, 08010 Barcelona, Spain. ; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA. ed@soe.ucsc.edu david.a.ray@ttu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504731" target="_blank"〉PubMed〈/a〉
    Keywords: Alligators and Crocodiles/classification/*genetics ; Animals ; Biological Evolution ; Birds/classification/*genetics ; Conserved Sequence ; DNA Transposable Elements ; Dinosaurs/classification/*genetics ; *Evolution, Molecular ; Genetic Variation ; *Genome ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; Reptiles/classification/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Transcriptome
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2014-08-26
    Description: Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chalhoub, Boulos -- Denoeud, France -- Liu, Shengyi -- Parkin, Isobel A P -- Tang, Haibao -- Wang, Xiyin -- Chiquet, Julien -- Belcram, Harry -- Tong, Chaobo -- Samans, Birgit -- Correa, Margot -- Da Silva, Corinne -- Just, Jeremy -- Falentin, Cyril -- Koh, Chu Shin -- Le Clainche, Isabelle -- Bernard, Maria -- Bento, Pascal -- Noel, Benjamin -- Labadie, Karine -- Alberti, Adriana -- Charles, Mathieu -- Arnaud, Dominique -- Guo, Hui -- Daviaud, Christian -- Alamery, Salman -- Jabbari, Kamel -- Zhao, Meixia -- Edger, Patrick P -- Chelaifa, Houda -- Tack, David -- Lassalle, Gilles -- Mestiri, Imen -- Schnel, Nicolas -- Le Paslier, Marie-Christine -- Fan, Guangyi -- Renault, Victor -- Bayer, Philippe E -- Golicz, Agnieszka A -- Manoli, Sahana -- Lee, Tae-Ho -- Thi, Vinh Ha Dinh -- Chalabi, Smahane -- Hu, Qiong -- Fan, Chuchuan -- Tollenaere, Reece -- Lu, Yunhai -- Battail, Christophe -- Shen, Jinxiong -- Sidebottom, Christine H D -- Wang, Xinfa -- Canaguier, Aurelie -- Chauveau, Aurelie -- Berard, Aurelie -- Deniot, Gwenaelle -- Guan, Mei -- Liu, Zhongsong -- Sun, Fengming -- Lim, Yong Pyo -- Lyons, Eric -- Town, Christopher D -- Bancroft, Ian -- Wang, Xiaowu -- Meng, Jinling -- Ma, Jianxin -- Pires, J Chris -- King, Graham J -- Brunel, Dominique -- Delourme, Regine -- Renard, Michel -- Aury, Jean-Marc -- Adams, Keith L -- Batley, Jacqueline -- Snowdon, Rod J -- Tost, Jorg -- Edwards, David -- Zhou, Yongming -- Hua, Wei -- Sharpe, Andrew G -- Paterson, Andrew H -- Guan, Chunyun -- Wincker, Patrick -- BB/E017363/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Aug 22;345(6199):950-3. doi: 10.1126/science.1253435. Epub 2014 Aug 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut National de Recherche Agronomique (INRA)/Universite d'Evry Val d'Essone, Unite de Recherche en Genomique Vegetale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Cremieux, 91057 Evry, France. chalhoub@evry.inra.fr. ; Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, BP5706, 91057 Evry, France. Universite d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. ; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China. ; Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada. chalhoub@evry.inra.fr. ; J. Craig Venter Institute, Rockville, MD 20850, USA. Center for Genomics and Biotechnology, Fujian Agriculture and Forestry, University, Fuzhou 350002, Fujian Province, China. ; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. Center of Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei 063000, China. ; Laboratoire de Mathematiques et Modelisation d'Evry-UMR 8071 CNRS/Universite d'Evry val d'Essonne-USC INRA, Evry, France. ; Institut National de Recherche Agronomique (INRA)/Universite d'Evry Val d'Essone, Unite de Recherche en Genomique Vegetale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Cremieux, 91057 Evry, France. ; Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany. ; Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, BP5706, 91057 Evry, France. ; INRA, Institut de Genetique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France. ; National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada. ; INRA, Etude du Polymorphisme des Genomes Vegetaux, US1279, Centre National de Genotypage, CEA-IG, 2 rue Gaston Cremieux, 91057 Evry, France. ; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. ; Laboratory for Epigenetics and Environment, Centre National de Genotypage, CEA-IG, 2 rue Gaston Cremieux, 91000 Evry, France. ; Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. ; Institut National de Recherche Agronomique (INRA)/Universite d'Evry Val d'Essone, Unite de Recherche en Genomique Vegetale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Cremieux, 91057 Evry, France. Cologne Center for Genomics, University of Cologne, Weyertal 115b, 50931 Koln, Germany. ; Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA. ; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA. ; Department of Botany, University of British Columbia, Vancouver, BC, Canada. ; Beijing Genome Institute-Shenzhen, Shenzhen 518083, China. ; Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, 27 rue Juliette Dodu, 75010 Paris, France. ; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China. ; College of Agronomy, Hunan Agricultural University, Changsha 410128, China. ; Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon-305764, South Korea. ; School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, USA. ; J. Craig Venter Institute, Rockville, MD 20850, USA. ; Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK. ; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China. ; Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA. ; Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia. ; Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia. ; Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia. chalhoub@evry.inra.fr. ; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China. chalhoub@evry.inra.fr. ; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China. chalhoub@evry.inra.fr. ; National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada. chalhoub@evry.inra.fr. ; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. chalhoub@evry.inra.fr. ; College of Agronomy, Hunan Agricultural University, Changsha 410128, China. chalhoub@evry.inra.fr. ; Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, BP5706, 91057 Evry, France. Universite d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. chalhoub@evry.inra.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25146293" target="_blank"〉PubMed〈/a〉
    Keywords: Brassica napus/cytology/*genetics ; *Chromosome Duplication ; *Evolution, Molecular ; *Genome, Plant ; *Polyploidy ; Seeds/*genetics
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  • 4
    Publication Date: 2014-05-17
    Description: Atmospheric new-particle formation affects climate and is one of the least understood atmospheric aerosol processes. The complexity and variability of the atmosphere has hindered elucidation of the fundamental mechanism of new-particle formation from gaseous precursors. We show, in experiments performed with the CLOUD (Cosmics Leaving Outdoor Droplets) chamber at CERN, that sulfuric acid and oxidized organic vapors at atmospheric concentrations reproduce particle nucleation rates observed in the lower atmosphere. The experiments reveal a nucleation mechanism involving the formation of clusters containing sulfuric acid and oxidized organic molecules from the very first step. Inclusion of this mechanism in a global aerosol model yields a photochemically and biologically driven seasonal cycle of particle concentrations in the continental boundary layer, in good agreement with observations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Riccobono, Francesco -- Schobesberger, Siegfried -- Scott, Catherine E -- Dommen, Josef -- Ortega, Ismael K -- Rondo, Linda -- Almeida, Joao -- Amorim, Antonio -- Bianchi, Federico -- Breitenlechner, Martin -- David, Andre -- Downard, Andrew -- Dunne, Eimear M -- Duplissy, Jonathan -- Ehrhart, Sebastian -- Flagan, Richard C -- Franchin, Alessandro -- Hansel, Armin -- Junninen, Heikki -- Kajos, Maija -- Keskinen, Helmi -- Kupc, Agnieszka -- Kurten, Andreas -- Kvashin, Alexander N -- Laaksonen, Ari -- Lehtipalo, Katrianne -- Makhmutov, Vladimir -- Mathot, Serge -- Nieminen, Tuomo -- Onnela, Antti -- Petaja, Tuukka -- Praplan, Arnaud P -- Santos, Filipe D -- Schallhart, Simon -- Seinfeld, John H -- Sipila, Mikko -- Spracklen, Dominick V -- Stozhkov, Yuri -- Stratmann, Frank -- Tome, Antonio -- Tsagkogeorgas, Georgios -- Vaattovaara, Petri -- Viisanen, Yrjo -- Vrtala, Aron -- Wagner, Paul E -- Weingartner, Ernest -- Wex, Heike -- Wimmer, Daniela -- Carslaw, Kenneth S -- Curtius, Joachim -- Donahue, Neil M -- Kirkby, Jasper -- Kulmala, Markku -- Worsnop, Douglas R -- Baltensperger, Urs -- New York, N.Y. -- Science. 2014 May 16;344(6185):717-21. doi: 10.1126/science.1243527.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Atmospheric Chemistry, Paul Scherrer Institute, Villigen, Switzerland. ; Department of Physics, University of Helsinki, Helsinki, Finland. ; School of Earth and Environment, University of Leeds, Leeds, UK. ; Institute for Atmospheric and Environmental Sciences, Goethe University of Frankfurt, Frankfurt am Main, Germany. ; Laboratory for Systems, Instrumentation, and Modeling in Science and Technology for Space and the Environment (SIM), University of Lisbon and University of Beira Interior, Lisbon, Portugal. ; Ionicon Analytik GmbH and University of Innsbruck, Institute for Ion and Applied Physics, Innsbruck, Austria. ; CERN (European Organization for Nuclear Research), Geneva, Switzerland. ; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA. ; Department of Physics, University of Helsinki, Helsinki, Finland. Helsinki Institute of Physics, University of Helsinki, Helsinki, Finland. ; University of Eastern Finland, Kuopio, Finland. ; Faculty of Physics, University of Vienna, Vienna, Austria. ; Solar and Cosmic Ray Research Laboratory, Lebedev Physical Institute, Moscow, Russia. ; Leibniz Institute for Tropospheric Research, Leipzig, Germany. ; Finnish Meteorological Institute, Helsinki, Finland. ; Center for Atmospheric Particle Studies, Carnegie Mellon University, Pittsburgh, PA 15213, USA. ; Institute for Atmospheric and Environmental Sciences, Goethe University of Frankfurt, Frankfurt am Main, Germany. CERN (European Organization for Nuclear Research), Geneva, Switzerland. ; Department of Physics, University of Helsinki, Helsinki, Finland. Aerodyne Research Incorporated, Billerica, MA 01821, USA. ; Laboratory of Atmospheric Chemistry, Paul Scherrer Institute, Villigen, Switzerland. urs.baltensperger@psi.ch.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24833386" target="_blank"〉PubMed〈/a〉
    Keywords: Aerosols/*chemistry ; Atmosphere/*chemistry ; *Climate Change ; Computer Simulation ; Models, Chemical ; Organic Chemicals/*chemistry ; Oxidation-Reduction ; Photochemical Processes ; Seasons ; Sulfuric Acids/*chemistry ; Volatilization
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  • 5
    Publication Date: 2014-09-06
    Description: Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Denoeud, France -- Carretero-Paulet, Lorenzo -- Dereeper, Alexis -- Droc, Gaetan -- Guyot, Romain -- Pietrella, Marco -- Zheng, Chunfang -- Alberti, Adriana -- Anthony, Francois -- Aprea, Giuseppe -- Aury, Jean-Marc -- Bento, Pascal -- Bernard, Maria -- Bocs, Stephanie -- Campa, Claudine -- Cenci, Alberto -- Combes, Marie-Christine -- Crouzillat, Dominique -- Da Silva, Corinne -- Daddiego, Loretta -- De Bellis, Fabien -- Dussert, Stephane -- Garsmeur, Olivier -- Gayraud, Thomas -- Guignon, Valentin -- Jahn, Katharina -- Jamilloux, Veronique -- Joet, Thierry -- Labadie, Karine -- Lan, Tianying -- Leclercq, Julie -- Lepelley, Maud -- Leroy, Thierry -- Li, Lei-Ting -- Librado, Pablo -- Lopez, Loredana -- Munoz, Adriana -- Noel, Benjamin -- Pallavicini, Alberto -- Perrotta, Gaetano -- Poncet, Valerie -- Pot, David -- Priyono -- Rigoreau, Michel -- Rouard, Mathieu -- Rozas, Julio -- Tranchant-Dubreuil, Christine -- VanBuren, Robert -- Zhang, Qiong -- Andrade, Alan C -- Argout, Xavier -- Bertrand, Benoit -- de Kochko, Alexandre -- Graziosi, Giorgio -- Henry, Robert J -- Jayarama -- Ming, Ray -- Nagai, Chifumi -- Rounsley, Steve -- Sankoff, David -- Giuliano, Giovanni -- Albert, Victor A -- Wincker, Patrick -- Lashermes, Philippe -- New York, N.Y. -- Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274. Epub 2014 Sep 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. ; CIRAD, UMR Amelioration Genetique et Adaptation des Plantes Mediterraneennes et Tropicales (AGAP), F-34398 Montpellier, France. ; IRD, UMR Diversite Adaptation et Developpement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France. ; Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy. ; Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. ; Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France. ; Nestle Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oe, BP 49716, 37097 Tours Cedex 2, France. ; ENEA Trisaia Research Center, 75026 Rotondella, Italy. ; Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France. ; Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. Center for Biotechnology, Universitat Bielefeld, Universitatsstrasse 27, D-33615 Bielefeld, Germany. AG Genominformatik, Technische Fakultat, Universitat Bielefeld, 33594 Bielefeld, Germany. ; Institut National de la Recherche Agronomique (INRA), Unite de Recherches en Genomique-Info (UR INRA 1164), Centre de Recherche de Versailles, 78026 Versailles Cedex, France. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. Department of Biology, Chongqing University of Science and Technology, 4000042 Chongqing, China. ; Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. ; Departament de Genetica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain. ; Department of Mathematics, University of Maryland, Mathematics Building 084, University of Maryland, College Park, MD 20742, USA. School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. ; Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. ; Indonesian Coffee and Cocoa Institute, Jember, East Java, Indonesia. ; Laboratorio de Genetica Molecular, Nucleo de Biotecnologia (NTBio), Embrapa Recursos Geneticos e Biotecnologia, Final Av. W/5 Norte, Parque Estacao Biologia, Brasilia-DF 70770-917, Brazil. ; CIRAD, UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France. ; Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. DNA Analytica Srl, Via Licio Giorgieri 5, 34127 Trieste, Italy. ; Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, Australia. ; Central Coffee Research Institute, Coffee Board, Coffee Research Station (Post) - 577 117 Chikmagalur District, Karnataka State, India. ; Hawaii Agriculture Research Center, Post Office Box 100, Kunia, HI 96759-0100, USA. ; BIO5 Institute, University of Arizona, 1657 Helen Street, Tucson, AZ 85721, USA. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr. ; Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25190796" target="_blank"〉PubMed〈/a〉
    Keywords: Caffeine/biosynthesis/*genetics ; Coffea/classification/*genetics ; *Evolution, Molecular ; *Genome, Plant ; Methyltransferases/genetics/*physiology ; Phylogeny ; Plant Proteins/genetics/*physiology
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  • 6
    Publication Date: 2014-06-14
    Description: Sediments cored along the southwestern Iberian margin during Integrated Ocean Drilling Program Expedition 339 provide constraints on Mediterranean Outflow Water (MOW) circulation patterns from the Pliocene epoch to the present day. After the Strait of Gibraltar opened (5.33 million years ago), a limited volume of MOW entered the Atlantic. Depositional hiatuses indicate erosion by bottom currents related to higher volumes of MOW circulating into the North Atlantic, beginning in the late Pliocene. The hiatuses coincide with regional tectonic events and changes in global thermohaline circulation (THC). This suggests that MOW influenced Atlantic Meridional Overturning Circulation (AMOC), THC, and climatic shifts by contributing a component of warm, saline water to northern latitudes while in turn being influenced by plate tectonics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hernandez-Molina, F Javier -- Stow, Dorrik A V -- Alvarez-Zarikian, Carlos A -- Acton, Gary -- Bahr, Andre -- Balestra, Barbara -- Ducassou, Emmanuelle -- Flood, Roger -- Flores, Jose-Abel -- Furota, Satoshi -- Grunert, Patrick -- Hodell, David -- Jimenez-Espejo, Francisco -- Kim, Jin Kyoung -- Krissek, Lawrence -- Kuroda, Junichiro -- Li, Baohua -- Llave, Estefania -- Lofi, Johanna -- Lourens, Lucas -- Miller, Madeline -- Nanayama, Futoshi -- Nishida, Naohisa -- Richter, Carl -- Roque, Cristina -- Pereira, Helder -- Sanchez Goni, Maria Fernanda -- Sierro, Francisco J -- Singh, Arun Deo -- Sloss, Craig -- Takashimizu, Yasuhiro -- Tzanova, Alexandrina -- Voelker, Antje -- Williams, Trevor -- Xuan, Chuang -- New York, N.Y. -- Science. 2014 Jun 13;344(6189):1244-50. doi: 10.1126/science.1251306.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK. javier.hernandez-molina@rhul.ac.uk. ; Institute of Petroleum Engineering, Heriot-Watt University, Edinburgh EH14 4AS, Scotland, UK. ; International Ocean Discovery Program, Department of Oceanography, Texas A&M University, College Station, TX 77845, USA. ; Department of Geography and Geology, Sam Houston State University, Huntsville, TX 77341, USA. ; Institute of Geosciences, University of Frankfurt, 60438 Frankfurt, Germany. ; Institute of Marine Sciences, University of California, Santa Cruz, CA 95064, USA. ; EPOC, Universite de Bordeaux, 33615 Pessac Cedex, France. ; School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA. ; Departamento de Geologia, Universidad de Salamanca, 3008 Salamanca, Spain. ; Department of Natural History Sciences, Hokkaido University, N10W8, Kita-ku, Sapporo 060-0810, Japan. ; Institute for Earth Sciences, University of Graz, A-8010 Graz, Austria. ; Godwin Laboratory for Palaeoclimate Research, University of Cambridge, Cambridge CB2 3EQ, UK. ; Department of Biogeochemistry, JAMSTEC, 237-0061 Yokosuka, Japan. ; Korea Institute of Ocean Science & Technology, Ansan 426-744, Korea. ; School of Earth Sciences, Ohio State University, Columbus, OH 43210, USA. ; Institute for Frontier Research on Earth Evolution (IFREE), JAMSTEC, 2-15 Natsushima-Cho, Yokosuka-city, Kanagawa 237-0061, Japan. ; Department of Micropalaeontology, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, P.R. China. ; Instituto Geologico y Minero de Espana, Rios Rosas 23, 28003 Madrid, Spain. ; Geosciences Montpellier, Universite Montpellier II, 34090 Montpellier, France, and Department of Geology, University of Leicester, Leicester LE1 7RH, UK. ; Institute of Earth Sciences, Utrecht University, 3584 CD Utrecht, Netherlands. ; Department of Mechanical Engineering, California Institute of Technology, Pasadena, CA 91125, USA. ; Institute of Geology and Geoinformation, Geological Survey of Japan (AIST), Ibaraki 305-8567, Japan. ; School of Geosciences, University of Louisiana, Lafayette, LA 70504, USA. ; Divisao de Geologia e Georecursos Marinhos, IPMA, 1749-077 Lisboa, Portugal. ; Grupo de Biologia e Geologia, Escola Secundaria de Loule, 8100-740 Loule, Portugal. ; Ecole Pratique des Hautes Etudes, EPOC, Universite de Bordeaux, 33615 Pessac, France. ; Department of Geology, Banaras Hindu University, Varanasi 221005, India. ; School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland 4001, Australia. ; Department of Geology, Faculty of Education, Niigata University, Niigata 950-2181, Japan. ; Department of Geological Sciences, Brown University, Providence, RI 02912, USA. ; Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, USA. ; Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Waterfront Campus, Southampton SO14 3ZH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24926012" target="_blank"〉PubMed〈/a〉
    Keywords: Atlantic Ocean ; *Climate Change ; Mediterranean Sea ; Paleontology ; *Seawater ; *Water Movements
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  • 7
    Publication Date: 2014-02-18
    Description: In this work, we investigate morphological differences between Arabidopsis thaliana, which has simple leaves, and its relative Cardamine hirsuta, which has dissected leaves comprising distinct leaflets. With the use of genetics, interspecific gene transfers, and time-lapse imaging, we show that leaflet development requires the REDUCED COMPLEXITY (RCO) homeodomain protein. RCO functions specifically in leaves, where it sculpts developing leaflets by repressing growth at their flanks. RCO evolved in the Brassicaceae family through gene duplication and was lost in A. thaliana, contributing to leaf simplification in this species. Species-specific RCO action with respect to its paralog results from its distinct gene expression pattern in the leaf base. Thus, regulatory evolution coupled with gene duplication and loss generated leaf shape diversity by modifying local growth patterns during organogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vlad, Daniela -- Kierzkowski, Daniel -- Rast, Madlen I -- Vuolo, Francesco -- Dello Ioio, Raffaele -- Galinha, Carla -- Gan, Xiangchao -- Hajheidari, Mohsen -- Hay, Angela -- Smith, Richard S -- Huijser, Peter -- Bailey, C Donovan -- Tsiantis, Miltos -- BB/H006974/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H011455/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Feb 14;343(6172):780-3. doi: 10.1126/science.1248384.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24531971" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/anatomy & histology/genetics ; Brassicaceae/*anatomy & histology/*genetics ; Chromosome Mapping ; *Evolution, Molecular ; Gene Duplication ; *Gene Expression Regulation, Plant ; *Genes, Homeobox ; Genetic Complementation Test ; Molecular Sequence Data ; Plant Leaves/*anatomy & histology/*genetics
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  • 8
    Publication Date: 2014-05-31
    Description: The most prominent pattern in global marine biogeography is the biodiversity peak in the Indo-Australian Archipelago. Yet the processes that underpin this pattern are still actively debated. By reconstructing global marine paleoenvironments over the past 3 million years on the basis of sediment cores, we assessed the extent to which Quaternary climate fluctuations can explain global variation in current reef fish richness. Comparing global historical coral reef habitat availability with the present-day distribution of 6316 reef fish species, we find that distance from stable coral reef habitats during historical periods of habitat loss explains 62% of the variation in fish richness, outweighing present-day environmental factors. Our results highlight the importance of habitat persistence during periods of climate change for preserving marine biodiversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pellissier, Loic -- Leprieur, Fabien -- Parravicini, Valeriano -- Cowman, Peter F -- Kulbicki, Michel -- Litsios, Glenn -- Olsen, Steffen M -- Wisz, Mary S -- Bellwood, David R -- Mouillot, David -- New York, N.Y. -- Science. 2014 May 30;344(6187):1016-9. doi: 10.1126/science.1249853.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Fribourg, Department of Biology, Chemin du Musee 10, CH-1700 Fribourg, Switzerland. Department of Bioscience, Aarhus University, 8000 C Aarhus, Denmark. ; Laboratoire Ecologie des Systemes Marins Cotiers UMR 5119, CNRS, Institut de Recherche pour le Developpement (IRD), Institut Francais de Recherche pour l'Exploitation de la Mer, UM2, UM1, cc 093, Place E. Bataillon, FR-34095 Montpellier Cedex 5, France. ; IRD, UR 227 CoReUs, LABEX (Laboratoire d'Excellence) Corail, Laboratoire Arago, Boite Postale 44, FR-66651 Banyuls/mer, France. CESAB (Centre de Synthese et d'Analyse sur la Biodiversite)-FRB (Fondation pour la Recherche sur la Biodiversite), Immeuble Henri Poincare, Domaine du Petit Arbois, FR-13857 Aix-en-Provence cedex 3, France. ; Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia. ; IRD, UR 227 CoReUs, LABEX (Laboratoire d'Excellence) Corail, Laboratoire Arago, Boite Postale 44, FR-66651 Banyuls/mer, France. ; Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland. Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland. ; Center for Ocean and Ice, Danish Meteorological Institute, Lyngbyvej 100, 2100 Copenhagen, Denmark. ; Department of Bioscience, Aarhus University, 8000 C Aarhus, Denmark. Department of Ecology and Environment, DHI Water and Environment, 2970 Horsholm, Denmark. ; Australian Research Council Centre of Excellence for Coral Reef Studies, and School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia. ; Laboratoire Ecologie des Systemes Marins Cotiers UMR 5119, CNRS, Institut de Recherche pour le Developpement (IRD), Institut Francais de Recherche pour l'Exploitation de la Mer, UM2, UM1, cc 093, Place E. Bataillon, FR-34095 Montpellier Cedex 5, France. Australian Research Council Centre of Excellence for Coral Reef Studies, and School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia. david.mouillot@univ-montp2.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24876495" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Australia ; *Biodiversity ; *Climate Change ; *Conservation of Natural Resources ; *Coral Reefs ; *Fishes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2014-01-25
    Description: Comparative genomic analyses have revealed that genes may arise from ancestrally nongenic sequence. However, the origin and spread of these de novo genes within populations remain obscure. We identified 142 segregating and 106 fixed testis-expressed de novo genes in a population sample of Drosophila melanogaster. These genes appear to derive primarily from ancestral intergenic, unexpressed open reading frames, with natural selection playing a significant role in their spread. These results reveal a heretofore unappreciated dynamism of gene content.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391638/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391638/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhao, Li -- Saelao, Perot -- Jones, Corbin D -- Begun, David J -- GM084056/GM/NIGMS NIH HHS/ -- R01 GM084056/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Feb 14;343(6172):769-72. doi: 10.1126/science.1248286. Epub 2014 Jan 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24457212" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Drosophila melanogaster/*genetics ; *Evolution, Molecular ; Female ; Gene Expression ; Gene Expression Regulation ; *Genes, Insect ; Genetic Association Studies ; Male ; Open Reading Frames ; Selection, Genetic ; Testis/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2014-12-17
    Description: 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Qi -- Zhang, Jilin -- Bachtrog, Doris -- An, Na -- Huang, Quanfei -- Jarvis, Erich D -- Gilbert, M Thomas P -- Zhang, Guojie -- GM076007/GM/NIGMS NIH HHS/ -- GM093182/GM/NIGMS NIH HHS/ -- R01 GM076007/GM/NIGMS NIH HHS/ -- R01 GM093182/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1246338. doi: 10.1126/science.1246338. Epub 2014 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Biology, University of California, Berkeley, CA94720, USA. zhouqi@berkeley.edu zhanggj@genomics.org.cn. ; China National Genebank, BGI-Shenzhen, Shenzhen, 518083. China. ; Department of Integrative Biology, University of California, Berkeley, CA94720, USA. ; Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia. ; China National Genebank, BGI-Shenzhen, Shenzhen, 518083. China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark. zhouqi@berkeley.edu zhanggj@genomics.org.cn.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504727" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Avian Proteins/genetics ; *Biological Evolution ; Birds/classification/*genetics ; Chickens/genetics ; Chromosome Inversion ; Chromosome Mapping ; *Evolution, Molecular ; Female ; Male ; Phylogeny ; Recombination, Genetic ; Sex Chromosomes/*genetics ; Species Specificity ; Struthioniformes/genetics ; Synteny ; Transcription Factors/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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