ALBERT

Description: We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849982/" 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/PMC2849982/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Werren, John H -- Richards, Stephen -- Desjardins, Christopher A -- Niehuis, Oliver -- Gadau, Jurgen -- Colbourne, John K -- Nasonia Genome Working Group -- Beukeboom, Leo W -- Desplan, Claude -- Elsik, Christine G -- Grimmelikhuijzen, Cornelis J P -- Kitts, Paul -- Lynch, Jeremy A -- Murphy, Terence -- Oliveira, Deodoro C S G -- Smith, Christopher D -- van de Zande, Louis -- Worley, Kim C -- Zdobnov, Evgeny M -- Aerts, Maarten -- Albert, Stefan -- Anaya, Victor H -- Anzola, Juan M -- Barchuk, Angel R -- Behura, Susanta K -- Bera, Agata N -- Berenbaum, May R -- Bertossa, Rinaldo C -- Bitondi, Marcia M G -- Bordenstein, Seth R -- Bork, Peer -- Bornberg-Bauer, Erich -- Brunain, Marleen -- Cazzamali, Giuseppe -- Chaboub, Lesley -- Chacko, Joseph -- Chavez, Dean -- Childers, Christopher P -- Choi, Jeong-Hyeon -- Clark, Michael E -- Claudianos, Charles -- Clinton, Rochelle A -- Cree, Andrew G -- Cristino, Alexandre S -- Dang, Phat M -- Darby, Alistair C -- de Graaf, Dirk C -- Devreese, Bart -- Dinh, Huyen H -- Edwards, Rachel -- Elango, Navin -- Elhaik, Eran -- Ermolaeva, Olga -- Evans, Jay D -- Foret, Sylvain -- Fowler, Gerald R -- Gerlach, Daniel -- Gibson, Joshua D -- Gilbert, Donald G -- Graur, Dan -- Grunder, Stefan -- Hagen, Darren E -- Han, Yi -- Hauser, Frank -- Hultmark, Da -- Hunter, Henry C 4th -- Hurst, Gregory D D -- Jhangian, Shalini N -- Jiang, Huaiyang -- Johnson, Reed M -- Jones, Andrew K -- Junier, Thomas -- Kadowaki, Tatsuhiko -- Kamping, Albert -- Kapustin, Yuri -- Kechavarzi, Bobak -- Kim, Jaebum -- Kim, Jay -- Kiryutin, Boris -- Koevoets, Tosca -- Kovar, Christie L -- Kriventseva, Evgenia V -- Kucharski, Robert -- Lee, Heewook -- Lee, Sandra L -- Lees, Kristin -- Lewis, Lora R -- Loehlin, David W -- Logsdon, John M Jr -- Lopez, Jacqueline A -- Lozado, Ryan J -- Maglott, Donna -- Maleszka, Ryszard -- Mayampurath, Anoop -- Mazur, Danielle J -- McClure, Marcella A -- Moore, Andrew D -- Morgan, Margaret B -- Muller, Jean -- Munoz-Torres, Monica C -- Muzny, Donna M -- Nazareth, Lynne V -- Neupert, Susanne -- Nguyen, Ngoc B -- Nunes, Francis M F -- Oakeshott, John G -- Okwuonu, Geoffrey O -- Pannebakker, Bart A -- Pejaver, Vikas R -- Peng, Zuogang -- Pratt, Stephen C -- Predel, Reinhard -- Pu, Ling-Ling -- Ranson, Hilary -- Raychoudhury, Rhitoban -- Rechtsteiner, Andreas -- Reese, Justin T -- Reid, Jeffrey G -- Riddle, Megan -- Robertson, Hugh M -- Romero-Severson, Jeanne -- Rosenberg, Miriam -- Sackton, Timothy B -- Sattelle, David B -- Schluns, Helge -- Schmitt, Thomas -- Schneider, Martina -- Schuler, Andreas -- Schurko, Andrew M -- Shuker, David M -- Simoes, Zila L P -- Sinha, Saurabh -- Smith, Zachary -- Solovyev, Victor -- Souvorov, Alexandre -- Springauf, Andreas -- Stafflinger, Elisabeth -- Stage, Deborah E -- Stanke, Mario -- Tanaka, Yoshiaki -- Telschow, Arndt -- Trent, Carol -- Vattathil, Selina -- Verhulst, Eveline C -- Viljakainen, Lumi -- Wanner, Kevin W -- Waterhouse, Robert M -- Whitfield, James B -- Wilkes, Timothy E -- Williamson, Michael -- Willis, Judith H -- Wolschin, Florian -- Wyder, Stefan -- Yamada, Takuji -- Yi, Soojin V -- Zecher, Courtney N -- Zhang, Lan -- Gibbs, Richard A -- 5R01GM070026-04/GM/NIGMS NIH HHS/ -- 5R01HG000747-14/HG/NHGRI NIH HHS/ -- 5R24GM084917-02/GM/NIGMS NIH HHS/ -- AI028309-13A2/AI/NIAID NIH HHS/ -- R01 AI055624/AI/NIAID NIH HHS/ -- R01 GM064864/GM/NIGMS NIH HHS/ -- R01 GM064864-04/GM/NIGMS NIH HHS/ -- R01 GM064864-05A2/GM/NIGMS NIH HHS/ -- R01 GM070026/GM/NIGMS NIH HHS/ -- R01 GM070026-04S1/GM/NIGMS NIH HHS/ -- R01 GM079484/GM/NIGMS NIH HHS/ -- R01 GM085163/GM/NIGMS NIH HHS/ -- R01 GM085163-01/GM/NIGMS NIH HHS/ -- R01 GM085233/GM/NIGMS NIH HHS/ -- R01 HG000747/HG/NHGRI NIH HHS/ -- R01 HG000747-14/HG/NHGRI NIH HHS/ -- R01GM064864/GM/NIGMS NIH HHS/ -- R24 GM084917/GM/NIGMS NIH HHS/ -- R24 GM084917-01/GM/NIGMS NIH HHS/ -- R24 GM084917-02/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- U54 HG003273-03/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Jan 15;327(5963):343-8. doi: 10.1126/science.1178028.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075255" target="_blank"〉PubMed〈/a〉

Description: Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166216/" 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/PMC3166216/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Banks, Jo Ann -- Nishiyama, Tomoaki -- Hasebe, Mitsuyasu -- Bowman, John L -- Gribskov, Michael -- dePamphilis, Claude -- Albert, Victor A -- Aono, Naoki -- Aoyama, Tsuyoshi -- Ambrose, Barbara A -- Ashton, Neil W -- Axtell, Michael J -- Barker, Elizabeth -- Barker, Michael S -- Bennetzen, Jeffrey L -- Bonawitz, Nicholas D -- Chapple, Clint -- Cheng, Chaoyang -- Correa, Luiz Gustavo Guedes -- Dacre, Michael -- DeBarry, Jeremy -- Dreyer, Ingo -- Elias, Marek -- Engstrom, Eric M -- Estelle, Mark -- Feng, Liang -- Finet, Cedric -- Floyd, Sandra K -- Frommer, Wolf B -- Fujita, Tomomichi -- Gramzow, Lydia -- Gutensohn, Michael -- Harholt, Jesper -- Hattori, Mitsuru -- Heyl, Alexander -- Hirai, Tadayoshi -- Hiwatashi, Yuji -- Ishikawa, Masaki -- Iwata, Mineko -- Karol, Kenneth G -- Koehler, Barbara -- Kolukisaoglu, Uener -- Kubo, Minoru -- Kurata, Tetsuya -- Lalonde, Sylvie -- Li, Kejie -- Li, Ying -- Litt, Amy -- Lyons, Eric -- Manning, Gerard -- Maruyama, Takeshi -- Michael, Todd P -- Mikami, Koji -- Miyazaki, Saori -- Morinaga, Shin-ichi -- Murata, Takashi -- Mueller-Roeber, Bernd -- Nelson, David R -- Obara, Mari -- Oguri, Yasuko -- Olmstead, Richard G -- Onodera, Naoko -- Petersen, Bent Larsen -- Pils, Birgit -- Prigge, Michael -- Rensing, Stefan A -- Riano-Pachon, Diego Mauricio -- Roberts, Alison W -- Sato, Yoshikatsu -- Scheller, Henrik Vibe -- Schulz, Burkhard -- Schulz, Christian -- Shakirov, Eugene V -- Shibagaki, Nakako -- Shinohara, Naoki -- Shippen, Dorothy E -- Sorensen, Iben -- Sotooka, Ryo -- Sugimoto, Nagisa -- Sugita, Mamoru -- Sumikawa, Naomi -- Tanurdzic, Milos -- Theissen, Gunter -- Ulvskov, Peter -- Wakazuki, Sachiko -- Weng, Jing-Ke -- Willats, William W G T -- Wipf, Daniel -- Wolf, Paul G -- Yang, Lixing -- Zimmer, Andreas D -- Zhu, Qihui -- Mitros, Therese -- Hellsten, Uffe -- Loque, Dominique -- Otillar, Robert -- Salamov, Asaf -- Schmutz, Jeremy -- Shapiro, Harris -- Lindquist, Erika -- Lucas, Susan -- Rokhsar, Daniel -- Grigoriev, Igor V -- GM065383/GM/NIGMS NIH HHS/ -- GM84051/GM/NIGMS NIH HHS/ -- HG004164/HG/NHGRI NIH HHS/ -- R01 GM043644/GM/NIGMS NIH HHS/ -- R01 GM084051/GM/NIGMS NIH HHS/ -- R01 GM084051-01A1/GM/NIGMS NIH HHS/ -- R01 HG004164/HG/NHGRI NIH HHS/ -- R01 HG004164-02/HG/NHGRI NIH HHS/ -- R01 HG004164-03/HG/NHGRI NIH HHS/ -- R01 HG004164-04/HG/NHGRI NIH HHS/ -- T32 GM007757/GM/NIGMS NIH HHS/ -- T32-HG00035/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810. Epub 2011 May 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA. banksj@purdue.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21551031" target="_blank"〉PubMed〈/a〉

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〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grayson, D K -- Meltzer, D J -- Buikstra, J E -- Flannery, K V -- Fowler, C S -- Marcus, J -- O'Connell, J F -- Piperno, D R -- Sabloff, J A -- Smith, B D -- Thomas, D H -- Willerslev, E -- Zeder, M A -- New York, N.Y. -- Science. 2014 Jul 25;345(6195):390. doi: 10.1126/science.345.6195.390-b. Epub 2014 Jul 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anthropology and Quaternary Research Center, University of Washington, Seattle, WA 98185, USA. grayson@uw.edu. ; Department of Anthropology, Southern Methodist University, Dallas, TX 75275, USA. ; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA. ; Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA. ; Department of Anthropology, University of Nevada, Reno, NV 89557, USA. ; Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA. ; Program in Human Ecology and Archaeobiology and Smithsonian Tropical Research Institute (Panama), National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA. ; Santa Fe Institute, Santa Fe, NM 87501, USA. ; Program in Human Ecology and Archaeobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA. ; Division of Anthropology, American Museum of Natural History, New York, NY 10024, USA. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25061197" target="_blank"〉PubMed〈/a〉

Description: Seismic interferometry applied to 120 hr of railroad traffic recorded by an array of vertical component seismographs along a railway within the Rio Grande rift has recovered surface and body waves characteristic of the geology beneath the railway. Linear and hyperbolic arrivals are retrieved that agree with surface (Rayleigh), direct and reflected P waves observed by nearby conventional seismic surveys. Train-generated Rayleigh waves span a range of frequencies significantly higher than those recovered from typical ambient noise interferometry studies. Direct P -wave arrivals have apparent velocities appropriate for the shallow geology of the survey area. Significant reflected P -wave energy is also present at relatively large offsets. A common midpoint stack produces a reflection image consistent with nearby conventional reflection data. We suggest that for sources at the free surface (e.g. trains) increasing the aperture of the array to record wide angle reflections, in addition to longer recording intervals, might allow the recovery of deeper geological structure from railroad traffic. Frequency–wavenumber analyses of these recordings indicate that the train source is symmetrical (i.e. approaching and receding) and that deeper refracted energy is present although not evident in the time-offset domain. These results confirm that train-generated vibrations represent a practical source of high-resolution subsurface information, with particular relevance to geotechnical and environmental applications.

Description: We constrain azimuthal anisotropy in the West Antarctic upper mantle using shear wave splitting parameters obtained from teleseismic SKS, SKKS and PKS phases recorded at 37 broad-band seismometres deployed by the POLENET/ANET project. We use an eigenvalue technique to linearize the rotated and shifted shear wave horizontal particle motions and determine the fast direction and delay time for each arrival. High-quality measurements are stacked to determine the best fitting splitting parameters for each station. Overall, fast anisotropic directions are oriented at large angles to the direction of Antarctic absolute plate motion in both hotspot and no-net-rotation frameworks, showing that the anisotropy does not result from shear due to plate motion over the mantle. Further, the West Antarctic directions are substantially different from those of East Antarctica, indicating that anisotropy across the continent reflects multiple mantle regimes. We suggest that the observed anisotropy along the central Transantarctic Mountains (TAM) and adjacent West Antarctic Rift System (WARS), one of the largest zones of extended continental crust on Earth, results from asthenospheric mantle strain associated with the final pulse of western WARS extension in the late Miocene. Strong and consistent anisotropy throughout the WARS indicate fast axes subparallel to the inferred extension direction, a result unlike reports from the East African rift system and rifts within the Basin and Range, which show much greater variation. We contend that ductile shearing rather than magmatic intrusion may have been the controlling mechanism for accumulation and retention of such coherent, widespread anisotropic fabric. Splitting beneath the Marie Byrd Land Dome (MBL) is weaker than that observed elsewhere within the WARS, but shows a consistent fast direction, possibly representative of anisotropy that has been ‘frozen-in’ to remnant thicker lithosphere. Fast directions observed inland from the Amundsen Sea appear to be radial to the dome and may indicate radial horizontal mantle flow associated with an MBL plume head and low upper mantle velocities in this region, or alternatively to lithospheric features associated with the complex Cenozoic tectonics at the far-eastern end of the WARS.

Description: We have investigated the seismic anisotropy beneath the Central Andean southern Puna plateau by applying shear wave splitting analysis and shear wave splitting tomography to local S waves and teleseismic SKS, SKKS and PKS phases. Overall, a very complex pattern of fast directions throughout the southern Puna plateau region and a circular pattern of fast directions around the region of the giant Cerro Galan ignimbrite complex are observed. In general, teleseismic lag times are much greater than those for local events which are interpreted to reflect a significant amount of sub and inner slab anisotropy. The complex pattern observed from shear wave splitting analysis alone is the result of a complex 3-D anisotropic structure under the southern Puna plateau. Our application of shear wave splitting tomography provides a 3-D model of anisotropy in the southern Puna plateau that shows different patterns depending on the driving mechanism of upper-mantle flow and seismic anisotropy. The trench parallel a -axes in the continental lithosphere above the slab east of 68W may be related to deformation of the overriding continental lithosphere since it is under compressive stresses which are orthogonal to the trench. The more complex pattern below the Cerro Galan ignimbrite complex and above the slab is interpreted to reflect delamination of continental lithosphere and upwelling of hot asthenosphere. The a -axes beneath the Cerro Galan, Cerro Blanco and Carachi Pampa volcanic centres at 100 km depth show some weak evidence for vertically orientated fast directions, which could be due to vertical asthenospheric flow around a delaminated block. Additionally, our splitting tomographic model shows that there is a significant amount of seismic anisotropy beneath the slab. The subslab mantle west of 68W shows roughly trench parallel horizontal a -axes that are probably driven by slab roll back and the relatively small coupling between the Nazca slab and the underlying mantle. In contrast, the subslab region (i.e. depths greater than 200 km) east of 68W shows a circular pattern of a -axes centred on a region with small strength of anisotropy (Cerro Galan and its eastern edge) which suggest the dominant mechanism is a combination of slab roll back and flow driven by an overlying abnormally heated slab or possibly a slab gap. There seems to be some evidence for vertical flow below the slab at depths of 200–400 km driven by the abnormally heated slab or slab gap. This cannot be resolved by the tomographic inversion due to the lack of ray crossings in the subslab mantle.

Description: An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the sister lineage to all other animals. Mnemiopsis lacks many of the genes found in bilaterian mesodermal cell types, suggesting that these cell types evolved independently. The set of neural genes in Mnemiopsis is similar to that of sponges, indicating that sponges may have lost a nervous system. These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920664/" 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/PMC3920664/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ryan, Joseph F -- Pang, Kevin -- Schnitzler, Christine E -- Nguyen, Anh-Dao -- Moreland, R Travis -- Simmons, David K -- Koch, Bernard J -- Francis, Warren R -- Havlak, Paul -- NISC Comparative Sequencing Program -- Smith, Stephen A -- Putnam, Nicholas H -- Haddock, Steven H D -- Dunn, Casey W -- Wolfsberg, Tyra G -- Mullikin, James C -- Martindale, Mark Q -- Baxevanis, Andreas D -- ZIA HG000140-13/Intramural NIH HHS/ -- ZIA HG000140-14/Intramural NIH HHS/ -- ZIA HG000140-15/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 13;342(6164):1242592. doi: 10.1126/science.1242592.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Technology Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24337300" target="_blank"〉PubMed〈/a〉

Description: The evolution of grasses using C4 photosynthesis and their sudden rise to ecological dominance 3 to 8 million years ago is among the most dramatic examples of biome assembly in the geological record. A growing body of work suggests that the patterns and drivers of C4 grassland expansion were considerably more complex than originally assumed. Previous research has benefited substantially from dialog between geologists and ecologists, but current research must now integrate fully with phylogenetics. A synthesis of grass evolutionary biology with grassland ecosystem science will further our knowledge of the evolution of traits that promote dominance in grassland systems and will provide a new context in which to evaluate the relative importance of C4 photosynthesis in transforming ecosystems across large regions of Earth.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Edwards, Erika J -- Osborne, Colin P -- Stromberg, Caroline A E -- Smith, Stephen A -- C4 Grasses Consortium -- Bond, William J -- Christin, Pascal-Antoine -- Cousins, Asaph B -- Duvall, Melvin R -- Fox, David L -- Freckleton, Robert P -- Ghannoum, Oula -- Hartwell, James -- Huang, Yongsong -- Janis, Christine M -- Keeley, Jon E -- Kellogg, Elizabeth A -- Knapp, Alan K -- Leakey, Andrew D B -- Nelson, David M -- Saarela, Jeffery M -- Sage, Rowan F -- Sala, Osvaldo E -- Salamin, Nicolas -- Still, Christopher J -- Tipple, Brett -- New York, N.Y. -- Science. 2010 Apr 30;328(5978):587-91. doi: 10.1126/science.1177216.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA. erika_edwards@brown.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20431008" target="_blank"〉PubMed〈/a〉

Description: Environmental change has been observed to generate simultaneous responses in population dynamics, life history, gene frequencies, and morphology in a number of species. But how common are such eco-evolutionary responses to environmental change likely to be? Are they inevitable, or do they require a specific type of change? Can we accurately predict eco-evolutionary responses? We address these questions using theory and data from the study of Yellowstone wolves. We show that environmental change is expected to generate eco-evolutionary change, that changes in the average environment will affect wolves to a greater extent than changes in how variable it is, and that accurate prediction of the consequences of environmental change will probably prove elusive.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coulson, Tim -- MacNulty, Daniel R -- Stahler, Daniel R -- vonHoldt, Bridgett -- Wayne, Robert K -- Smith, Douglas W -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2011 Dec 2;334(6060):1275-8. doi: 10.1126/science.1209441.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK. t.coulson@imperial.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22144626" target="_blank"〉PubMed〈/a〉