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Read, Betsy A. ; Kegel, Jessica ; Klute, Mary J. ; Kuo, Alan ; Lefebvre, Stephane C. ; Maumus, Florian ; Mayer, Christoph ; Miller, John ; Monier, Adam ; Salamov, Asaf ; Young, Jeremy ; Aguilar, Maria ; Claverie, Jean-Michel ; Frickenhaus, Stephan ; Gonzalez, Karina ; Herman, Emily K. ; Lin, Yao-Cheng ; Napier, Johnathan ; Ogata, Hiroyuki ; Sarno, Analissa F. ; Shmutz, Jeremy ; Schroeder, Declan ; de Vargas, Colomban ; Verret, Frederic ; von Dassow, Peter ; Valentin, Klaus ; Van de Peer, Yves ; Wheeler, Glen ; Dacks, Joel B. ; Delwiche, Charles F. ; Dyhrman, Sonya T. ; Glöckner, Gernot ; John, Uwe ; Richards, Thomas ; Worden, Alexandra Z. ; Zhang, Xiaoyu ; Grigoriev, Igor V. ; Allen, Andrew E. ; Bidle, Kay ; Borodovsky, M. ; Bowler, C. ; Brownlee, Colin ; Cock, J. Mark ; Elias, Marek ; Gladyshev, Vadim N. ; Groth, Marco ; Guda, Chittibabu ; Hadaegh, Ahmad ; Iglesias-Rodriguez, Maria Debora ; Jenkins, J. ; Jones, Bethan M. ; Lawson, Tracy ; Leese, Florian ; Lindquist, Erika ; Lobanov, Alexei ; Lomsadze, Alexandre ; Malik, Shehre-Banoo ; Marsh, Mary E. ; Mackinder, Luke ; Mock, Thomas ; Müller-Röber, Bernd ; Pagarete, Antonio ; Parker, Micaela ; Probert, Ian ; Quesneville, Hadi ; Raines, Christine ; Rensing, Stefan A. ; Riano-Pachon, Diego Mauricio ; Richier, Sophie ; Rokitta, Sebastian ; Shiraiwa, Yoshihiro ; Soanes, Darren M. ; van der Giezen, Mark ; Wahlund, Thomas M. ; Williams, Bryony ; Wilson, Willie ; Wolfe, Gordon ; Wurch, Louie L.
Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
Palkopoulou, Eleftheria ; Lipson, Mark ; Mallick, Swapan ; Nielsen, Svend ; Rohland, Nadin ; Baleka, Sina Isabelle ; Karpinski, Emil ; Ivancevici, Atma M. ; Thu-Hien To ; Kortschak, Daniel ; Raison, Joy M. ; Qu, Zhipeng ; Chin, Tat-Jun ; Alt, Kurt W. ; Claesson, Stefan ; Dalen, Love ; MacPhee, Ross D. E. ; Meller, Harald ; Rocar, Alfred L. ; Ryder, Oliver A. ; Heiman, David ; Young, Sarah ; Breen, Matthew ; Williams, Christina ; Aken, Bronwen L. ; Ruffier, Magali ; Karlsson, Elinor ; Johnson, Jeremy ; Di Palma, Federica ; Alfoldi, Jessica ; Adelsoni, David L. ; Mailund, Thomas ; Munch, Kasper ; Lindblad-Toh, Kerstin ; Hofreiter, Michael ; Poinar, Hendrik ; Reich, David
Brodeur, Abel ; Mikola, Derek ; Cook, Nikolai ; Brailey, Thomas ; Briggs, Ryan ; Gendre, Alexandra de ; Dupraz, Yannick ; Fiala, Lenka ; Gabani, Jacopo ; Gauriot, Romain ; Haddad, Joanne ; Lima, Goncalo ; Ankel-Peters, Jörg ; Dreber, Anna ; Campbell, Douglas ; Kattan, Lamis ; Fages, Diego Marino ; Mierisch, Fabian ; Sun, Pu ; Wright, Taylor ; Connolly, Marie ; Hoces de la Guardia, Fernando ; Johannesson, Magnus ; Miguel, Edward ; Vilhuber, Lars ; Abarca, Alejandro ; Acharya, Mahesh ; Adjisse, Sossou Simplice ; Akhtar, Ahwaz ; Lizardi, Eduardo Alberto Ramirez ; Albrecht, Sabina ; Andersen, Synve Nygaard ; Andlib, Zubaria ; Arrora, Falak ; Ash, Thomas ; Bacher, Etienne ; Bachler, Sebastian ; Bacon, Félix ; Bagues, Manuel ; Balogh, Timea ; Batmanov, Alisher ; Barschkett, Mara ; Basdil, B. Kaan ; Dower, Jaromneda ; Castek, Ondrej ; Caviglia-Harris, Jill ; Strand, Gabriella Chauca ; Chen, Shi ; Chzhen, Asya ; Chung, Jong ; Collins, Jason ; Coppock, Alexander ; Cordeau, Hugo ; Couillard, Ben ; Crechet, Jonathan ; Crippa, Lorenzo ; Cui, Jeanne ; Czymara, Christian ; Daarstad, Haley ; Dao, Danh Chi ; Dao, Dong ; Schmandt, Marco David ; Linde, Astrid de ; Melo, Lucas De ; Deer, Lachlan ; Vera, Micole De ; Dimitrova, Velichka ; Dollbaum, Jan Fabian ; Dollbaum, Jan Matti ; Donnelly, Michael ; Huynh, Luu Duc Toan ; Dumbalska, Tsvetomira ; Duncan, Jamie ; Duong, Kiet Tuan ; Duprey, Thibaut ; Dworschak, Christoph ; Ellingsrud, Sigmund ; Elminejad, Ali ; Eissa, Yasmine ; Erhart, Andrea ; Etingin-Frati, Giulian ; Fatemi-Pour, Elaheh ; Federice, Alexa ; Feld, Jan ; Fenig, Guidon ; Firouzjaeiangalougah, Mojtaba ; Fleisje, Erlend ; Fortier-Chouinard, Alexandre ; Engel, Julia Francesca ; Fries, Tilman ; Fortier, Reid ; Fréchet, Nadjim ; Galipeau, Thomas ; Gallegos, Sebastián ; Gangji, Areez ; Gao, Xiaoying ; Garnache, Cloé ; Gáspár, Attila ; Gavrilova, Evelina ; Ghosh, Arijit ; Gibney, Garreth ; Gibson, Grant ; Godager, Geir ; Goff, Leonard ; Gong, Da ; González, Javier ; Gretton, Jeremy ; Griffa, Cristina ; Grigoryeva, Idaliya ; Grtting, Maja ; Guntermann, Eric ; Guo, Jiaqi ; Gugushvili, Alexi ; Habibnia, Hooman ; Häffner, Sonja ; Hall, Jonathan D. ; Hammar, Olle ; Kordt, Amund Hanson ; Hashimoto, Barry ; Hartley, Jonathan S. ; Hausladen, Carina I. ; Havránek, Tomáš ; Hazen, Jacob ; He, Harry ; Hepplewhite, Matthew ; Herrera-Rodriguez, Mario ; Heuer, Felix ; Heyes, Anthony ; Ho, Anson T. Y. ; Holmes, Jonathan ; Holzknecht, Armando ; Hsu, Yu-Hsiang Dexter ; Hu, Shiang-Hung ; Huang, Yu-Shiuan ; Huebener, Mathias ; Huber, Christoph ; Huynh, Kim P. ; Irsova, Zuzana ; Isler, Ozan ; Jakobsson, Niklas ; Frith, Michael James ; Jananji, Raphaël ; Jayalath, Tharaka A. ; Jetter, Michael ; John, Jenny ; Forshaw, Rachel Joy ; Juan, Felipe ; Kadriu, Valon ; Karim, Sunny ; Kelly, Edmund ; Dang, Duy Khanh Hoang ; Khushboo, Tazia ; Kim, Jin ; Kjellsson, Gustav ; Kjelsrud, Anders ; Kotsadam, Andreas ; Korpershoek, Jori ; Krashinsky, Lewis ; Kundu, Suranjana ; Kustov, Alexander ; Lalayev, Nurlan ; Langlois, Audrée ; Laufer, Jill ; Lee-Whiting, Blake ; Leibing, Andreas ; Lenz, Gabriel ; Levin, Joel ; Li, Peng ; Li, Tongzhe ; Lin, Yuchen ; Listo, Ariel ; Liu, Dan ; Lu, Xuewen ; Lukmanova, Elvina ; Luscombe, Alex ; Lusher, Lester R. ; Lyu, Ke ; Ma, Hai ; Mäder, Nicolas ; Makate, Clifton ; Malmberg, Alice ; Maitra, Adit ; Mandas, Marco ; Marcus, Jan ; Margaryan, Shushanik ; Márk, Lili ; Martignano, Andres ; Marsh, Abigail ; Masetto, Isabella ; McCanny, Anthony ; McManus, Emma ; McWay, Ryan ; Metson, Lennard ; Kinge, Jonas Minet ; Mishra, Sumit ; Mohnen, Myra ; Möller, Jakob ; Montambeault, Rosalie ; Montpetit, Sébastien ; Morin, Louis-Philippe ; Morris, Todd ; Moser, Scott ; Motoki, Fabio ; Muehlenbachs, Lucija ; Musulan, Andreea ; Musumeci, Marco ; Nabin, Munirul ; Nchare, Karim ; Neubauer, Florian ; Nguyen, Quan M. P. ; Nguyen, Tuan ; Nguyen-Tien, Viet ; Niazi, Ali ; Nikolaishvili, Giorgi ; Nordstrom, Ardyn ; Nü, Patrick ; Odermatt, Angela ; Olson, Matt ; ien, Henning ; Ölkers, Tim ; Vert, Miquel Oliver i. ; Oral, Emre ; Oswald, Christian ; Ousman, Ali ; Özak, Ömer ; Pandey, Shubham ; Pavlov, Alexandre ; Pelli, Martino ; Penheiro, Romeo ; Park, RyuGyung ; Martel, Eva Pérez ; Petrovičová, Tereza ; Phan, Linh ; Prettyman, Alexa ; Procházka, Jakub ; Putri, Aqila ; Quandt, Julian ; Qiu, Kangyu ; Nguyen, Loan Quynh Thi ; Rahman, Andaleeb ; Rea, Carson H. ; Reiremo, Adam ; Renée, Laëtitia ; Richardson, Joseph ; Rivers, Nicholas ; Rodrigues, Bruno ; Roelofs, William ; Roemer, Tobias ; Rogeberg, Ole ; Rose, Julian ; Roskos-Ewoldsen, Andrew ; Rosmer, Paul ; Sabada, Barbara ; Saberian, Soodeh ; Salamanca, Nicolas ; Sator, Georg ; Sawyer, Antoine ; Scates, Daniel ; Schlüter, Elmar ; Sells, Cameron ; Sen, Sharmi ; Sethi, Ritika ; Shcherbiak, Anna ; Sogaolu, Moyosore ; Soosalu, Matt ; Srensen, Erik ; Sovani, Manali ; Spencer, Noah ; Staubli, Stefan ; Stans, Renske ; Stewart, Anya ; Stips, Felix ; Stockley, Kieran ; Strobel, Stephenson ; Struby, Ethan ; Tang, John ; Tanrisever, Idil ; Yang, Thomas Tao ; Tastan, Ipek ; Tatić, Dejan ; Tatlow, Benjamin ; Seuyong, Féraud Tchuisseu ; Thériault, Rémi ; Thivierge, Vincent ; Tian, Wenjie ; Toma, Filip-Mihai ; Totarelli, Maddalena ; Tran, Van-Anh ; Truong, Hung ; Tsoy, Nikita ; Tuzcuoglu, Kerem ; Ubfal, Diego ; Villalobos, Laura ; Walterskirchen, Julian ; Wang, Joseph Taoyi ; Wattal, Vasudha ; Webb, Matthew D. ; Weber, Bryan ; Weisser, Reinhard ; Weng, Wei-Chien ; Westheide, Christian ; White, Kimberly ; Winter, Jacob ; Wochner, Timo ; Woerman, Matt ; Wong, Jared ; Woodard, Ritchie ; Wroński, Marcin ; Yazbeck, Myra ; Yang, Gustav Chung ; Yap, Luther ; Yassin, Kareman ; Ye, Hao ; Yoon, Jin Young ; Yurris, Chris ; Zahra, Tahreen ; Zaneva, Mirela ; Zayat, Aline ; Zhang, Jonathan ; Zhao, Ziwei ; Yaolang, Zhong
This study pushes our understanding of research reliability by reproducing and replicating claims from 110 papers in leading economic and political science journals. The analysis involves computational reproducibility checks and robustness assessments. It reveals several patterns. First, we uncover a high rate of fully computationally reproducible results (over 85%). Second, excluding minor issues like missing packages or broken pathways, we uncover coding errors for about 25% of studies, with some studies containing multiple errors. Third, we test the robustness of the results to 5,511 re-analyses. We find a robustness reproducibility of about 70%. Robustness reproducibility rates are relatively higher for re-analyses that introduce new data and lower for re-analyses that change the sample or the definition of the dependent variable. Fourth, 52% of re-analysis effect size estimates are smaller than the original published estimates and the average statistical significance of a re-analysis is 77% of the original. Lastly, we rely on six teams of researchers working independently to answer eight additional research questions on the determinants of robustness reproducibility. Most teams find a negative relationship between replicators' experience and reproducibility, while finding no relationship between reproducibility and the provision of intermediate or even raw data combined with the necessary cleaning codes.
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