TY - JOUR A1 - Middeldorp, Christel M. A1 - Mahajan, Anubha A1 - Horikoshi, Momoko A1 - Robertson, Neil R. A1 - Beaumont, Robin N. A1 - Bradfield, Jonathan P. A1 - Bustamante, Mariona A1 - Cousminer, Diana L. A1 - Day, Felix R. A1 - De Silva, N. Maneka A1 - Guxens, Monica A1 - Mook-Kanamori, Dennis O. A1 - St Pourcain, Beate A1 - Warrington, Nicole M. A1 - Adair, Linda S. A1 - Ahlqvist, Emma A1 - Ahluwalia, Tarunveer Singh A1 - Almgren, Peter A1 - Ang, Wei A1 - Atalay, Mustafa A1 - Auvinen, Juha A1 - Bartels, Meike A1 - Beckmann, Jacques S. A1 - Bilbao, Jose Ramon A1 - Bond, Tom A1 - Borja, Judith B. A1 - Cavadino, Alana A1 - Charoen, Pimphen A1 - Chen, Zhanghua A1 - Coin, Lachlan A1 - Cooper, Cyrus A1 - Curtin, John A. A1 - Custovic, Adnan A1 - Das, Shikta A1 - Davies, Gareth E. A1 - Dedoussis, George V. A1 - Duijts, Liesbeth A1 - Eastwood, Peter R. A1 - Eliasen, Anders U. A1 - Elliott, Paul A1 - Eriksson, Johan G. A1 - Estivill, Xavier A1 - Fadista, Joao A1 - Fedko, Iryna O. A1 - Frayling, Timothy M. A1 - Gaillard, Romy A1 - Gauderman, W. James A1 - Geller, Frank A1 - Gilliland, Frank A1 - Gilsanz, Vincente A1 - Granell, Raquel A1 - Grarup, Niels A1 - Groop, Leif A1 - Hadley, Dexter A1 - Hakonarson, Hakon A1 - Hansen, Torben A1 - Hartman, Catharina A. A1 - Hattersley, Andrew T. A1 - Hayes, M. Geoffrey A1 - Hebebrand, Johannes A1 - Heinrich, Joachim A1 - Helgeland, Oyvind A1 - Henders, Anjali K. A1 - Henderson, John A1 - Henriksen, Tine B. A1 - Hirschhorn, Joel N. A1 - Hivert, Marie-France A1 - Hocher, Berthold A1 - Holloway, John W. A1 - Holt, Patrick A1 - Hottenga, Jouke-Jan A1 - Hypponen, Elina A1 - Iniguez, Carmen A1 - Johansson, Stefan A1 - Jugessur, Astanand A1 - Kahonen, Mika A1 - Kalkwarf, Heidi J. A1 - Kaprio, Jaakko A1 - Karhunen, Ville A1 - Kemp, John P. A1 - Kerkhof, Marjan A1 - Koppelman, Gerard H. A1 - Korner, Antje A1 - Kotecha, Sailesh A1 - Kreiner-Moller, Eskil A1 - Kulohoma, Benard A1 - Kumar, Ashish A1 - Kutalik, Zoltan A1 - Lahti, Jari A1 - Lappe, Joan M. A1 - Larsson, Henrik A1 - Lehtimaki, Terho A1 - Lewin, Alexandra M. A1 - Li, Jin A1 - Lichtenstein, Paul A1 - Lindgren, Cecilia M. A1 - Lindi, Virpi A1 - Linneberg, Allan A1 - Liu, Xueping A1 - Liu, Jun A1 - Lowe, William L. A1 - Lundstrom, Sebastian A1 - Lyytikainen, Leo-Pekka A1 - Ma, Ronald C. W. A1 - Mace, Aurelien A1 - Magi, Reedik A1 - Magnus, Per A1 - Mamun, Abdullah A. A1 - Mannikko, Minna A1 - Martin, Nicholas G. A1 - Mbarek, Hamdi A1 - McCarthy, Nina S. A1 - Medland, Sarah E. A1 - Melbye, Mads A1 - Melen, Erik A1 - Mohlke, Karen L. A1 - Monnereau, Claire A1 - Morgen, Camilla S. A1 - Morris, Andrew P. A1 - Murray, Jeffrey C. A1 - Myhre, Ronny A1 - Najman, Jackob M. A1 - Nivard, Michel G. A1 - Nohr, Ellen A. A1 - Nolte, Ilja M. A1 - Ntalla, Ioanna A1 - Oberfield, Sharon E. A1 - Oken, Emily A1 - Oldehinkel, Albertine J. A1 - Pahkala, Katja A1 - Palviainen, Teemu A1 - Panoutsopoulou, Kalliope A1 - Pedersen, Oluf A1 - Pennell, Craig E. A1 - Pershagen, Goran A1 - Pitkanen, Niina A1 - Plomin, Robert A1 - Power, Christine A1 - Prasad, Rashmi B. A1 - Prokopenko, Inga A1 - Pulkkinen, Lea A1 - Raikkonen, Katri A1 - Raitakari, Olli T. A1 - Reynolds, Rebecca M. A1 - Richmond, Rebecca C. A1 - Rivadeneira, Fernando A1 - Rodriguez, Alina A1 - Rose, Richard J. A1 - Salem, Rany A1 - Santa-Marina, Loreto A1 - Saw, Seang-Mei A1 - Schnurr, Theresia M. A1 - Scott, James G. A1 - Selzam, Saskia A1 - Shepherd, John A. A1 - Simpson, Angela A1 - Skotte, Line A1 - Sleiman, Patrick M. A. A1 - Snieder, Harold A1 - Sorensen, Thorkild I. A. A1 - Standl, Marie A1 - Steegers, Eric A. P. A1 - Strachan, David P. A1 - Straker, Leon A1 - Strandberg, Timo A1 - Taylor, Michelle A1 - Teo, Yik-Ying A1 - Thiering, Elisabeth A1 - Torrent, Maties A1 - Tyrrell, Jessica A1 - Uitterlinden, Andre G. A1 - van Beijsterveldt, Toos A1 - van der Most, Peter J. A1 - van Duijn, Cornelia M. A1 - Viikari, Jorma A1 - Vilor-Tejedor, Natalia A1 - Vogelezang, Suzanne A1 - Vonk, Judith M. A1 - Vrijkotte, Tanja G. M. A1 - Vuoksimaa, Eero A1 - Wang, Carol A. A1 - Watkins, William J. A1 - Wichmann, H-Erich A1 - Willemsen, Gonneke A1 - Williams, Gail M. A1 - Wilson, James F. A1 - Wray, Naomi R. A1 - Xu, Shujing A1 - Xu, Cheng-Jian A1 - Yaghootkar, Hanieh A1 - Yi, Lu A1 - Zafarmand, Mohammad Hadi A1 - Zeggini, Eleftheria A1 - Zemel, Babette S. A1 - Hinney, Anke A1 - Lakka, Timo A. A1 - Whitehouse, Andrew J. O. A1 - Sunyer, Jordi A1 - Widen, Elisabeth E. A1 - Feenstra, Bjarke A1 - Sebert, Sylvain A1 - Jacobsson, Bo A1 - Njolstad, Pal R. A1 - Stoltenberg, Camilla A1 - Smith, George Davey A1 - Lawlor, Debbie A. A1 - Paternoster, Lavinia A1 - Timpson, Nicholas J. A1 - Ong, Ken K. A1 - Bisgaard, Hans A1 - Bonnelykke, Klaus A1 - Jaddoe, Vincent W. V. A1 - Tiemeier, Henning A1 - Jarvelin, Marjo-Riitta A1 - Evans, David M. A1 - Perry, John R. B. A1 - Grant, Struan F. A. A1 - Boomsma, Dorret I. A1 - Freathy, Rachel M. A1 - McCarthy, Mark I. A1 - Felix, Janine F. T1 - The Early Growth Genetics (EGG) and EArly Genetics and Lifecourse Epidemiology (EAGLE) consortia BT - design, results and future prospects JF - European journal of epidemiology N2 - The impact of many unfavorable childhood traits or diseases, such as low birth weight and mental disorders, is not limited to childhood and adolescence, as they are also associated with poor outcomes in adulthood, such as cardiovascular disease. Insight into the genetic etiology of childhood and adolescent traits and disorders may therefore provide new perspectives, not only on how to improve wellbeing during childhood, but also how to prevent later adverse outcomes. To achieve the sample sizes required for genetic research, the Early Growth Genetics (EGG) and EArly Genetics and Lifecourse Epidemiology (EAGLE) consortia were established. The majority of the participating cohorts are longitudinal population-based samples, but other cohorts with data on early childhood phenotypes are also involved. Cohorts often have a broad focus and collect(ed) data on various somatic and psychiatric traits as well as environmental factors. Genetic variants have been successfully identified for multiple traits, for example, birth weight, atopic dermatitis, childhood BMI, allergic sensitization, and pubertal growth. Furthermore, the results have shown that genetic factors also partly underlie the association with adult traits. As sample sizes are still increasing, it is expected that future analyses will identify additional variants. This, in combination with the development of innovative statistical methods, will provide detailed insight on the mechanisms underlying the transition from childhood to adult disorders. Both consortia welcome new collaborations. Policies and contact details are available from the corresponding authors of this manuscript and/or the consortium websites. KW - Genetics KW - Consortium KW - Childhood traits and disorders KW - Longitudinal Y1 - 2019 U6 - https://doi.org/10.1007/s10654-019-00502-9 SN - 0393-2990 SN - 1573-7284 VL - 34 IS - 3 SP - 279 EP - 300 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Chipman, Ariel D. A1 - Ferrier, David E. K. A1 - Brena, Carlo A1 - Qu, Jiaxin A1 - Hughes, Daniel S. T. A1 - Schroeder, Reinhard A1 - Torres-Oliva, Montserrat A1 - Znassi, Nadia A1 - Jiang, Huaiyang A1 - Almeida, Francisca C. A1 - Alonso, Claudio R. A1 - Apostolou, Zivkos A1 - Aqrawi, Peshtewani A1 - Arthur, Wallace A1 - Barna, Jennifer C. J. A1 - Blankenburg, Kerstin P. A1 - Brites, Daniela A1 - Capella-Gutierrez, Salvador A1 - Coyle, Marcus A1 - Dearden, Peter K. A1 - Du Pasquier, Louis A1 - Duncan, Elizabeth J. A1 - Ebert, Dieter A1 - Eibner, Cornelius A1 - Erikson, Galina A1 - Evans, Peter D. A1 - Extavour, Cassandra G. A1 - Francisco, Liezl A1 - Gabaldon, Toni A1 - Gillis, William J. A1 - Goodwin-Horn, Elizabeth A. A1 - Green, Jack E. A1 - Griffiths-Jones, Sam A1 - Grimmelikhuijzen, Cornelis J. P. A1 - Gubbala, Sai A1 - Guigo, Roderic A1 - Han, Yi A1 - Hauser, Frank A1 - Havlak, Paul A1 - Hayden, Luke A1 - Helbing, Sophie A1 - Holder, Michael A1 - Hui, Jerome H. L. A1 - Hunn, Julia P. A1 - Hunnekuhl, Vera S. A1 - Jackson, LaRonda A1 - Javaid, Mehwish A1 - Jhangiani, Shalini N. A1 - Jiggins, Francis M. A1 - Jones, Tamsin E. A1 - Kaiser, Tobias S. A1 - Kalra, Divya A1 - Kenny, Nathan J. A1 - Korchina, Viktoriya A1 - Kovar, Christie L. A1 - Kraus, F. Bernhard A1 - Lapraz, Francois A1 - Lee, Sandra L. A1 - Lv, Jie A1 - Mandapat, Christigale A1 - Manning, Gerard A1 - Mariotti, Marco A1 - Mata, Robert A1 - Mathew, Tittu A1 - Neumann, Tobias A1 - Newsham, Irene A1 - Ngo, Dinh N. A1 - Ninova, Maria A1 - Okwuonu, Geoffrey A1 - Ongeri, Fiona A1 - Palmer, William J. A1 - Patil, Shobha A1 - Patraquim, Pedro A1 - Pham, Christopher A1 - Pu, Ling-Ling A1 - Putman, Nicholas H. A1 - Rabouille, Catherine A1 - Ramos, Olivia Mendivil A1 - Rhodes, Adelaide C. A1 - Robertson, Helen E. A1 - Robertson, Hugh M. A1 - Ronshaugen, Matthew A1 - Rozas, Julio A1 - Saada, Nehad A1 - Sanchez-Gracia, Alejandro A1 - Scherer, Steven E. A1 - Schurko, Andrew M. A1 - Siggens, Kenneth W. A1 - Simmons, DeNard A1 - Stief, Anna A1 - Stolle, Eckart A1 - Telford, Maximilian J. A1 - Tessmar-Raible, Kristin A1 - Thornton, Rebecca A1 - van der Zee, Maurijn A1 - von Haeseler, Arndt A1 - Williams, James M. A1 - Willis, Judith H. A1 - Wu, Yuanqing A1 - Zou, Xiaoyan A1 - Lawson, Daniel A1 - Muzny, Donna M. A1 - Worley, Kim C. A1 - Gibbs, Richard A. A1 - Akam, Michael A1 - Richards, Stephen T1 - The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima JF - PLoS biology N2 - Myriapods (e. g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pbio.1002005 SN - 1545-7885 VL - 12 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Read, Betsy A. A1 - Kegel, Jessica A1 - Klute, Mary J. A1 - Kuo, Alan A1 - Lefebvre, Stephane C. A1 - Maumus, Florian A1 - Mayer, Christoph A1 - Miller, John A1 - Monier, Adam A1 - Salamov, Asaf A1 - Young, Jeremy A1 - Aguilar, Maria A1 - Claverie, Jean-Michel A1 - Frickenhaus, Stephan A1 - Gonzalez, Karina A1 - Herman, Emily K. A1 - Lin, Yao-Cheng A1 - Napier, Johnathan A1 - Ogata, Hiroyuki A1 - Sarno, Analissa F. A1 - Shmutz, Jeremy A1 - Schroeder, Declan A1 - de Vargas, Colomban A1 - Verret, Frederic A1 - von Dassow, Peter A1 - Valentin, Klaus A1 - Van de Peer, Yves A1 - Wheeler, Glen A1 - Dacks, Joel B. A1 - Delwiche, Charles F. A1 - Dyhrman, Sonya T. A1 - Glöckner, Gernot A1 - John, Uwe A1 - Richards, Thomas A1 - Worden, Alexandra Z. A1 - Zhang, Xiaoyu A1 - Grigoriev, Igor V. A1 - Allen, Andrew E. A1 - Bidle, Kay A1 - Borodovsky, M. A1 - Bowler, C. A1 - Brownlee, Colin A1 - Cock, J. Mark A1 - Elias, Marek A1 - Gladyshev, Vadim N. A1 - Groth, Marco A1 - Guda, Chittibabu A1 - Hadaegh, Ahmad A1 - Iglesias-Rodriguez, Maria Debora A1 - Jenkins, J. A1 - Jones, Bethan M. A1 - Lawson, Tracy A1 - Leese, Florian A1 - Lindquist, Erika A1 - Lobanov, Alexei A1 - Lomsadze, Alexandre A1 - Malik, Shehre-Banoo A1 - Marsh, Mary E. A1 - Mackinder, Luke A1 - Mock, Thomas A1 - Müller-Röber, Bernd A1 - Pagarete, Antonio A1 - Parker, Micaela A1 - Probert, Ian A1 - Quesneville, Hadi A1 - Raines, Christine A1 - Rensing, Stefan A. A1 - Riano-Pachon, Diego Mauricio A1 - Richier, Sophie A1 - Rokitta, Sebastian A1 - Shiraiwa, Yoshihiro A1 - Soanes, Darren M. A1 - van der Giezen, Mark A1 - Wahlund, Thomas M. A1 - Williams, Bryony A1 - Wilson, Willie A1 - Wolfe, Gordon A1 - Wurch, Louie L. T1 - Pan genome of the phytoplankton Emiliania underpins its global distribution JF - Nature : the international weekly journal of science N2 - 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. Y1 - 2013 U6 - https://doi.org/10.1038/nature12221 SN - 0028-0836 SN - 1476-4687 VL - 499 IS - 7457 SP - 209 EP - 213 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Maddock, Simon T. A1 - Childerstone, Aaron A1 - Fry, Bryan Grieg A1 - Williams, David J. A1 - Barlow, Axel A1 - Wuester, Wolfgang T1 - Multi-locus phylogeny and species delimitation of Australo-Papuan blacksnakes (Pseudechis Wagler, 1830: Elapidae: Serpentes) JF - Molecular phylogenetics and evolution N2 - Genetic analyses of Australasian organisms have resulted in the identification of extensive cryptic diversity across the continent. The venomous elapid snakes are among the best-studied organismal groups in this region, but many knowledge gaps persist: for instance, despite their iconic status, the species-level diversity among Australo-Papuan blacksnakes (Pseudechis) has remained poorly understood due to the existence of a group of cryptic species within the P. australis species complex, collectively termed "pygmy mulga snakes". Using two mitochondrial and three nuclear loci we assess species boundaries within the genus using Bayesian species delimitation methods and reconstruct their phylogenetic history using multispecies coalescent approaches. Our analyses support the recognition of 10 species, including all of the currently described pygmy mulga snakes and one undescribed species from the Northern Territory of Australia. Phylogenetic relationships within the genus are broadly consistent with previous work, with the recognition of three major groups, the viviparous red-bellied black snake P. porphyriacus forming the sister species to two clades consisting of ovoviviparous species. KW - Australia KW - New Guinea KW - Molecular phylogenetics KW - BPP KW - Snakes KW - Multispecies coalescent Y1 - 2017 U6 - https://doi.org/10.1016/j.ympev.2016.09.005 SN - 1055-7903 SN - 1095-9513 VL - 107 SP - 48 EP - 55 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Kefi, Sonia A1 - Berlow, Eric L. A1 - Wieters, Evie A. A1 - Navarrete, Sergio A. A1 - Petchey, Owen L. A1 - Wood, Spencer A. A1 - Boit, Alice A1 - Joppa, Lucas N. A1 - Lafferty, Kevin D. A1 - Williams, Richard J. A1 - Martinez, Neo D. A1 - Menge, Bruce A. A1 - Blanchette, Carol A. A1 - Iles, Alison C. A1 - Brose, Ulrich T1 - More than a meal ... integrating non-feeding interactions into food webs JF - Ecology letters N2 - Organisms eating each other are only one of many types of well documented and important interactions among species. Other such types include habitat modification, predator interference and facilitation. However, ecological network research has been typically limited to either pure food webs or to networks of only a few (<3) interaction types. The great diversity of non-trophic interactions observed in nature has been poorly addressed by ecologists and largely excluded from network theory. Herein, we propose a conceptual framework that organises this diversity into three main functional classes defined by how they modify specific parameters in a dynamic food web model. This approach provides a path forward for incorporating non-trophic interactions in traditional food web models and offers a new perspective on tackling ecological complexity that should stimulate both theoretical and empirical approaches to understanding the patterns and dynamics of diverse species interactions in nature. KW - Ecological network KW - ecosystem engineering KW - facilitation KW - food web KW - interaction modification KW - non-trophic interactions KW - trophic interactions Y1 - 2012 U6 - https://doi.org/10.1111/j.1461-0248.2011.01732.x SN - 1461-023X VL - 15 IS - 4 SP - 291 EP - 300 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Boit, Alice A1 - Martinez, Neo D. A1 - Williams, Richard J. A1 - Gaedke, Ursula T1 - Mechanistic theory and modelling of complex food-web dynamics in Lake Constance JF - Ecology letters N2 - Mechanistic understanding of consumer-resource dynamics is critical to predicting the effects of global change on ecosystem structure, function and services. Such understanding is severely limited by mechanistic models inability to reproduce the dynamics of multiple populations interacting in the field. We surpass this limitation here by extending general consumer-resource network theory to the complex dynamics of a specific ecosystem comprised by the seasonal biomass and production patterns in a pelagic food web of a large, well-studied lake. We parameterised our allometric trophic network model of 24 guilds and 107 feeding relationships using the lakes food web structure, initial spring biomasses and body-masses. Adding activity respiration, the detrital loop, minimal abiotic forcing, prey resistance and several empirically observed rates substantially increased the model's fit to the observed seasonal dynamics and the size-abundance distribution. This process illuminates a promising approach towards improving food-web theory and dynamic models of specific habitats. KW - Allometric Trophic Network model KW - community ecology KW - food web KW - multi-trophic dynamics KW - seasonal plankton succession Y1 - 2012 U6 - https://doi.org/10.1111/j.1461-0248.2012.01777.x SN - 1461-023X VL - 15 IS - 6 SP - 594 EP - 602 PB - Wiley-Blackwell CY - Hoboken ER -