The Origins of Genome Complexity

Lynch, Michael, Conery, John S.·2003·Science
DOI 10.1126/science.1089370

Cited by (1,001)

Items 201–300 of 1,001

  1. Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals
    Giulia Irene Maria Pasquesi, Richard H. Jr. Adams, Daren C. Card, Drew R. Schield, Andrew B. Corbin, Blair W. Perry, Jacobo Reyes‐Velasco, Robert P. Ruggiero, Michael W. Vandewege, Jonathan Shortt et al. · 2018 · Nature Communications
  2. The hybrid nature of the Eukaryota and a consilient view of life on Earth
    James O. McInerney, Mary J. O’Connell, Davide Pisani · 2014 · Nature Reviews Microbiology
  3. Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays
    Paul Bilinski, Patrice S. Albert, Jeremy J. Berg, James A. Birchler, Mark N. Grote, Anne Lorant, Juvenal Quezada, Kelly Swarts, Jinliang Yang, Jeffrey Ross‐Ibarra · 2018 · PLoS Genetics
  4. Getting Started in Gene Orthology and Functional Analysis
    Gang Fang, Nitin Bhardwaj, R. Robilotto, M. Gerstein · 2010 · PLoS Comput. Biol.
  5. Why genes overlap in viruses
    Nicola Chirico, Alberto Vianelli, Robert D. Belshaw · 2010 · Proceedings of the Royal Society B Biological Sciences
  6. Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation–Accumulation Experiments
    Way Sung, Matthew S. Ackerman, Jean-François Goût, Samuel F. Miller, Emily Williams, Patricia L. Foster, Michael Lynch · 2015 · Molecular Biology and Evolution
  7. Fungal Genomes and Insights into the Evolution of the Kingdom
    Jason Stajich · 2017 · Microbiology Spectrum
  8. Modes of pre-Ediacaran multicellularity
    Nicholas J.F. Butterfield · 2009 · Precambrian Research
  9. Genetics and the understanding of selection
    Laurence D. Hurst · 2009 · Nature Reviews Genetics
  10. LTR Retrotransposons in Fungi
    Anna Muszewska, Marta Hoffman‐Sommer, Marcin Grynberg · 2011 · PLoS ONE
  11. Role of mRNA structure in the control of protein folding
    Guilhem Faure, Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Eugene V. Koonin · 2016 · Nucleic Acids Research
  12. Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate
    Liedtke, H. Christoph, Gower, David J., Wilkinson, Mark, Gomez-Mestre, Ivan · 2018 · Nature Ecology & Evolution
  13. Ion Channel Clustering at the Axon Initial Segment and Node of Ranvier Evolved Sequentially in Early Chordates
    Alexis S. Hill, Atsuo Nishino, Koichi Nakajo, Giuxin Zhang, Jaime R. Fineman, Michael E. Selzer, Yasushi Okamura, Edward C. Cooper · 2008 · PLoS Genetics
  14. Hybridization and genome size evolution: timing and magnitude of nuclear DNA content increases in Helianthus homoploid hybrid species
    Eric J. Baack, Kenneth D. Whitney, Loren H. Rieseberg · 2005 · New Phytologist
  15. Evolution of Exon-Intron Structure and Alternative Splicing
    Tomasz E. Koralewski, Konstantin V. Krutovsky · 2011 · PLoS ONE
  16. From biophysics to evolutionary genetics: statistical aspects of gene regulation
    Michael Lässig · 2007 · BMC Bioinformatics
  17. Comparative genomic analysis of fungal genomes reveals intron-rich ancestors
    Jason Stajich, Fred S. Dietrich, Scott William Roy · 2007 · Genome biology
  18. Molecular Evolution, Functional Variation, and Proposed Nomenclature of the Gene Family That Includes Sphingomyelinase D in Sicariid Spider Venoms
    Greta J. Binford, Melissa R. Bodner, Matthew H. J. Cordes, Katherine L. Baldwin, Melody R. Rynerson, Shuntele N. Burns, Pamela A. Zobel-Thropp · 2008 · Molecular Biology and Evolution
  19. Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes
    Janna L. Fierst, John H. Willis, Cristel G. Thomas, Wei Wang, Rose M. Reynolds, Timothy E. Ahearne, Asher D. Cutter, Patrick C. Phillips · 2015 · PLoS Genetics
  20. Transposable Elements and Factors Influencing their Success in Eukaryotes
    Ellen J. Pritham · 2009 · Journal of Heredity
  21. The Footprint of Genome Architecture in the Largest Genome Expansion in RNA Viruses
    Chris Lauber, Jelle J. Goeman, Maria del Carmen Parquet, Phan Thi Nga, Eric J. Snijder, Kouichi Morita, Alexander E. Gorbalenya · 2013 · PLoS Pathogens
  22. Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements
    Jae Young Choi, Yuh Chwen G. Lee · 2020 · PLoS Genetics
  23. Cryptic Genetic Variation Is Enriched for Potential Adaptations
    Joanna Masel · 2005 · Genetics
  24. What Is Speciation?
    B. Jesse Shapiro, Jean‐Baptiste Leducq, James Mallet · 2016 · PLoS Genetics
  25. Exceptionally High Density of NUMTs in the Honeybee Genome
    Pekka Pamilo, Lumi Viljakainen, Anu Vihavainen · 2007 · Molecular Biology and Evolution
  26. High Spontaneous Rate of Gene Duplication in Caenorhabditis elegans
    Kendra J. Lipinski, James C. Farslow, Kelly A. Fitzpatrick, Michael Lynch, Vaishali Katju, Ulfar Bergthorsson · 2011 · Current Biology
  27. The determinants of genetic diversity in butterflies
    Alexander Mackintosh, Dominik R. Laetsch, Alexander Hayward, Brian Charlesworth, Martin Waterfall, Roger Vila, Konrad Lohse · 2019 · Nature Communications
  28. Assembling metagenomes, one community at a time
    A.J. van der Walt, Marc W. Van Goethem, Jean‐Baptiste Ramond, Thulani Peter Makhalanyane, Oleg N. Reva, Don Arthur Cowan · 2017 · BMC Genomics
  29. Genome downsizing after polyploidy: mechanisms, rates and selection pressures
    Xiaotong Wang, Joseph A. Morton, Jaume Pellicer, Ilia J. Leitch, Andrew Rowland Leitch · 2021 · The Plant Journal
  30. The evolution of bet-hedging adaptations to rare scenarios
    Oliver D. King, Joanna Masel · 2007 · Theoretical Population Biology
  31. The genome‐centric concept: resynthesis of evolutionary theory
    Henry H. Heng · 2009 · BioEssays
  32. Families of transposable elements, population structure and the origin of species
    J. Jurka, Wei-Dong Bao, K. Kojima · 2011 · Biology Direct
  33. Horizontal Gene Transfer and the History of Life
    Vincent Daubin, Gergely J. Szöllősi · 2016 · Cold Spring Harbor Perspectives in Biology
  34. Less effective selection leads to larger genomes
    Lefébure Tristan, Claire Morvan, Florian Malard, Clémentine M. Francois, Lara Konecny‐Dupré, Laurent Guéguen, Michèle Weiss‐Gayet, Andaine Seguin‐Orlando, Luca Ermini, Clio S. I. Der Sarkissian et al. · 2017 · Genome Research
  35. Extraordinary genome stability in the ciliate Paramecium tetraurelia
    Way Sung, Abraham E. Tucker, Thomas G. Doak, Eunjin Choi, W. Kelley Thomas, Michael Lynch · 2012 · Proceedings of the National Academy of Sciences
  36. Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding
    Luciana F. Santoferrara, Fabien Burki, Sabine Filker, Ramiro Logares, Micah Dunthorn, George B. McManus · 2020 · Journal of Eukaryotic Microbiology
  37. Genome size evolution: towards new model systems for old questions
    Blommaert, Julie · 2020 · Proceedings of the Royal Society B: Biological Sciences
  38. Non-adaptive origins of interactome complexity
    Ariel Fernández, Michael Lynch · 2011 · Nature
  39. Evolutionary construction by staying together and coming together
    Tarnita, Corina E., Taubes, Clifford H., Nowak, Martin A. · 2013 · Journal of Theoretical Biology
  40. Splendor and misery of adaptation, or the importance of neutral null for understanding evolution
    Eugene V. Koonin · 2016 · BMC Biology
  41. The Origin of Subfunctions and Modular Gene Regulation
    Allan G. Force, William A. Cresko, F. Bryan Pickett, Steven R Proulx, Chris T. Amemiya, Michael Lynch · 2005 · Genetics
  42. Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores
    Ichiro Hiratani, Amanda Leskovar, David M. Gilbert · 2004 · Proceedings of the National Academy of Sciences
  43. Evolution favors protein mutational robustness in sufficiently large populations
    Bloom, Jesse D, Lu, Zhongyi, Chen, David, Raval, Alpan, Venturelli, Ophelia S, Arnold, Frances H · 2007 · BMC Biology
  44. Tempo and Mode of Transposable Element Activity in Drosophila
    Robert Kofler, Viola Nolte, Christian Schlötterer · 2015 · PLoS Genetics
  45. Pericentromeric Effects Shape the Patterns of Divergence, Retention, and Expression of Duplicated Genes in the Paleopolyploid Soybean
    Jianchang Du, Zhixi Tian, Yi Sui, Meixia Zhao, Qijian Song, Steven B. Cannon, Perry B. Cregan, Jianxin Ma · 2012 · The Plant Cell
  46. Correlation between Nuclear Plastid DNA Abundance and Plastid Number Supports the Limited Transfer Window Hypothesis
    D. Smith, K. Crosby, Robert W. Lee · 2011 · Genome Biology and Evolution
  47. Comparative Analysis of Mycobacterium tuberculosis pe and ppe Genes Reveals High Sequence Variation and an Apparent Absence of Selective Constraints
    Christopher R. E. McEvoy, Ruben E.A. Cloete, Borna Müller, Anita C. Schürch, Paul D. van Helden, Sébastien Gagneux, Robin M. Warren, Nicolaas C. Gey van Pittius · 2012 · PLoS ONE
  48. Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli
    Valerie W. C. Soo, Paulina Hanson‐Manful, Wayne M. Patrick · 2010 · Proceedings of the National Academy of Sciences
  49. Why Genes Evolve Faster on Secondary Chromosomes in Bacteria
    Vaughn S. Cooper, Samuel H. Vohr, Sarah C. Wrocklage, Philip J. Hatcher · 2010 · PLoS Computational Biology
  50. Ecological genomics in Daphnia: stress responses and environmental sex determination
    Brian D. Eads, Justen Andrews, John K. Colbourne · 2007 · Heredity
  51. Intra-Genomic Variation in the Ribosomal Repeats of Nematodes
    Holly M. Bik, David Fournier, Way Sung, R. Daniel Bergeron, W. Kelley Thomas · 2013 · PLoS ONE
  52. Intron retention enhances gene regulatory complexity in vertebrates
    Ulf Schmitz, Natalia Pinello, Fangzhi Jia, Sultan Alasmari, William Ritchie, Maria-Cristina Keightley, S. Shini, Graham John Lieschke, Justin J. -L. Wong, John E.J. Rasko · 2017 · Genome biology
  53. Transposable elements contribute to fungal genes and impact fungal lifestyle
    Anna Muszewska, Kamil Steczkiewicz, Marta M. Stepniewska-Dziubinska, Krzysztof Ginalski · 2019 · Scientific Reports
  54. Adaptive and nonadaptive genome size evolution in Karst endemic flora of China
    Ming Kang, Junjie Tao, Jing Wang, Chen Ren, Qingwen Qi, Qiu‐Yun Xiang, Hongwen Huang · 2014 · New Phytologist
  55. Evolution of complexity in signaling pathways
    Orkun S. Soyer, Sebastian Bonhoeffer · 2006 · Proceedings of the National Academy of Sciences
  56. Estimating Translational Selection in Eukaryotic Genomes
    Mario dos Reis, Lorenz Wernisch · 2008 · Molecular Biology and Evolution
  57. Origin and early evolution of neural circuits for the control of ciliary locomotion
    Jékely, Gáspár · 2011 · Proceedings of the Royal Society B: Biological Sciences
  58. Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution
    Christopher R. Baker, V. Hanson-Smith, Alexander D. Johnson · 2013 · Science
  59. Phagocytosis-like cell engulfment by a planctomycete bacterium
    Takashi Shiratori, S. Suzuki, Yukako Kakizawa, Ken‐ichiro Ishida · 2019 · Nature Communications
  60. Intron Delays and Transcriptional Timing during Development
    Ian A. Swinburne, Pamela A. Silver · 2008 · Developmental Cell
  61. Genes with a large intronic burden show greater evolutionary conservation on the protein level
    Olga Y. Gorlova, Alexey N. Fedorov, Christopher J. Logothetis, Christopher Ian Amos, Ivan P. Gorlov · 2014 · BMC Evolutionary Biology
  62. Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution
    Yuh Chwen G. Lee, Gary H. Karpen · 2017 · eLife
  63. Energy efficiency trade-offs drive nucleotide usage in transcribed regions
    Wei-Hua Chen, Guanting Lu, Peer Bork, Songnian Hu, Martin J. Lercher · 2016 · Nature Communications
  64. The Mutation Rate and the Age of the Sex Chromosomes in Silene latifolia
    Marc Krasovec, Michael Chester, Kate E. Ridout, Dmitry A. Filatov · 2018 · Current Biology
  65. Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata
    Steven Lockton, Jeffrey Ross‐Ibarra, Brandon S. Gaut · 2008 · Proceedings of the National Academy of Sciences
  66. Mouse duplicate genes are as essential as singletons
    Ben‐Yang Liao, Jianzhi Zhang · 2007 · Trends in Genetics
  67. Small genomes dominate in plants growing on serpentine soils in West Balkans, an exhaustive study of 8 habitats covering 308 taxa
    Fatima Pustahija, Spencer Brown, Faruk Bogunić, Neđad Bašić, Edina Muratović, Sébastien Ollier, Oriane Hidalgo, Mickaël Bourge, Vladimir Stevanović, Sonja Šiljak-Yakovlev · 2013 · Plant and Soil
  68. Shift happens! Shifting balance and the evolution of diversity in warning colour and mimicry
    James Mallet · 2010 · Ecological Entomology
  69. A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family M elanthiaceae
    Jaume Pellicer, Laura J. Kelly, Ilia J. Leitch, Wendy B. Zomlefer, Michael F. Fay · 2013 · New Phytologist
  70. The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics
    Anthony Levasseur, Pierre Pontarotti · 2011 · Biology Direct
  71. Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus
    Olga Zhaxybayeva, W. Ford Doolittle, R. Thane Papke, Johann Peter Gogarten · 2009 · Genome Biology and Evolution
  72. The Limits of Natural Selection in a Nonequilibrium World
    Yaniv J Brandvain, Stephen Wright · 2016 · Trends in Genetics
  73. Gene Complexity and Gene Duplicability
    Xionglei He, Jianzhi Zhang · 2005 · Current Biology
  74. Simple sequence repeats in proteins and their significance for network evolution
    John M. Hancock, Michelle Simon · 2004 · Gene
  75. Nucleosomes Suppress Spontaneous Mutations Base-Specifically in Eukaryotes
    Xiaoshu Chen, Zhidong Chen, Han Chen, Zhijian Su, Jianfeng Yang, Fangqin Lin, Suhua Shi, Xionglei He · 2012 · Science
  76. Small genome of the fungus Escovopsis weberi , a specialized disease agent of ant agriculture
    Tom J. B. de Man, Jason Stajich, Christian Peter Kubicek, Clotilde Teiling, Komal Chenthamara, Lea Atanasova, Irina S. Druzhinina, Natasha Levenkova, Stephanie S.L. Birnbaum, Seth Michael Barribeau et al. · 2016 · Proceedings of the National Academy of Sciences
  77. Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans
    Kristian Alfsnes, Hans Petter Leinaas, Dag O. Hessen · 2017 · Ecology and Evolution
  78. Plant Genome Diversity Volume 1
    Jonathan F. Wendel, J. Greilhuber, Jaroslav Doležel, Ilia J. Leitch · 2012 · Springer eBooks
  79. Origin and Neofunctionalization of a Drosophila Paternal Effect Gene Essential for Zygote Viability
    Benjamin Loppin, David Lepetit, Steve Dorus, Pierre Couble, Timothy L. Karr · 2005 · Current Biology
  80. Sequence diversity of the mucABD locus in Pseudomonas aeruginosa isolates from patients with cystic fibrosis
    Alessandra Bragonzi, Lutz Wiehlmann, Jens Klockgether, Nina Cramer, Dieter Worlitzsch, Gerd Döring, Burkhard Tümmler · 2006 · Microbiology
  81. Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat
    Alexander Belyayev, Ruslan N. Kalendar, Leonid Brodsky, Eviatar Nevo, Alan Howard Schulman, Olga Raskina · 2010 · Mobile DNA
  82. Gene length and expression level shape genomic novelties
    V. Grishkevich, I. Yanai · 2014 · Genome Research
  83. AS1DHRS4, a head-to-head natural antisense transcript, silences the DHRS4 gene cluster in cis and trans
    Qi Li, Zhongjing Su, Xiaoyuan Xu, Gefei Liu, Xuhong Song, Ruijian Wang, Xuxia Sui, Ting Liu, Xiaolan Chang, Dongyang Huang · 2012 · Proceedings of the National Academy of Sciences
  84. Muller's Ratchet and compensatory mutation in Caenorhabditis briggsae mitochondrial genome evolution
    Dana K. Howe, Dee R. Denver · 2008 · BMC Evolutionary Biology
  85. Discovery of Highly Divergent Repeat Landscapes in Snake Genomes Using High-Throughput Sequencing
    Todd A. Castoe, Kathryn T. Hall, Marcel L. Guibotsy Mboulas, Wanjun Gu, A. P. Jason de Koning, Samuel E. Fox, Alexander W. Poole, Vijetha Vemulapalli, Juan M. Daza, Todd C. Mockler et al. · 2011 · Genome Biology and Evolution
  86. NATURAL TRANSFORMATION INCREASES THE RATE OF ADAPTATION IN THE HUMAN PATHOGEN HELICOBACTER PYLORI
    David A. Baltrus, Karen J. Guillemin, Patrick C. Phillips · 2007 · Evolution
  87. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies
    Camille Sessegolo, Nelly Burlet, Annabelle Haudry · 2016 · Biology Letters
  88. Similar Ratios of Introns to Intergenic Sequence across Animal Genomes
    Warren Russell Francis, Gert Wörheide · 2017 · Genome Biology and Evolution
  89. The Loss of Adaptive Plasticity during Long Periods of Environmental Stasis
    Joanna Masel A, Oliver D. King, Heather Maughan · 2006 · The American Naturalist
  90. Co-evolution between transposable elements and their hosts: a major factor in genome size evolution?
    J. Arvid Ågren, Stephen Wright · 2011 · Chromosome Research
  91. Allopatric origins of microbial species
    Rachel J. Whitaker · 2006 · Philosophical Transactions of the Royal Society B Biological Sciences
  92. The GH18 family of chitinases: Their domain architectures, functions and evolutions
    Qian‐Sheng Huang, Xiaolan Xie, Ge Liang, Fang Gong, Ye Wang, Xiaoqian Wei, Qin Wang, Zhi‐Liang Ji, Qing‐Xi Chen · 2011 · Glycobiology
  93. The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi
    María Victoria Aguilar Pontes, Julian Brandl, Erin McDonnell, Kimchi Strasser, Thi Truc Minh Nguyen, Robert W. Riley, Stephen James Mondo, Asaf Salamov, J.L. Nybo, Tammi Vesth et al. · 2018 · Studies in Mycology
  94. New target carotenoids for CCD4 enzymes are revealed with the characterization of a novel stress-induced carotenoid cleavage dioxygenase gene from Crocus sativus
    Ángela Rubio‐Moraga, José Luís Rambla, Asun Fernández‐del‐Carmen, Almudena Trapero‐Mozos, Oussama Ahrazem, Diego Orzáez, Antonio Granell, Lourdes Gómez‐Gómez · 2014 · Plant Molecular Biology
  95. Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability
    Kirsten ten Tusscher, Paulien Hogeweg · 2011 · PLoS Computational Biology
  96. Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum
    Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael P. H. Stumpf, Sylvia T. Richardson, Carsten Wiuf · 2005 · PLoS Computational Biology
  97. Comparative analysis of pseudogenes across three phyla
    Cristina Sisu, Baikang Pei, Jing Leng, Adam Frankish, Yan Zhang, Suganthi Balasubramanian, Rachel Harte, Daifeng Wang, Michael Rutenberg-Schoenberg, Wyatt Travis Clark et al. · 2014 · Proceedings of the National Academy of Sciences
  98. Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments
    Zihao Yuan, Shikai Liu, Tao Zhou, Changxu Tian, Lisui Bao, Rex A. Dunham, Zhanjiang Liu · 2018 · BMC Genomics
  99. Causes and effects of nuclear genome reduction
    Patrick J. Keeling, Claudio H. Slamovits · 2005 · Current Opinion in Genetics & Development
  100. Contrasting evolutionary dynamics between angiosperm and mammalian genomes
    Eduard Kejnovský, Ilia J. Leitch, Andrew Rowland Leitch · 2009 · Trends in Ecology & Evolution