The origins of genome complexity

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

Cited by (1,002)

Items 601–700 of 1,002

  1. Elusive Origins of the Extra Genes in Aspergillus oryzae
    Nora Khaldi, Kenneth H. Wolfe · 2008 · PLoS ONE
  2. Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: investigating the origins of genome architecture
    David Roy Smith, Robert William Lee · 2008 · BMC Evolutionary Biology
  3. Interaction between Selection and Biased Gene Conversion in Mammalian Protein-Coding Sequence Evolution Revealed by a Phylogenetic Covariance Analysis
    Nicolas Lartillot · 2012 · Molecular Biology and Evolution
  4. Evolution of the vertebrate twist family and synfunctionalization: a mechanism for differential gene loss through merging of expression domains
    Inna Gitelman · 2007 · Molecular Biology and Evolution
  5. Objects that make objects: the population dynamics of structural complexity
    James P. Crutchfield, Olof Görnerup · 2006 · Journal of The Royal Society Interface
  6. The evolutionary significance of variation in sperm–egg interactions
    Timothy L. Karr, William J. Swanson, Rhonda R. Snook · 2009 · Elsevier eBooks
  7. The Complex Intron Landscape and Massive Intron Invasion in a Picoeukaryote Provides Insights into Intron Evolution
    Bram Verhelst, Yves Van de Peer, Pierre Rouzé · 2013 · Genome Biology and Evolution
  8. Nearly Neutral Evolution across the Drosophila melanogaster Genome
    David Castellano, Jennifer James, Adam Eyre‐Walker · 2018 · Molecular Biology and Evolution
  9. Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species
    Chun Shen Lim, Brooke N. Weinstein, Scott William Roy, Chris M. Brown · 2021 · Molecular Biology and Evolution
  10. Declining Population Sizes and Loss of Genetic Diversity in Commercial Fishes: A Simple Method for a First Diagnostic
    Natalia Petit, Min Liu, Iris Ziying Tan, Arthur C.-K. Chung, Bàrbara Terrasa, Beatríz Guijarro, Francesc Ordines, Sergio Ramírez‐Amaro, Enric Massutı́, Celia Schunter · 2022 · Frontiers in Marine Science
  11. Habitat Variability Correlates with Duplicate Content of Drosophila Genomes
    Takashi T Makino, Masakado Kawata · 2012 · Molecular Biology and Evolution
  12. Quantitative PCR-based genome size estimation of the astigmatid mites Sarcoptes scabiei, Psoroptes ovis and Dermatophagoides pteronyssinus
    Kate E. Mounsey, Charlene Willis, Stewart T. G. Burgess, Deborah C. Holt, James S. McCarthy, Katja Fischer · 2012 · Parasites & Vectors
  13. Informational laws of genome structures
    Bonnici, Vincenzo, Manca, Vincenzo · 2016 · Scientific Reports
  14. Repeated ecological and life cycle transitions make salamanders an ideal model for evolution and development
    Bonett, Ronald M., Ledbetter, Nicholus M., Hess, Alexander J., Herrboldt, Madison A., Denoël, Mathieu · 2022 · Developmental Dynamics
  15. Pangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus Flavobacterium
    Min‐Ji Kim, In‐Tae Cha, Ki‐Eun Lee, Meng Li, Soo-Je Park · 2023 · Microbiology Spectrum
  16. Consensus features of microsatellite distribution: Microsatellite contents are universally correlated with recombination rates and are preferentially depressed by centromeres in multicellular eukaryotic genomes
    Wen-Jiu Guo, Jun Ling, Ping Li · 2009 · Genomics
  17. Towards a postmodern synthesis of evolutionary biology
    Eugene V. Koonin · 2009 · Cell Cycle
  18. On the Tempo of Genome Size Evolution in Angiosperms
    Jeremy M. Beaulieu, Stephen A. Smith, Ilia J. Leitch · 2010 · Journal of Botany
  19. Contrasting evolutionary trajectories of multiple retrotransposons following independent allopolyploidy in wild wheats
    Natacha Senerchia, François Felber, Christian Parisod · 2014 · New Phytologist
  20. Meiosis Gene Inventory of Four Ciliates Reveals the Prevalence of a Synaptonemal Complex-Independent Crossover Pathway
    Jingyun Chi, Frédéric Mahé, Josef Loidl, John M. Logsdon Jr., Micah Dunthorn · 2013 · Molecular Biology and Evolution
  21. Symbiogenesis, gradualism, and mitochondrial energy in eukaryote origin
    Martin, William F. · 2017 · Periodicum Biologorum
  22. A New Standard for Crustacean Genomes: The Highly Contiguous, Annotated Genome Assembly of the Clam Shrimp Eulimnadia texana Reveals HOX Gene Order and Identifies the Sex Chromosome
    James G. Baldwin-Brown, Stephen C. Weeks, Anthony D. Long · 2017 · Genome Biology and Evolution
  23. Rapid Divergence of Genome Architectures Following the Origin of an Ectomycorrhizal Symbiosis in the Genus Amanita
    Jaqueline Hess, Inger Skrede, Maryam Chaib De Mares, Matthieu Hainaut, Bernard Henrissat, Anne Pringle · 2018 · Molecular Biology and Evolution
  24. Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species
    Carina F. Mugal, Verena Esther Kutschera, Fidel Botero-Castro, Jochen B. W. Wolf, Ingemar Kaj · 2019 · Molecular Biology and Evolution
  25. Miniaturization, Genome Size, and Biological Size in a Diverse Clade of Salamanders
    Louis Paul Decena-Segarra, Lilijana Bizjak Mali, Aleš Kladnik, Stanley K. Sessions, Sean M. Rovito · 2020 · The American Naturalist
  26. A Network Model for the Correlation between Epistasis and Genomic Complexity
    Rafael Sanjuán, Miguel R. Nebot · 2008 · PLoS ONE
  27. Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon pufferfish lineages
    Daniel E. Neafsey, Daniel L. Hartl · 2005 · Gene
  28. Parlez-vous VUS?
    Gregory M. Cooper · 2015 · Genome Research
  29. Novel genome sequence of Chinese cavefish ( Triplophysa rosa ) reveals pervasive relaxation of natural selection in cavefish genomes
    Qingyuan Zhao, Feng Shao, Yanping Li, Soojin V. Yi, Zuogang Peng · 2022 · Molecular Ecology
  30. Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery
    Phred M. Benham, Carla Cicero, Merly Escalona, Eric Beraut, Colin W Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Madhusudan Sahasrabudhe, Benjamin L. King, W. Kelley Thomas et al. · 2024 · Genome Biology and Evolution
  31. In with the Old, in with the New: The Promiscuity of the Duplication Process Engenders Diverse Pathways for Novel Gene Creation
    Vaishali Katju · 2012 · International Journal of Evolutionary Biology
  32. Path lengths in protein–protein interaction networks and biological complexity
    Ke Xu, Ivona Bezáková, Leonid Bunimovich, Soojin V. Yi · 2011 · PROTEOMICS
  33. A Living Fossil in the Genome of a Living Fossil: Harbinger Transposons in the Coelacanth Genome
    Jeramiah J. Smith, Kenta Sumiyama, Chris T. Amemiya · 2011 · Molecular Biology and Evolution
  34. Adaptation of mRNA structure to control protein folding
    Guilhem Faure, Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Eugene V. Koonin · 2017 · RNA Biology
  35. Natural Selection Drives Rapid Functional Evolution of Young Drosophila Duplicate Genes
    Xueyuan Jiang, Raquel Assis · 2017 · Molecular Biology and Evolution
  36. Genetic diversity and structure of the round-tailed paradise fish (Macropodus ocellatus): Implications for population management
    Qingzheng Zhang, Cheng‐He Sun, Ying Zhu, Nan Xu, Hongyi Liu · 2019 · Global Ecology and Conservation
  37. A Survey of the Brassica rapa Genome by BAC-End Sequence Analysis and Comparison with Arabidopsis thaliana
    Chang Pyo Hong, Prikshit Plaha, Dal‐Hoe Koo, Tae‐Jin Yang, Su Ryun Choi, Young Ki Lee, Taesik Uhm, Jae-Wook Bang, David Edwards, Ian Bancroft et al. · 2006 · Molecules and Cells
  38. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord
    Gergely J. Szöllősi, Vincent Daubin · 2012 · Methods in molecular biology
  39. Pyoverdine Receptor: a Case of Positive Darwinian Selection inPseudomonas aeruginosa
    Burkhard Tümmler, Pierre Cornélis · 2005 · Journal of Bacteriology
  40. Novelties That Change Carrying Capacity
    Erwin, Douglas H. · 2012 · Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
  41. Species-specific chromatin landscape determines how transposable elements shape genome evolution
    Yuheng Huang, Harsh G. Shukla, Yuh Chwen G. Lee · 2022 · eLife
  42. Forces driving transposable element load variation during Arabidopsis range expansion
    Juan Jiang, Yong‐Chao Xu, Zhiqin Zhang, Jia‐Fu Chen, Xiao‐Min Niu, Xing-Hui Hou, Xin-Tong Li, Li Wang, Yong E. Zhang, Song Ge et al. · 2023 · The Plant Cell
  43. Lizards and LINEs: Selection and Demography Affect the Fate of L1 Retrotransposons in the Genome of the Green Anole (Anolis carolinensis)
    Marc Tollis, Stéphane Boissinot · 2013 · Genome Biology and Evolution
  44. Natural taxonomy in light of horizontal gene transfer
    Cheryl P. Andam, David Williams, Johann Peter Gogarten · 2010 · Biology & Philosophy
  45. Response to Comment on "The Origins of Genome Complexity"
    Michael Lynch, John S. Conery · 2004 · Science
  46. Widespread Recurrent Evolution of Genomic Features
    Ignacio Maeso, Scott William Roy, Manuel Irimia · 2012 · Genome Biology and Evolution
  47. Simple evolutionary pathways to complex proteins
    Michael Lynch · 2005 · Protein Science
  48. Accommodating the load
    Cushla J. Metcalfe, Didier Casañe · 2013 · Mobile Genetic Elements
  49. Selfish Mitochondrial DNA Proliferates and Diversifies in Small, but not Large, Experimental Populations ofCaenorhabditis briggsae
    Wendy Phillips, Anna L Coleman-Hulbert, Emily S. Bellis, Dana K. Howe, Sita Ping, Riana I. Wernick, Suzanne Estes, Dee R. Denver · 2015 · Genome Biology and Evolution
  50. Virtual Genomes in Flux: An Interplay of Neutrality and Adaptability Explains Genome Expansion and Streamlining
    Thomas D. Cuypers, Paulien Hogeweg · 2012 · Genome Biology and Evolution
  51. Whole Genome Duplications Shaped the Receptor Tyrosine Kinase Repertoire of Jawed Vertebrates
    Frédéric Brunet, Jean‐Nicolas Volff, Manfred Schartl · 2016 · Genome Biology and Evolution
  52. Transposable element abundance correlates with mode of transmission in microsporidian parasites
    Nathalia Rammé Medeiros de Albuquerque, Dieter Ebert, Karen Luisa Haag · 2020 · Mobile DNA
  53. Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer
    Koji Yahara, Masaki Fukuyo, Akira Sasaki, Ichizo Kobayashi · 2009 · Proceedings of the National Academy of Sciences
  54. Is ectopic expression caused by deregulatory mutations or due to gene‐regulation leaks with evolutionary potential?
    Francisco Rodrı́guez-Trelles, Rosa Tarrı́o, Francisco J. Ayala · 2005 · BioEssays
  55. Evolutionary Dynamics of Introns in Plastid-Derived Genes in Plants: Saturation Nearly Reached but Slow Intron Gain Continues
    M. K. Basu, Igor B. Rogozin, Oliver Deusch, Tal Dagan, William F. Martin, Eugene V. Koonin · 2007 · Molecular Biology and Evolution
  56. Chromosome Size in Diploid Eukaryotic Species Centers on the Average Length with a Conserved Boundary
    Xianran Li, C. Zhu, Zhongxu Lin, Y. Wu, Dawei Zhang, Guihua Bai, Wen Song, Jianxin Ma, Gary J. Muehlbauer, Michael J. Scanlon et al. · 2011 · Molecular Biology and Evolution
  57. Evolution of the Nervous System in Fishes
    Mario F. Wullimann, Philippe Vernier · 2007 · Elsevier eBooks
  58. Independent evolution of genomic characters during major metazoan transitions
    Oleg Simakov, Takeshi Kawashima · 2016 · Developmental Biology
  59. Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch
    Grant Kinsler, Kara Schmidlin, Daphne Newell, Rachel Eder, Sam Apodaca, Grace Lam, Dmitri A. Petrov, Kerry Geiler‐Samerotte · 2023 · Journal of Molecular Evolution
  60. Evidence of Adaptive Evolution of Accessory Gland Proteins in Closely Related Species of the Drosophila repleta Group
    F. C. Almeida, Rob DeSalle · 2008 · Molecular Biology and Evolution
  61. Characterization and evolution of 5′ and 3′ untranslated regions in eukaryotes
    Honglei Liu, Jiaming Yin, Meili Xiao, Caihua Gao, Annaliese S. Mason, Zunkang Zhao, Yingchun Liu, Jiana Li, Donghui Fu · 2012 · Gene
  62. Lessons for inductive germline determination
    Riyad N. H. Seervai, Gary M. Wessel · 2013 · Molecular Reproduction and Development
  63. Construction of high-resolution recombination maps in Asian seabass
    Le Wang, Bin Bai, Peng Liu, Shu Qing Huang, Zi Yi Wan, Elaine Chua, Baoqing Ye, Gen Hua Yue · 2017 · BMC Genomics
  64. Latitudinal variation in genome size in crustaceans
    Kristin M. Hultgren, Nicholas W. Jeffery, A Moran, T. Ryan Gregory · 2018 · Biological Journal of the Linnean Society
  65. Genome size evolution is associated with climate seasonality and glucosinolates, but not life history, soil nutrients or range size, across a clade of mustards
    N. Ivalú Cacho, Patrick J. McIntyre, Daniel J. Kliebenstein, Sharon Y. Strauss · 2021 · Annals of Botany
  66. Population size and genome size in fishes: a closer look
    T. Ryan Gregory, Jonathan D. S. Witt · 2008 · Genome
  67. The evolution of individuality revisited
    Arunas L. Radzvilavicius, Neil W. Blackstone · 2018 · Biological reviews/Biological reviews of the Cambridge Philosophical Society
  68. Non‐adaptive evolution of genome complexity
    Soojin V. Yi · 2006 · BioEssays
  69. Birth-and-Death Evolution of the Cecropin Multigene Family in Drosophila
    Humberto Quesada, Sebastian Ernesto Ramos-Onsins, Montserrat Aguadé · 2005 · Journal of Molecular Evolution
  70. The metazoan history of the COE transcription factors. Selection of a variant HLH motif by mandatory inclusion of a duplicated exon in vertebrates
    Virginie Daburon, Sébastien Mella, Jean-Louis Plouhinec, Sylvie Mazan, Michèle Crozatier, Alain Vincent · 2008 · BMC Evolutionary Biology
  71. The origin of RNA interference: Adaptive or neutral evolution?
    Alessandro Torri, Johannes Jaeger, Thomas Pradeu, Maria‐Carla Saleh · 2022 · PLoS Biology
  72. A Test of the Coordinated Expression Hypothesis for the Origin and Maintenance of the GAL Cluster in Yeast
    Gregory I. Lang, David Botstein · 2011 · PLoS ONE
  73. Highly Abundant Proteins Favor More Stable 3D Structures in Yeast
    Adrian W.R. Serohijos, S. Y. Ryan Lee, Eugene I. Shakhnovich · 2013 · Biophysical Journal
  74. Ecological perspectives on the sequenced genome collection
    Jennifer B. H. Martiny, Dawn Field · 2005 · Ecology Letters
  75. An Unusually Low Microsatellite Mutation Rate in Dictyostelium discoideum, an Organism With Unusually Abundant Microsatellites
    R. P. McConnell, Sara Middlemist, Clea Scala, Joan E. Strassmann, David C. Queller · 2007 · Genetics
  76. Different Regulatory Mechanisms Underlie Similar Transposable Element Profiles in Pufferfish and Fruitflies
    Daniel E. Neafsey, Justin P. Blumenstiel, Daniel L. Hartl · 2004 · Molecular Biology and Evolution
  77. The Common Ancestor Process for a Wright-Fisher Diffusion
    Jesse Earl Taylor · 2007 · Electronic Journal of Probability
  78. Haplotype‐phased and chromosome‐level genome assembly of Puccinia polysora , a giga‐scale fungal pathogen causing southern corn rust
    Junmin Liang, Yuanjie Li, Peter N. Dodds, Melania Figueroa, Jana Sperschneider, Shiling Han, Clement K. M. Tsui, Keyu Zhang, Leifu Li, Zhanhong Ma et al. · 2022 · Molecular Ecology Resources
  79. Selection on synonymous sites: the unwanted transcript hypothesis
    Sofia Radrizzani, Grzegorz R. Kudla, Zsuzsanna Izsvák, Laurence D. Hurst · 2024 · Nature Reviews Genetics
  80. Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy
    David A. Liberles, Makayla D. M. Tisdell, Johan A. Grahnen · 2011 · Proceedings of the Royal Society B Biological Sciences
  81. Evaluating the Fitness Cost of Protein Expression in Saccharomyces cerevisiae
    Katarzyna Tomala, Ryszard Korona · 2013 · Genome Biology and Evolution
  82. Criticality in tumor evolution and clinical outcome
    Erez Persi, Yuri I. Wolf, Mark D.M. Leiserson, Eugene V. Koonin, Eytan Ruppin · 2018 · Proceedings of the National Academy of Sciences
  83. Co-adaption of tRNA gene copy number and amino acid usage influences translation rates in three life domains
    Meng‐Ze Du, Wen Wei, Lei Qin, Shuo Liu, Anying Zhang, Yong Zhang, Hong Zhou, Feng‐Biao Guo · 2017 · DNA Research
  84. ModEst: Accurate estimation of genome size from next generation sequencing data
    Markus Pfenninger, Philipp Schönnenbeck, Tilman Schell · 2021 · Molecular Ecology Resources
  85. Consistency of genome‐based methods in measuring Metazoan evolution
    Evgeny M. Zdobnov, Christian von Mering, Ivica Letunić, Peer Bork B · 2005 · FEBS Letters
  86. The Evolution of Genome Size Variation in Drumstick Onions (Allium subgenus Melanocrommyum)
    Maia Gurushidze, Jörg Fuchs, Frank R. Blattner · 2012 · Systematic Botany
  87. Recent evolutionary diversification of a protist lineage
    Ramiro Logares, Niels Daugbjerg, Andrés Boltovskoy, Anke Kremp, Johanna Laybourn‐Parry, Karin Rengefors · 2008 · Environmental Microbiology
  88. CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation
    Julien Prunier, Sébastien Caron, John J. MacKay · 2017 · BMC Genomics
  89. The Chromosome-Level Genome Assembly of European Grayling Reveals Aspects of a Unique Genome Evolution Process Within Salmonids
    Tiina Sävilammi, Craig Robert Primmer, Srinidhi Varadharajan, René Guyomard, Yann Guiguen, Simen R. Sandve, Leif Asbjørn Vøllestad, Spiros Papakostas, Sigbjørn Lien · 2019 · G3 Genes Genomes Genetics
  90. DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses
    Shengwei Hou, Tianqi Tang, Siliangyu Cheng, Yuanhao Liu, Tian Xia, Ting Chen, Jed A. Fuhrman, Fengzhu Sun · 2024 · NAR Genomics and Bioinformatics
  91. The other eukaryotes in light of evolutionary protistology
    Maureen A. O’Malley, Alastair G. B. Simpson, Andrew J. Roger · 2012 · Biology & Philosophy
  92. No evidence that sex and transposable elements drive genome size variation in evening primroses
    J. Arvid Ågren, Stephan Greiner, Marc T. J. Johnson, Stephen Wright · 2015 · Evolution
  93. Trail of decryption of molecular research on Botryosphaeriaceae in woody plants
    Kandawatte W. Thilini Chethana, Xinghong Li, Wei Zhang, Kevin D. Hyde, Jiye Yan · 2016 · DOAJ (DOAJ: Directory of Open Access Journals)
  94. AMPK/Mitochondria in Metabolic Diseases
    Pedro Bullón, Fabiola Marín‐Aguilar, Lourdes Román-Malo · 2016 · Proceedings of the Fourth International Symposium on Polarization Phenomena in Nuclear Reactions
  95. Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing
    Corrinne E. Grover, Mark A. Arick, Justin L. Conover, Adam Thrash, Guanjing Hu, William S. Sanders, Chuan-Yu Hsu, Rubab Zahra Naqvi, Muhammad Farooq, Xiaochong Li et al. · 2017 · Genome Biology and Evolution
  96. Ligand Binding Site Structure Influences the Evolution of Protein Complex Function and Topology
    György Abrusán, Joseph A. Marsh · 2018 · Cell Reports
  97. Genome-wide identification and expression analysis of major latex protein (MLP) family genes in the apple (Malus domestica Borkh.) genome
    Gaopeng Yuan, Shanshan He, Shuxun Bian, Xiaolei Han, Kai Liu, Peihua Cong, Cai‐Xia Zhang · 2019 · Gene
  98. Ecological and evolutionary genomics of marine photosynthetic organisms
    Susana M. Coelho, Nathalie Simon, Sophia Ahmed, Jeremy Mark Cock, Frédéric Partensky · 2012 · Molecular Ecology
  99. Robust Yet Fragile: Expression Noise, Protein Misfolding, and Gene Dosage in the Evolution of Genomes
    J. Chris Pires, Gavin C. Conant · 2016 · Annual Review of Genetics
  100. An evolving approach to understanding plant adaptation
    Glenn T. Howe, Amy M. Brunner · 2005 · New Phytologist