IDEAS home Printed from https://ideas.repec.org/a/eee/ecomod/v224y2012i1p124-129.html
   My bibliography  Save this article

Computer modeling of genome complexity variation trends in prokaryotic communities under varying habitat conditions

Author

Listed:
  • Lashin, Sergey A.
  • Matushkin, Yury G.
  • Suslov, Valentin V.
  • Kolchanov, Nikolay A.

Abstract

There are two types of organisms’ grouping in nature: mono-species populations and multi-species communities. Here at during the process of evolution the adaptability of a trait is to be tested both at population and ecocenotic levels. Size of a genome is one of the major adaptive traits, which widely varies in eukaryotic species. By contrast, prokaryotes with their small genomes are considered to have genome reduction evolutionary trend. Domination of this trend is mostly founded on population-level models. In this paper we in silico study interactions of ecocenotic and population levels. The trend of genome and metabolism reduction in prokaryotic communities was shown to be major only in comfortable environmental conditions. In subcomfortable conditions, genome and metabolism reduction leads to community simplification (in extreme case to community death). Pessimum conditions promote metabolism integration of a community and induce reciprocal genes acquiring.

Suggested Citation

  • Lashin, Sergey A. & Matushkin, Yury G. & Suslov, Valentin V. & Kolchanov, Nikolay A., 2012. "Computer modeling of genome complexity variation trends in prokaryotic communities under varying habitat conditions," Ecological Modelling, Elsevier, vol. 224(1), pages 124-129.
    • Handle: RePEc:eee:ecomod:v:224:y:2012:i:1:p:124-129
    DOI: 10.1016/j.ecolmodel.2011.11.004
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0304380011005230
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.ecolmodel.2011.11.004?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Sean B. Carroll, 2001. "Chance and necessity: the evolution of morphological complexity and diversity," Nature, Nature, vol. 409(6823), pages 1102-1109, February.
    2. Maria C. Rivera & James A. Lake, 2004. "The ring of life provides evidence for a genome fusion origin of eukaryotes," Nature, Nature, vol. 431(7005), pages 152-155, September.
    3. Howard Ochman & Jeffrey G. Lawrence & Eduardo A. Groisman, 2000. "Lateral gene transfer and the nature of bacterial innovation," Nature, Nature, vol. 405(6784), pages 299-304, May.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Klimenko, Alexandra I. & Matushkin, Yury G. & Kolchanov, Nikolay A. & Lashin, Sergey A., 2019. "Spatial heterogeneity promotes antagonistic evolutionary scenarios in microbial community explained by ecological stratification: a simulation study," Ecological Modelling, Elsevier, vol. 399(C), pages 66-76.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Tazzyman, Samuel J. & Bonhoeffer, Sebastian, 2013. "Fixation probability of mobile genetic elements such as plasmids," Theoretical Population Biology, Elsevier, vol. 90(C), pages 49-55.
    2. Aletheia Atzinger & Jeffrey G Lawrence, 2020. "Selection for ancient periodic motifs that do not impart DNA bending," PLOS Genetics, Public Library of Science, vol. 16(10), pages 1-25, October.
    3. Fabien Lafuma & Ian J. Corfe & Julien Clavel & Nicolas Di-Poï, 2021. "Multiple evolutionary origins and losses of tooth complexity in squamates," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    4. João F Matias Rodrigues & Andreas Wagner, 2009. "Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks," PLOS Computational Biology, Public Library of Science, vol. 5(12), pages 1-11, December.
    5. Nara Figueroa-Bossi & Rocío Fernández-Fernández & Patricia Kerboriou & Philippe Bouloc & Josep Casadesús & María Antonia Sánchez-Romero & Lionello Bossi, 2024. "Transcription-driven DNA supercoiling counteracts H-NS-mediated gene silencing in bacterial chromatin," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Fan Xu & Zeng Zhou & Sergio Fagherazzi & Andrea D’Alpaos & Ian Townend & Kun Zhao & Weiming Xie & Leicheng Guo & Xianye Wang & Zhong Peng & Zhicheng Yang & Chunpeng Chen & Guangcheng Cheng & Yuan Xu &, 2024. "Anomalous scaling of branching tidal networks in global coastal wetlands and mudflats," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    7. Brian D. Huang & Dowan Kim & Yongjoon Yu & Corey J. Wilson, 2024. "Engineering intelligent chassis cells via recombinase-based MEMORY circuits," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    8. Ernestina Hauptfeld & Nikolaos Pappas & Sandra Iwaarden & Basten L. Snoek & Andrea Aldas-Vargas & Bas E. Dutilh & F. A. Bastiaan Meijenfeldt, 2024. "Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    9. Rohan Maddamsetti & Yi Yao & Teng Wang & Junheng Gao & Vincent T. Huang & Grayson S. Hamrick & Hye-In Son & Lingchong You, 2024. "Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    10. Rajaram, R. & Castellani, B., 2016. "An entropy based measure for comparing distributions of complexity," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 453(C), pages 35-43.
    11. Jennifer Kuzma & James Romanchek & Adam Kokotovich, 2008. "Upstream Oversight Assessment for Agrifood Nanotechnology: A Case Studies Approach," Risk Analysis, John Wiley & Sons, vol. 28(4), pages 1081-1098, August.
    12. Xiaotong Li & Jason Karpac, 2023. "A distinct Acyl-CoA binding protein (ACBP6) shapes tissue plasticity during nutrient adaptation in Drosophila," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    13. Voorhoeve, Niels & Allan, Douglas C. & Moret, M.A. & Zebende, G.F. & Phillips, J.C., 2018. "Why human milk is more nutritious than cow milk," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 497(C), pages 302-309.
    14. Jenny Wachter & Britney Cheff & Chad Hillman & Valentina Carracoi & David W. Dorward & Craig Martens & Kent Barbian & Glenn Nardone & L. Renee Olano & Margie Kinnersley & Patrick R. Secor & Patricia A, 2023. "Coupled induction of prophage and virulence factors during tick transmission of the Lyme disease spirochete," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    15. Sotir Sotirov & Evdokia Sotirova & Vassia Atanassova & Krassimir Atanassov & Oscar Castillo & Patricia Melin & Todor Petkov & Stanimir Surchev, 2018. "A Hybrid Approach for Modular Neural Network Design Using Intercriteria Analysis and Intuitionistic Fuzzy Logic," Complexity, Hindawi, vol. 2018, pages 1-11, April.
    16. Rajeev K Azad & Jeffrey G Lawrence, 2005. "Use of Artificial Genomes in Assessing Methods for Atypical Gene Detection," PLOS Computational Biology, Public Library of Science, vol. 1(6), pages 1-13, November.
    17. Benedetta Tuvo & Michela Scarpaci & Sara Bracaloni & Enrica Esposito & Anna Laura Costa & Martina Ioppolo & Beatrice Casini, 2023. "Microplastics and Antibiotic Resistance: The Magnitude of the Problem and the Emerging Role of Hospital Wastewater," IJERPH, MDPI, vol. 20(10), pages 1-14, May.
    18. Yi-Long Hao & Gang Li & Zu-Fei Xiao & Ning Liu & Muhammad Azeem & Yi Zhao & Yao-Yang Xu & Xin-Wei Yu, 2021. "Distribution and Influence on the Microbial Ecological Relationship of Antibiotic Resistance Genes in Soil at a Watershed Scale," Sustainability, MDPI, vol. 13(17), pages 1-16, August.
    19. Tom A Williams & T Martin Embley & Eva Heinz, 2011. "Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-11, June.
    20. Ari J S Ferreira & Rania Siam & João C Setubal & Ahmed Moustafa & Ahmed Sayed & Felipe S Chambergo & Adam S Dawe & Mohamed A Ghazy & Hazem Sharaf & Amged Ouf & Intikhab Alam & Alyaa M Abdel-Haleem & H, 2014. "Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses," PLOS ONE, Public Library of Science, vol. 9(6), pages 1-11, June.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:ecomod:v:224:y:2012:i:1:p:124-129. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/ecological-modelling .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.