IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v106y2015icp22-31.html
   My bibliography  Save this article

Extinction probabilities and stationary distributions of mobile genetic elements in prokaryotes: The birth–death-diversification model

Author

Listed:
  • Drakos, Nicole E.
  • Wahl, Lindi M.

Abstract

Theoretical approaches are essential to our understanding of the complex dynamics of mobile genetic elements (MGEs) within genomes. Recently, the birth–death-diversification model was developed to describe the dynamics of mobile promoters (MPs), a particular class of MGEs in prokaryotes. A unique feature of this model is that genetic diversification of elements was included. To explore the implications of diversification on the longterm fate of MGE lineages, in this contribution we analyze the extinction probabilities, extinction times and equilibrium solutions of the birth–death-diversification model. We find that diversification increases both the survival and growth rate of MGE families, but the strength of this effect depends on the rate of horizontal gene transfer (HGT). We also find that the distribution of MGE families per genome is not necessarily monotonically decreasing, as observed for MPs, but may have a peak in the distribution that is related to the HGT rate. For MPs specifically, we find that new families have a high extinction probability, and predict that the number of MPs is increasing, albeit at a very slow rate. Additionally, we develop an extension of the birth–death-diversification model which allows MGEs in different regions of the genome, for example coding and non-coding, to be described by different rates. This extension may offer a potential explanation as to why the majority of MPs are located in non-promoter regions of the genome.

Suggested Citation

  • Drakos, Nicole E. & Wahl, Lindi M., 2015. "Extinction probabilities and stationary distributions of mobile genetic elements in prokaryotes: The birth–death-diversification model," Theoretical Population Biology, Elsevier, vol. 106(C), pages 22-31.
    • Handle: RePEc:eee:thpobi:v:106:y:2015:i:c:p:22-31
    DOI: 10.1016/j.tpb.2015.09.001
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580915000866
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.tpb.2015.09.001?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. Andreas Wagner, 2006. "Cooperation is Fleeting in the World of Transposable Elements," PLOS Computational Biology, Public Library of Science, vol. 2(12), pages 1-8, December.
    Full references (including those not matched with items on IDEAS)

    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. Startek, Michał & Le Rouzic, Arnaud & Capy, Pierre & Grzebelus, Dariusz & Gambin, Anna, 2013. "Genomic parasites or symbionts? Modeling the effects of environmental pressure on transposition activity in asexual populations," Theoretical Population Biology, Elsevier, vol. 90(C), pages 145-151.

    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:thpobi:v:106:y:2015:i:c:p:22-31. 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: https://www.journals.elsevier.com/intelligence .

    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.