IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/0020102.html
   My bibliography  Save this article

Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families

Author

Listed:
  • Guohui Ding
  • Jiuhong Kang
  • Qi Liu
  • Tieliu Shi
  • Gang Pei
  • Yixue Li

Abstract

The evolution of new gene families subsequent to gene duplication may be coupled to the fluctuation of population and environment variables. Based upon that, we presented a systematic analysis of the animal transmembrane gene duplication events on a macroevolutionary scale by integrating the palaeontology repository. The age of duplication events was calculated by maximum likelihood method, and the age distribution was estimated by density histogram and normal kernel density estimation. We showed that the density of the duplicates displays a positive correlation with the estimates of maximum number of cell types of common ancestors, and the oxidation events played a key role in the major transitions of this density trace. Next, we focused on the Phanerozoic phase, during which more macroevolution data are available. The pulse mass extinction timepoints coincide with the local peaks of the age distribution, suggesting that the transmembrane gene duplicates fixed frequently when the environment changed dramatically. Moreover, a 61-million-year cycle is the most possible cycle in this phase by spectral analysis, which is consistent with the cycles recently detected in biodiversity. Our data thus elucidate a strong coupling of duplication events and macroevolution; furthermore, our method also provides a new way to address these questions.Synopsis: The interplay of information-processing life and force-driven environment has characterized Earth's evolutionary history since its beginning some 4 billion years ago. The study of macroevolution has seen a growing appreciation of this interplay. Previously, a large-scale effort was mounted to collect and analyze the paleontological and geochemical data. In the meantime, more and more genomes have been sequenced. The growing molecular sequence database with these paleontological data will provide important opportunities to investigate this interplay. Using the transmembrane proteins of 12 genomes, Ding and his colleagues have devised a sophisticated pipeline to date 1,651 duplication events grouped into 786 gene families, and have mapped the distribution of duplication events to the profile of macroevolution. They showed that the oxidation events played a key role in the major transitions of this density trace, and that the pulse mass extinction time points in the Phanerozoic phase coincide with the local peaks of the age distribution. Through some mathematical transformation of the density trace of the transmembrane gene duplicates during the Phanerozoic phase, they reported a potential cycle similar to the cycle detected by paleontologists. They concluded that a dramatically changed environment affected the evolution of life and left some imprint in the molecular level that can be detected.

Suggested Citation

  • Guohui Ding & Jiuhong Kang & Qi Liu & Tieliu Shi & Gang Pei & Yixue Li, 2006. "Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families," PLOS Computational Biology, Public Library of Science, vol. 2(8), pages 1-7, August.
  • Handle: RePEc:plo:pcbi00:0020102
    DOI: 10.1371/journal.pcbi.0020102
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0020102
    Download Restriction: no

    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020102&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pcbi.0020102?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
    ---><---

    References listed on IDEAS

    as
    1. Timothy M. Lenton, 1998. "Gaia and natural selection," Nature, Nature, vol. 394(6692), pages 439-447, July.
    2. Paul Kenrick & Peter R. Crane, 1997. "The origin and early evolution of plants on land," Nature, Nature, vol. 389(6646), pages 33-39, September.
    3. Carl C. Swisher & Yuan-qing Wang & Xiao-lin Wang & Xing Xu & Yuan Wang, 1999. "Cretaceous age for the feathered dinosaurs of Liaoning, China," Nature, Nature, vol. 400(6739), pages 58-61, July.
    4. Robert A. Rohde & Richard A. Muller, 2005. "Cycles in fossil diversity," Nature, Nature, vol. 434(7030), pages 208-210, March.
    5. Yanan Shen & Andrew H. Knoll & Malcolm R. Walter, 2003. "Evidence for low sulphate and anoxia in a mid-Proterozoic marine basin," Nature, Nature, vol. 423(6940), pages 632-635, June.
    6. John M. Hayes, 2002. "A lowdown on oxygen," Nature, Nature, vol. 417(6885), pages 127-128, May.
    7. James W. Kirchner & Anne Weil, 2000. "Delayed biological recovery from extinctions throughout the fossil record," Nature, Nature, vol. 404(6774), pages 177-180, March.
    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. Bruce S Lieberman & Adrian L Melott, 2007. "Considering the Case for Biodiversity Cycles: Re-Examining the Evidence for Periodicity in the Fossil Record," PLOS ONE, Public Library of Science, vol. 2(8), pages 1-9, August.
    2. Puetz, Stephen J. & Prokoph, Andreas & Borchardt, Glenn & Mason, Edward W., 2014. "Evidence of synchronous, decadal to billion year cycles in geological, genetic, and astronomical events," Chaos, Solitons & Fractals, Elsevier, vol. 62, pages 55-75.

    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. Bruce S Lieberman & Adrian L Melott, 2007. "Considering the Case for Biodiversity Cycles: Re-Examining the Evidence for Periodicity in the Fossil Record," PLOS ONE, Public Library of Science, vol. 2(8), pages 1-9, August.
    2. Jorge E. Horvath, 2014. "Towards a Mathematical Description of Biodiversity Evolution," Challenges, MDPI, vol. 5(2), pages 1-10, September.
    3. Puetz, Stephen J. & Prokoph, Andreas & Borchardt, Glenn & Mason, Edward W., 2014. "Evidence of synchronous, decadal to billion year cycles in geological, genetic, and astronomical events," Chaos, Solitons & Fractals, Elsevier, vol. 62, pages 55-75.
    4. Folk, György, 2019. "Weal: the universal core of human well-being," MPRA Paper 97082, University Library of Munich, Germany.
    5. Haitao Shang & Daniel H. Rothman & Gregory P. Fournier, 2022. "Oxidative metabolisms catalyzed Earth’s oxygenation," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    6. Granville Tunnicliffe Wilson & John Haywood & Lynda Petherick, 2022. "Modeling cycles and interdependence in irregularly sampled geophysical time series," Environmetrics, John Wiley & Sons, Ltd., vol. 33(2), March.
    7. Gual, Miguel A. & Norgaard, Richard B., 2010. "Bridging ecological and social systems coevolution: A review and proposal," Ecological Economics, Elsevier, vol. 69(4), pages 707-717, February.
    8. David Moody, 2012. "Seven misconceptions regarding the Gaia hypothesis," Climatic Change, Springer, vol. 113(2), pages 277-284, July.
    9. Adrian L Melott, 2008. "Long-Term Cycles in the History of Life: Periodic Biodiversity in the Paleobiology Database," PLOS ONE, Public Library of Science, vol. 3(12), pages 1-5, December.
    10. Constantin Udriste & Massimiliano Ferrara & Dorel Zugravescu & Florin Munteanu & Ionel Tevy, 2018. "Geobiodynamics and Roegenian Economic Systems," Papers 1812.07961, arXiv.org.
    11. Rodrigue, Michelle & Romi, Andrea M., 2022. "Environmental escalations to social inequities: Some reflections on the tumultuous state of Gaia," CRITICAL PERSPECTIVES ON ACCOUNTING, Elsevier, vol. 82(C).
    12. Leonardo A. A. Terra & João L. Passador, 2016. "Symbiotic Dynamic: The Strategic Problem from the Perspective of Complexity," Systems Research and Behavioral Science, Wiley Blackwell, vol. 33(2), pages 235-248, March.
    13. Anastasios Xepapadeas & Gustav Engstrom, 2013. "Solow meets Lovelock: Economic growth in Daisyworld," DEOS Working Papers 1333, Athens University of Economics and Business.
    14. Babu, M S Umesh & Nautiyal, Sunil, 2013. "Historical issues and perspectives of land resource management in India: A review," Working Papers 309, Institute for Social and Economic Change, Bangalore.
    15. Richters, Oliver & Siemoneit, Andreas, 2019. "Marktwirtschaft reparieren: Entwurf einer freiheitlichen, gerechten und nachhaltigen Utopie," EconStor Books, ZBW - Leibniz Information Centre for Economics, number 213814, December.
    16. Rory Osborne & Laura Rehneke & Silke Lehmann & Jemma Roberts & Melina Altmann & Stefan Altmann & Yingqi Zhang & Eva Köpff & Ana Dominguez-Ferreras & Emeka Okechukwu & Chrysi Sergaki & Charlotte Rich-G, 2023. "Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of growth promotion," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    17. Na Wei & Wen-Jie Xie & Wei-Xing Zhou, 2024. "Resilience of international oil trade networks under extreme event shock-recovery simulations," Papers 2406.11467, arXiv.org.
    18. Gatti, Roberto Cazzolla & Hordijk, Wim & Kauffman, Stuart, 2017. "Biodiversity is autocatalytic," Ecological Modelling, Elsevier, vol. 346(C), pages 70-76.
    19. Yaser Saffar Talori & Jing-Shan Zhao & Yun-Fei Liu & Wen-Xiu Lu & Zhi-Heng Li & Jingmai Kathleen O'Connor, 2019. "Identification of avian flapping motion from non-volant winged dinosaurs based on modal effective mass analysis," PLOS Computational Biology, Public Library of Science, vol. 15(5), pages 1-16, May.

    More about this item

    Statistics

    Access and download statistics

    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:plo:pcbi00:0020102. 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: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    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.