IDEAS home Printed from https://ideas.repec.org/a/plo/pgen00/0030147.html
   My bibliography  Save this article

Adaptive Evolution of Conserved Noncoding Elements in Mammals

Author

Listed:
  • Su Yeon Kim
  • Jonathan K Pritchard

Abstract

Conserved noncoding elements (CNCs) are an abundant feature of vertebrate genomes. Some CNCs have been shown to act as cis-regulatory modules, but the function of most CNCs remains unclear. To study the evolution of CNCs, we have developed a statistical method called the “shared rates test” to identify CNCs that show significant variation in substitution rates across branches of a phylogenetic tree. We report an application of this method to alignments of 98,910 CNCs from the human, chimpanzee, dog, mouse, and rat genomes. We find that ∼68% of CNCs evolve according to a null model where, for each CNC, a single parameter models the level of constraint acting throughout the phylogeny linking these five species. The remaining ∼32% of CNCs show departures from the basic model including speed-ups and slow-downs on particular branches and occasionally multiple rate changes on different branches. We find that a subset of the significant CNCs have evolved significantly faster than the local neutral rate on a particular branch, providing strong evidence for adaptive evolution in these CNCs. The distribution of these signals on the phylogeny suggests that adaptive evolution of CNCs occurs in occasional short bursts of evolution. Our analyses suggest a large set of promising targets for future functional studies of adaptation.: Conservation of DNA sequences across evolutionary history is a highly informative signal for identifying regions with important biological functions. In particular, conserved noncoding regions have been shown to be good candidates for containing regulatory elements that have roles in gene regulation. Recent studies have found that there are many thousands of conserved noncoding elements (CNCs) in vertebrate genomes and have suggested possible functions for some of these elements, but the function of most CNCs remains unknown. To study the evolution of CNCs, we developed a statistical method to identify CNCs that show changes in evolutionary rates on particular branches of the mammalian phylogenetic tree. Those rate changes may indicate changes in the function of a CNC. We applied our method to CNCs of five mammalian genomes, and found that, indeed, many CNCs have experienced rate changes during their evolution. We also found a subset of CNCs showing accelerations in evolutionary rate that actually exceed the neutral rates, suggesting that adaptive evolution has shaped the evolution of those elements.

Suggested Citation

  • Su Yeon Kim & Jonathan K Pritchard, 2007. "Adaptive Evolution of Conserved Noncoding Elements in Mammals," PLOS Genetics, Public Library of Science, vol. 3(9), pages 1-15, September.
  • Handle: RePEc:plo:pgen00:0030147
    DOI: 10.1371/journal.pgen.0030147
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0030147
    Download Restriction: no

    File URL: https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.0030147&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pgen.0030147?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. Yoav Gilad & Alicia Oshlack & Gordon K. Smyth & Terence P. Speed & Kevin P. White, 2006. "Expression profiling in primates reveals a rapid evolution of human transcription factors," Nature, Nature, vol. 440(7081), pages 242-245, March.
    2. Katherine S. Pollard & Sofie R. Salama & Nelle Lambert & Marie-Alexandra Lambot & Sandra Coppens & Jakob S. Pedersen & Sol Katzman & Bryan King & Courtney Onodera & Adam Siepel & Andrew D. Kern & Cole, 2006. "An RNA gene expressed during cortical development evolved rapidly in humans," Nature, Nature, vol. 443(7108), pages 167-172, September.
    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. Xinru Zhang & Bohao Fang & Yi-Fei Huang, 2023. "Transcription factor binding sites are frequently under accelerated evolution in primates," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

    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. Oscar Westesson & Gerton Lunter & Benedict Paten & Ian Holmes, 2012. "Accurate Reconstruction of Insertion-Deletion Histories by Statistical Phylogenetics," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-12, April.
    2. Noah Dukler & Mehreen R. Mughal & Ritika Ramani & Yi-Fei Huang & Adam Siepel, 2022. "Extreme purifying selection against point mutations in the human genome," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Kazi Abdul, Mannan, 2020. "The Theory of Matriarchism: The Universal Origin of Human," MPRA Paper 101353, University Library of Munich, Germany, revised 2020.
    4. Xinru Zhang & Bohao Fang & Yi-Fei Huang, 2023. "Transcription factor binding sites are frequently under accelerated evolution in primates," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    5. Kirsten E Eilertson & James G Booth & Carlos D Bustamante, 2012. "SnIPRE: Selection Inference Using a Poisson Random Effects Model," PLOS Computational Biology, Public Library of Science, vol. 8(12), pages 1-14, December.
    6. Adam Safron, 2019. "Multilevel evolutionary developmental optimization (MEDO): A theoretical framework for understanding preferences and selection dynamics," Papers 1910.13443, arXiv.org, revised Nov 2019.
    7. Kazi Abdul, Mannan, 2020. "A Theory of Matriarchism: The Universal Origins of Humanity," MPRA Paper 105016, University Library of Munich, Germany, revised 2020.

    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:pgen00:0030147. 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: plosgenetics (email available below). General contact details of provider: https://journals.plos.org/plosgenetics/ .

    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.