IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1004812.html
   My bibliography  Save this article

Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

Author

Listed:
  • Andrej Kuritzin
  • Tabea Kischka
  • Jürgen Schmitz
  • Gennady Churakov

Abstract

Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Fortunately, such misleading fixed cases are relatively rare but nevertheless, need to be considered. Here, we present novel, comprehensive statistical models applicable for (1) analyzing any pattern of rare genomic changes, (2) testing and differentiating conflicting phylogenetic reconstructions based on rare genomic changes caused by incomplete lineage sorting or/and ancestral hybridization, and (3) differentiating between search strategies involving genome information from one or several lineages. When the new statistics are applied, in non-conflicting cases a minimum of three elements present in both of two species and absent in a third group are considered significant support (p

Suggested Citation

  • Andrej Kuritzin & Tabea Kischka & Jürgen Schmitz & Gennady Churakov, 2016. "Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data," PLOS Computational Biology, Public Library of Science, vol. 12(3), pages 1-20, March.
    • Handle: RePEc:plo:pcbi00:1004812
    DOI: 10.1371/journal.pcbi.1004812
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004812
    Download Restriction: no
    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004812&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pcbi.1004812?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. Alexander Suh & Martin Paus & Martin Kiefmann & Gennady Churakov & Franziska Anni Franke & Jürgen Brosius & Jan Ole Kriegs & Jürgen Schmitz, 2011. "Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds," Nature Communications, Nature, vol. 2(1), pages 1-7, September.
    2. Mitsuru Shimamura & Hiroshi Yasue & Kazuhiko Ohshima & Hideaki Abe & Hidehiro Kato & Toshiya Kishiro & Mutsuo Goto & Isao Munechika & Norihiro Okada, 1997. "Molecular evidence from retroposons that whales form a clade within even-toed ungulates," Nature, Nature, vol. 388(6643), pages 666-670, August.
    3. Meng, Chen & Kubatko, Laura Salter, 2009. "Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model," Theoretical Population Biology, Elsevier, vol. 75(1), pages 35-45.
    4. Nicolas Heslot & Jessica Rutkoski & Jesse Poland & Jean-Luc Jannink & Mark E Sorrells, 2013. "Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-8, 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. Ran Tian & Yaolei Zhang & Hui Kang & Fan Zhang & Zhihong Jin & Jiahao Wang & Peijun Zhang & Xuming Zhou & Janet M. Lanyon & Helen L. Sneath & Lucy Woolford & Guangyi Fan & Songhai Li & Inge Seim, 2024. "Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria," Nature Communications, Nature, vol. 15(1), pages 1-19, 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. Nicola F. Müller & Kathryn E. Kistler & Trevor Bedford, 2022. "A Bayesian approach to infer recombination patterns in coronaviruses," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    2. Mark S Hibbins & Matthew W Hahn, 2021. "The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes," PLOS Genetics, Public Library of Science, vol. 17(11), pages 1-20, November.
    3. Pahl, Cameron C. & Ruedas, Luis A., 2021. "Carnosaurs as Apex Scavengers: Agent-based simulations reveal possible vulture analogues in late Jurassic Dinosaurs," Ecological Modelling, Elsevier, vol. 458(C).
    4. Md Shamsuzzoha Bayzid & Siavash Mirarab & Bastien Boussau & Tandy Warnow, 2015. "Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-40, June.
    5. Md. S. Islam & Per McCord & Quentin D. Read & Lifang Qin & Alexander E. Lipka & Sushma Sood & James Todd & Marcus Olatoye, 2022. "Accuracy of Genomic Prediction of Yield and Sugar Traits in Saccharum spp. Hybrids," Agriculture, MDPI, vol. 12(9), pages 1-22, September.
    6. Haque Md Rejuan & Kubatko Laura, 2024. "A global test of hybrid ancestry from genome-scale data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 23(1), pages 1-18, January.
    7. Gabriel Cardona & Joan Carles Pons & Celine Scornavacca, 2019. "Generation of Binary Tree-Child phylogenetic networks," PLOS Computational Biology, Public Library of Science, vol. 15(9), pages 1-29, September.
    8. Qian Jin & Li-Jun He & Ai-Bing Zhang, 2012. "A Simple 2D Non-Parametric Resampling Statistical Approach to Assess Confidence in Species Identification in DNA Barcoding—An Alternative to Likelihood and Bayesian Approaches," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-11, December.

    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:pcbi00:1004812. 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.