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Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

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  • Meng, Chen
  • Kubatko, Laura Salter

Abstract

The application of phylogenetic inference methods, to data for a set of independent genes sampled randomly throughout the genome, often results in substantial incongruence in the single-gene phylogenetic estimates. Among the processes known to produce discord between single-gene phylogenies, two of the best studied in a phylogenetic context are hybridization and incomplete lineage sorting. Much recent attention has focused on the development of methods for estimating species phylogenies in the presence of incomplete lineage sorting, but phylogenetic models that allow for hybridization have been more limited. Here we propose a model that allows incongruence in single-gene phylogenies to be due to both hybridization and incomplete lineage sorting, with the goal of determining the contribution of hybridization to observed gene tree incongruence in the presence of incomplete lineage sorting. Using our model, we propose methods for estimating the extent of the role of hybridization in both a likelihood and a Bayesian framework. The performance of our methods is examined using both simulated and empirical data.

Suggested Citation

  • 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.
    • Handle: RePEc:eee:thpobi:v:75:y:2009:i:1:p:35-45
    DOI: 10.1016/j.tpb.2008.10.004
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    Cited by:

    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. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.

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