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Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

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  • Roch, Sebastien
  • Steel, Mike

Abstract

The reconstruction of a species tree from genomic data faces a double hurdle. First, the (gene) tree describing the evolution of each gene may differ from the species tree, for instance, due to incomplete lineage sorting. Second, the aligned genetic sequences at the leaves of each gene tree provide merely an imperfect estimate of the topology of the gene tree. In this note, we demonstrate formally that a basic statistical problem arises if one tries to avoid accounting for these two processes and analyses the genetic data directly via a concatenation approach. More precisely, we show that, under the multispecies coalescent with a standard site substitution model, maximum likelihood estimation on sequence data that has been concatenated across genes and performed under the incorrect assumption that all sites have evolved independently and identically on a fixed tree is a statistically inconsistent estimator of the species tree. Our results provide a formal justification of simulation results described of Kubatko and Degnan (2007) and others, and complements recent theoretical results by DeGIorgio and Degnan (2010) and Chifman and Kubtako (2014).

Suggested Citation

  • Roch, Sebastien & Steel, Mike, 2015. "Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent," Theoretical Population Biology, Elsevier, vol. 100(C), pages 56-62.
    • Handle: RePEc:eee:thpobi:v:100:y:2015:i:c:p:56-62
    DOI: 10.1016/j.tpb.2014.12.005
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    1. Antonis Rokas & Barry L. Williams & Nicole King & Sean B. Carroll, 2003. "Genome-scale approaches to resolving incongruence in molecular phylogenies," Nature, Nature, vol. 425(6960), pages 798-804, October.
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    Cited by:

    1. Degnan, James H. & Rhodes, John A., 2015. "There are no caterpillars in a wicked forest," Theoretical Population Biology, Elsevier, vol. 105(C), pages 17-23.
    2. Nazifa Ahmed Moumi & Badhan Das & Zarin Tasnim Promi & Nishat Anjum Bristy & Md Shamsuzzoha Bayzid, 2019. "Quartet-based inference of cell differentiation trees from ChIP-Seq histone modification data," PLOS ONE, Public Library of Science, vol. 14(9), pages 1-25, September.
    3. Ruriko Yoshida & Kenji Fukumizu & Chrysafis Vogiatzis, 2019. "Multilocus phylogenetic analysis with gene tree clustering," Annals of Operations Research, Springer, vol. 276(1), pages 293-313, May.

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