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The gene tree delusion.

Mark S Springer1, John Gatesy1

  • 1Department of Biology, University of California, Riverside, CA 92521, USA.

Molecular Phylogenetics and Evolution
|August 5, 2015
PubMed
Summary
This summary is machine-generated.

Shortcut coalescence methods are not suitable for deep phylogenetic problems due to short effective gene lengths and data errors. Re-analysis suggests the multispecies coalescent explains minimal gene tree conflicts, challenging prior conclusions.

Keywords:
C-geneConcatalescenceDeep coalescenceGene treeSpecies tree

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Area of Science:

  • Systematics and Phylogenetics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Higher-level placental mammal relationships are largely resolved, but some deep-level phylogenies remain contentious.
  • Shortcut coalescence methods (e.g., MP-EST, STAR) were proposed to resolve these deep-level phylogenetic issues, assuming no within-locus recombination.
  • Previous studies claimed these methods outperform concatenation for complex phylogenetic problems.

Purpose of the Study:

  • To reanalyze phylogenomic data from Song et al. (2012) to critically evaluate the efficacy of shortcut coalescence methods.
  • To investigate issues in phylogenetics including the recombination ratchet, gene tree stoichiometry, and sources of gene tree incongruence.
  • To compare the performance of coalescence and concatenation methods in species tree estimation using simulations.

Main Methods:

  • Re-analysis of phylogenomic data previously used by Song et al. (2012).
  • Empirical estimation of coalescence gene (c-gene) lengths considering recombination breakpoints and the recombination ratchet.
  • Data curation to identify and correct errors in the original dataset, followed by phylogenetic analyses using improved models and methods (e.g., ASTRAL).
  • Comparative simulations assessing species tree estimation methods.

Main Results:

  • The true mean length of loci in the dataset is significantly longer (139.6 kb) than reported, and effective c-genes are drastically shorter (∼12 bp) than assumed by coalescence methods.
  • The original dataset contained substantial errors, including switched names, duplicated/misaligned loci, missing data, and inadequate tree searches, leading to erroneous deep coalescences.
  • Re-analysis with curated data and superior methods supports a Scandentia+Glires clade and contradicts key conclusions of Song et al. (2012).
  • The multispecies coalescent likely explains only a small fraction (⩽15%) of gene tree conflicts, contrary to previous claims (77%).

Conclusions:

  • Shortcut coalescence methods are ill-suited for complete protein-coding sequences due to amalgamated c-genes with different evolutionary histories and distorted gene tree stoichiometry.
  • The assumption of long c-genes required for accurate species tree reconstruction using these methods is unfounded.
  • Coalescence approaches using single nucleotide polymorphisms (SNPs) spaced widely across the genome warrant further investigation to overcome recombination issues.