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Divergence and support among slightly suboptimal likelihood gene trees.

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Phylogenomic analyses using RAxML may produce over-resolved gene trees and inflated support values. Re-analyzing gene trees revealed frequent issues with optimal topology searches and clade support, highlighting the need for improved methods.

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Area of Science:

  • Phylogenomics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenomic studies often use two-step coalescent analyses to infer gene trees via maximum likelihood.
  • Popular programs like RAxML may present fully resolved gene trees despite ambiguous support or insufficient phylogenetic signal.
  • Concerns exist regarding inexact computer arithmetic and over-reliance on the single most likely tree, potentially leading to over-resolved topologies and inflated bootstrap support.

Purpose of the Study:

  • To investigate the frequency of issues in RAxML-based gene tree inference within contemporary phylogenomic studies.
  • To evaluate the impact of suboptimal gene trees and assess the reliability of standard support measures.
  • To identify effective strategies for robust gene tree inference and species tree reconstruction.

Main Methods:

  • Re-analysis of 100 genes from ten diverse phylogenomic studies using RAxML.
  • Systematic evaluation of gene tree topologies, including slightly suboptimal trees.
  • Comparison of Shimodaira-Hasegawa-like approximate likelihood ratio test (SH-aLRT) with bootstrap support and minimum-length branch collapsing.
  • Assessment of different RAxML optimization strategies and tree search models (GTRCAT vs. GTRGAMMA).

Main Results:

  • RAxML search replicates were often insufficient to find optimal gene tree topologies.
  • Significant topological variation exists among slightly suboptimal gene trees, often ignored in standard analyses.
  • SH-aLRT effectively identified dubiously supported clades, outperforming bootstrap and branch collapsing.
  • Bootstrap support rarely reflected support among suboptimal trees; GTRGAMMA generally outperformed GTRCAT for tree searches.
  • Gene tree sampling strategies impacted coalescent branch lengths, species tree topology, and branch support.

Conclusions:

  • Standard RAxML analyses in phylogenomics may yield unreliable gene trees and support values.
  • SH-aLRT is a more robust method for assessing clade support compared to bootstrap.
  • Careful consideration of tree search strategies, model parameters, and gene tree sampling is crucial for accurate phylogenomic inference.