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Incongruence among different mitochondrial regions: a case study using complete mitogenomes.

Kelly A Meiklejohn1, Melany J Danielson1, Brant C Faircloth2

  • 1Department of Biology, University of Florida, Gainesville, FL, United States.

Molecular Phylogenetics and Evolution
|June 15, 2014
PubMed
Summary

Mitochondrial DNA (DNA) phylogenetic analyses can yield conflicting results even when using the entire genome. Researchers found that analyzing individual mitochondrial DNA regions in birds often produced incongruent evolutionary trees, complicating phylogenetic interpretations.

Keywords:
Codon modelsGalliformesMixture modelsNoise reductionTaxon sampling

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Area of Science:

  • Evolutionary Biology
  • Genomics
  • Bioinformatics

Background:

  • Mitochondrial DNA (DNA) is widely used for phylogenetic studies due to ease of access and rapid evolution.
  • Mitochondrial genomes are generally considered to lack recombination, implying a single gene tree for the entire genome.
  • However, incongruence among phylogenetic estimates from different mitochondrial DNA regions has been observed, particularly in galliform birds.

Purpose of the Study:

  • To investigate the causes of phylogenetic incongruence among mitochondrial DNA regions in galliform birds.
  • To evaluate different analytical methods for resolving conflicts in mitochondrial DNA phylogenies.
  • To assess the reliability of complete mitogenome versus individual region analyses for inferring evolutionary relationships.

Main Methods:

  • Expanded sampling to 47 galliform mitogenomes, including new representatives from two families.
  • Analyzed complete mitogenomes and individual mitochondrial DNA regions.
  • Tested various analytical strategies to mitigate incongruence, such as partitioning by codon position, using mixture and codon-based models, RY coding, and excluding potentially misleading sites.

Main Results:

  • Analysis of complete mitogenomes yielded a well-supported topology consistent with multi-locus studies.
  • Analysis of individual mitochondrial DNA regions showed conflicting phylogenetic positions for Odontophoridae (New World quail) and other relationships.
  • No tested analytical strategy consistently resolved the incongruence among mitochondrial DNA regions; increasing taxa sometimes exacerbated conflicting signals.

Conclusions:

  • Phylogenetic analysis of mitochondrial DNA data remains challenging due to inherent incongruence among regions.
  • Complete mitogenome analysis provides a more robust estimate of the mitochondrial gene tree compared to individual regions.
  • The biological characteristics of misleading and non-misleading sites appear similar, suggesting complex evolutionary processes at play.