Compositional heterogeneity in true bug mitochondrial phylogenomics.

Area of Science:

• Evolutionary Biology
• Genomics
• Entomology

Background:

• Mitochondrial phylogenomics is crucial for understanding deep evolutionary relationships but can be complicated by data heterogeneity.
• Increasing mitochondrial genome data offers opportunities to improve phylogenetic accuracy and assess biases.

Purpose of the Study:

• To investigate phylogenetic relationships within Heteroptera (insects) using mitochondrial genome data.
• To assess the impact of nucleotide composition and evolutionary rate heterogeneity on phylogenetic inference.
• To evaluate the performance of site-heterogeneous mixture models in resolving Heteroptera phylogeny.

Main Methods:

• Gathered 76 mitochondrial genome sequences for Heteroptera, including 17 new sequences.
• Analyzed data using site-homogeneous models, identifying biases due to base composition and evolutionary rates.
• Employed Bayesian analyses with a site-heterogeneous mixture CAT+GTR model for robust phylogenetic reconstruction.

Main Results:

• Heteroptera mitochondrial genomes exhibit significant base composition and evolutionary rate heterogeneity.
• Site-homogeneous models produced inaccurate groupings, while site-heterogeneous models yielded topologies congruent with accepted phylogeny.
• Confirmed monophyly of six Heteroptera infraorders, with Cimicomorpha appearing paraphyletic; recovered monophyly of Terheteroptera and Panheteroptera.

Conclusions:

• Site-heterogeneous mixture models are powerful tools for resolving complex phylogenetic relationships in mitochondrial phylogenomics.
• Model adequacy is critical for accurate phylogenetic tree reconstruction, especially with heterogeneous mitochondrial genome data.
• This study provides an improved phylogenetic framework for Heteroptera, highlighting the utility of advanced modeling approaches.