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Updated: May 11, 2026
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Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for
Jenniffer Roa Lozano1,2, Mahamad Sayab Miya1,2, Emma Turner1,2
1Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, 72701, USA.
Journal of Molecular Evolution
|May 9, 2026
Summary
Hidden phylogenetic conflict, or gene-tree discordance from incomplete lineage sorting (ILS), can trick evolutionary models. Even simple DNA evolution can appear complex, leading to incorrect model selection in phylogenomic analyses.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Computational Biology
Background:
- Phylogenetic conflict, especially from incomplete lineage sorting (ILS), is common in multilocus and phylogenomic data.
- The impact of this hidden gene-tree discordance on nucleotide substitution model selection is not well understood.
- Modern phylogenomics uses concatenated alignments, increasing potential for analysis heterogeneity.
Purpose of the Study:
- To investigate if intra-alignment genealogical conflict influences standard model selection.
- To determine if conflict can lead to favoring parameter-rich models even under simple evolutionary processes.
- To assess the impact of varying levels of conflict on model selection outcomes.
Main Methods:
- Simulated sequence evolution under the Jukes-Cantor (JC69) model.
- Generated concatenated alignments as mosaics of loci evolving under the multispecies coalescent.
- Manipulated conditions to increase ILS and gene-tree heterogeneity, embedding hidden genealogies.
Main Results:
- Model selection frequently favored complex models (e.g., with among-site rate variation, GTR) despite data generated under the simple JC69 model.
- Sensitivity to conflict varied with taxon number and selection criteria.
- Extreme conflict increasingly favored richer substitution models.
Conclusions:
- Hidden phylogenetic conflict can mimic substitutional and rate heterogeneity in concatenated analyses.
- Model selection procedures may incorrectly compensate for conflict by adding unnecessary parameters.
- This highlights challenges in modeling molecular evolution for large phylogenomic datasets.
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