On correctness of gene tree tagging under a unified model of gene duplication, loss, and coalescence

2026/01/21 by Rachel A. Parsons, Yunzhuo Liu, Parth Dua +2 · 1 voice · 1 citation
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Chromosomal and Genetic Variations #Genetic diversity and population structure #Genomics and Phylogenetic Studies

paper · pdf · doi:10.64898/2026.01.20.700722

openalex publication_date 2026/01/21 · openalex created_date 2026/01/23 · openalex updated_date 2026/07/14

Abstract

A bstract ASTRAL-pro is the leading method for reconstructing species trees under complex evolutionary scenarios involving gene duplication, loss, and coalescence, commonly modeled by DLCoal. A unique aspect of A-pro is that it utilizes rooted gene trees, with internal vertices labeled as duplications or speciations, to modify its objective function compared to the traditional ASTRAL method. Although there is a natural event-based definition of correct tagging when genes evolve with only gene duplications and losses, it cannot be applied when there is deep coalescence. Here, we introduce a definition of correct tagging that is broadly applicable, proposing that a gene tree vertex is correctly tagged as a duplication if it is the most recent common ancestor of at least one pair of gene copies related via a duplication event. Using this definition, we study some statistical properties of ASTRAL-pro’s objective function under the DLCoal model and evaluate the accuracy of ASTRAL-pro’s tagging algorithm in simulations.

Citations

• IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
• Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration
• Improved Robustness to Gene Tree Incompleteness, Estimation Errors, and Systematic Homology Errors with Weighted TREE-QMC

Cited by

• On the consistency of duplication, loss, and deep coalescence gene tree parsimony costs under the multispecies coalescent

Discussions

• On the correctness of gene tree tagging and the consistency of ASTRAL-pro under a unified model of gene duplication, loss, and coalescence doi.org/10.64898/202... DupyliCate - mining, classifying, an [bsky, 1 points, 0 comments]

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