Quartet-based Genome-scale Species Tree Inference using Multicopy Gene Family Trees DOI
Abdur Rafi, Ahmed Mahir Sultan Rumi, Sheikh Azizul Hakim

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 10, 2025

Abstract Species tree estimation from genome-wide data has transformed evolutionary studies, particularly in the presence of gene discordance. Gene trees often differ species due to factors like incomplete lineage sorting (ILS) and duplication loss (GDL). Quartet-based methods have gained substantial popularity for their accuracy statistical guarantee. However, most these (e.g., ASTRAL, wQFM, wQMC) rely on single-copy models ILS not GDL, limiting applicability large genomic datasets. ASTRAL-Pro, a recent advancement, refined quartet similarity measures incorporate both orthology paralogy, improving inference under GDL. Among other quartet-based methods, wQFM-DISCO converts multicopy family into using DISCO applies wQFM algorithm trees. ASTRAL-Pro remained only summary method explicitly model loss. In this study, we extend (which requires decomposition) wQFM-TREE operates directly trees) by modeling loss, leveraging concept speciation-driven quartets introduced ASTRAL-Pro. Our consistently outperforms across conditions, offering promising alternative

Language: Английский

Quartet-based Genome-scale Species Tree Inference using Multicopy Gene Family Trees DOI
Abdur Rafi, Ahmed Mahir Sultan Rumi, Sheikh Azizul Hakim

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 10, 2025

Abstract Species tree estimation from genome-wide data has transformed evolutionary studies, particularly in the presence of gene discordance. Gene trees often differ species due to factors like incomplete lineage sorting (ILS) and duplication loss (GDL). Quartet-based methods have gained substantial popularity for their accuracy statistical guarantee. However, most these (e.g., ASTRAL, wQFM, wQMC) rely on single-copy models ILS not GDL, limiting applicability large genomic datasets. ASTRAL-Pro, a recent advancement, refined quartet similarity measures incorporate both orthology paralogy, improving inference under GDL. Among other quartet-based methods, wQFM-DISCO converts multicopy family into using DISCO applies wQFM algorithm trees. ASTRAL-Pro remained only summary method explicitly model loss. In this study, we extend (which requires decomposition) wQFM-TREE operates directly trees) by modeling loss, leveraging concept speciation-driven quartets introduced ASTRAL-Pro. Our consistently outperforms across conditions, offering promising alternative

Language: Английский

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