An efficient and robust ABC approach to infer the rate and strength of adaptation
Murga-Moreno, Jesus (University of Arizona)
Casillas Viladerrams, Sònia (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Barbadilla Prados, Antonio (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Uricchio, Lawrence (Tufts University (Medford, Estats Units d'Amèrica))
Enard, David (University of Arizona)

Date:	2024
Abstract:	Inferring the effects of positive selection on genomes remains a critical step in characterizing the ultimate and proximate causes of adaptation across species, and quantifying positive selection remains a challenge due to the confounding effects of many other evolutionary processes. Robust and efficient approaches for adaptation inference could help characterize the rate and strength of adaptation in nonmodel species for which demographic history, mutational processes, and recombination patterns are not currently well-described. Here, we introduce an efficient and user-friendly extension of the McDonald-Kreitman test (ABC-MK) for quantifying long-term protein adaptation in specific lineages of interest. We characterize the performance of our approach with forward simulations and find that it is robust to many demographic perturbations and positive selection configurations, demonstrating its suitability for applications to nonmodel genomes. We apply ABC-MK to the human proteome and a set of known virus interacting proteins (VIPs) to test the long-term adaptation in genes interacting wit142677h viruses. We find substantially stronger signatures of positive selection on RNA-VIPs than DNA-VIPs, suggesting that RNA viruses may be an important driver of human adaptation over deep evolutionary time scales.
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Mcdonald and Kreitman test ; Natural selection ; Viral interacting proteins
Published in:	G3, Vol. 14 (february 2024) , ISSN 2160-1836

DOI: 10.1093/g3journal/jkae031
PMID: 38365205

23 p, 2.3 MB

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