TY - JOUR
T1 - An efficient and robust ABC approach to infer the rate and strength of adaptation
AU - Casillas Viladerrams, Sònia
AU - Barbadilla Prados, Antonio
AU - Uricchio, Lawrence
AU - Enard, David
N1 - Publisher Copyright:
© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.
PY - 2024/2/14
Y1 - 2024/2/14
N2 - 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.
AB - 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.
KW - Mcdonald and Kreitman test
KW - natural selection
KW - viral interacting proteins
UR - http://www.scopus.com/inward/record.url?scp=85189858975&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/a0246105-41ad-3541-b8d4-51cc270bf1c1/
U2 - 10.1093/G3JOURNAL/JKAE031
DO - 10.1093/G3JOURNAL/JKAE031
M3 - Article
C2 - 38365205
SN - 2160-1836
VL - 14
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
ER -