Clonal interference can cause wavelet-like oscillations of multilocus linkage disequilibrium

Garcia, Victor; Glassberg, Emily C.; Harpak, Arbel; Feldman, Marcus W.

doi:10.1098/rsif.2017.0921

Publication type:	Article in scientific journal
Type of review:	Peer review (publication)
Title:	Clonal interference can cause wavelet-like oscillations of multilocus linkage disequilibrium
Authors:	Garcia, Victor Glassberg, Emily C. Harpak, Arbel Feldman, Marcus W.
DOI:	10.1098/rsif.2017.0921
Published in:	Journal of the Royal Society Interface
Volume(Issue):	15
Issue:	140
Issue Date:	21-Mar-2018
Publisher / Ed. Institution:	The Royal Society
ISSN:	1742-5689 1742-5662
Language:	English
Subjects:	Genetic interference; Human immunodeficiency virus; Multilocus linkage disequilibrium
Subject (DDC):	572: Biochemistry 616: Internal medicine and diseases
Abstract:	Within-host adaptation of pathogens such as human immunodeficiency virus (HIV) often occurs at more than two loci. Multiple beneficial mutations may arise simultaneously on different genetic backgrounds and interfere, affecting each other's fixation trajectories. Here, we explore how these evolutionary dynamics are mirrored in multilocus linkage disequilibrium (MLD), a measure of multi-way associations between alleles. In the parameter regime corresponding to HIV, we show that deterministic early infection models induce MLD to oscillate over time in a wavelet-like fashion. We find that the frequency of these oscillations is proportional to the rate of adaptation. This signature is robust to drift, but can be eroded by high variation in fitness effects of beneficial mutations. Our findings suggest that MLD oscillations could be used as a signature of interference among multiple equally advantageous mutations and may aid the interpretation of MLD in data.
URI:	https://digitalcollection.zhaw.ch/handle/11475/7498
Fulltext version:	Published version
License (according to publishing contract):	Licence according to publishing contract
Departement:	Life Sciences and Facility Management
Organisational Unit:	Institute of Computational Life Sciences (ICLS)
Appears in collections:	Publikationen Life Sciences und Facility Management

Files in This Item:

There are no files associated with this item.

Show full item record

Garcia, V., Glassberg, E. C., Harpak, A., & Feldman, M. W. (2018). Clonal interference can cause wavelet-like oscillations of multilocus linkage disequilibrium. Journal of the Royal Society Interface, 15(140). https://doi.org/10.1098/rsif.2017.0921

Garcia, V. et al. (2018) ‘Clonal interference can cause wavelet-like oscillations of multilocus linkage disequilibrium’, Journal of the Royal Society Interface, 15(140). Available at: https://doi.org/10.1098/rsif.2017.0921.

V. Garcia, E. C. Glassberg, A. Harpak, and M. W. Feldman, “Clonal interference can cause wavelet-like oscillations of multilocus linkage disequilibrium,” Journal of the Royal Society Interface, vol. 15, no. 140, Mar. 2018, doi: 10.1098/rsif.2017.0921.

GARCIA, Victor, Emily C. GLASSBERG, Arbel HARPAK und Marcus W. FELDMAN, 2018. Clonal interference can cause wavelet-like oscillations of multilocus linkage disequilibrium. Journal of the Royal Society Interface. 21 März 2018. Bd. 15, Nr. 140. DOI 10.1098/rsif.2017.0921

Garcia, Victor, Emily C. Glassberg, Arbel Harpak, and Marcus W. Feldman. 2018. “Clonal Interference Can Cause Wavelet-like Oscillations of Multilocus Linkage Disequilibrium.” Journal of the Royal Society Interface 15 (140). https://doi.org/10.1098/rsif.2017.0921.

Garcia, Victor, et al. “Clonal Interference Can Cause Wavelet-like Oscillations of Multilocus Linkage Disequilibrium.” Journal of the Royal Society Interface, vol. 15, no. 140, Mar. 2018, https://doi.org/10.1098/rsif.2017.0921.