Tag Archives: soft sweep

Manuscript on HIV sweeps and clonal interference posted on BioRxiv

13 Feb

Kadie-Ann Williams and I posted a new manuscript on the BioRiv. It is 30 pages with 28 figures and a supplement of 118 figures! I guess we could call it an HIV drug resistance evolution picture book!

P00089Muller

Muller plot showing clonal interference in patient 89.

Nowadays, drug resistance evolution is quite rare, but in the late 1990s, HIV populations within patients on treatment were undergoing soft sweeps, hard sweeps, clonal interference and other things. If you like sequence data, you’ll enjoy looking at our pictures!

Title: Drug resistance evolution in HIV in the late 1990s: hard sweeps, soft sweeps, clonal interference and the accumulation of drug resistance mutations

https://www.biorxiv.org/content/10.1101/548198v1

Abtract

The goal of this paper is to provide examples of evolutionary dynamics of HIV within patients who are treated with antiretrovirals. We hope that the figures in this paper will be used in evolution and population genetics classes. We show a wide variety of patterns, specifically: soft sweeps, hard sweeps, softening sweeps and hardening sweeps, simultaneous sweeps, accumulation of mutations and clonal interference.

Kadie

Kadie-Ann Williams, SFSU BSc 2014, MSc 2017

Download the paper 2019WilliamsPennings2019_Feb

Download the supplemental figures 2019WilliamsPennings2019_Supplement118Patients

 

New video about soft sweeps

12 Jul

I made a new video about why soft sweeps are more common than you may think!

This is a second video about a paper I published in 2017 with Joachim Hermisson.

I hope that these videos make it easy to understand some of the main conclusions from our paper!

 

It’s the sequel to this one:

 

Hermisson, J. and Pennings, P.S. 2017, Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation. Methods Ecol Evol, 8: 700–716. 2017Hermisson_Pennings_Methods_in_Ecology_and_Evolution.

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