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Big thanks to @dylanclark.bsky.social for an assist on the simulations, and Lillian Cohn on interpreting these data. Please check out the paper and let us know what you think!

Major takeaways: HIV can fix escape mutations while retaining nearly all genetic diversity, and sweep signatures can be so soft as to be effectively invisible in genetic data (except at the exact site of escape itself). This totally blew my mind, even as someone who appreciates HIV mutability.

She ran HIV-matched forward simulations in SLiM and found that sweeps need to be spreading on 50 or more genetic backgrounds before they generate these types of signatures. Beyond that point, you can’t really tell because there’s not really any signature to see!

But what Elena found is that in 8/10 HIV populations, haplotype lengths were basically exactly the same before, during and after the sweep. It seems like these sweeps are basically so soft that they’re not changing the linkage structure of the population??

But, we know that soft sweeps retain more genetic diversity than hard sweeps, so Elena looked at haplotype homozygosity. This should be considerably more sensitive.

Our classical sweep signature is a loss of diversity surrounding the adaptive locus. Elena found that following 10-1074 escape, 10 HIV populations are basically just as diverse as they were before the sweep, and consistently *more* diverse at the adaptive locus itself.

A few months ago, @elena-romero.bsky.social published a paper showing that HIV escape from broadly neutralizing antibody 10-1074 is driven by very recurrent mutation. In her latest, she asks - just how soft are the signatures of these sweeps? www.biorxiv.org/content/10.6...

She ran HIV-matched forward simulations in SLiM and found that sweeps need to be spreading on 50 or more genetic backgrounds before they generate these types of signatures. Beyond that point, you can’t really tell because there’s not really any signature to see!

But what Elena found is that in 8/10 HIV populations, haplotype homozygosity was basically exactly the same before, during and after the sweep. It seems like these sweeps are basically so soft that they’re often not changing the linkage structure of the population??

But, we know that soft sweeps retain more genetic diversity than hard sweeps, so Elena looked at haplotype homozygosity. This should be considerably more sensitive.

Our classical sweep signature is a loss of diversity surrounding the adaptive locus. Elena found that following 10-1074 escape, 10 HIV populations are basically just as diverse as they were before the sweep, and consistently *more* diverse at the adaptive locus itself.

Cannot be more excited about the lineup for the inaugural Function of Evolving Systems GRC conference I am co-organizing with the amazing Joy Bergelson. Less than a month away: August 9 - 14, 2026. Still a few spots left! And do check out the amazing list of speakers: www.grc.org/function-of-...

Genuine question for folx who look at bacterial phylogenies: How do you interpret the bootstrap support and posterior probabilities that you get on your tree estimates? Do you take them seriously? Do you think: "Wow, all 99%, that must be a reliable tree!"? 1/

It's go time!

Very proud of this preprint out of my lab, our first (of hopefully many) host-microbe spatial transcriptomics paper. www.biorxiv.org/content/10.6... Amazing insights into P. aeruginosa biology and chronic airway disease @cysticfibrosis.org.uk @sangerinstitute.bsky.social @asthmaandlung.org.uk

Inaugural post! We are a brand new lab @pasteur.fr studying how pathogen antigens evolve and how we can exploit these proteins' evolution to make better vaccines! Read a few words from the currently sole member of the lab @spyroslytras.bsky.social below! 😁 www.pasteur.fr/en/research-...

Folks in the #QVEU have been busy! We recently published two reviews in #JVI @jvico-eics.bsky.social! Check them out to learn more about the tools we use in the lab and the questions we are excited to pursue in the coming years… 🧵

Pls share: U of Washington has an opening for a tenure-track faculty position at the rank of Assistant Professor. This position is expected to specialize in molecular virology or bacteriology. Here is a link: microbiology.washington.edu/index.php/ne...

What if an embryo made immune cells before it finished building the tissue they usually come from? In our new preprint, we show that annual killifish embryos specify neutrophils before germ layers are fully resolved. www.biorxiv.org/content/10.6... Huge thanks to my PI, @ohnolog.bsky.social ! 🧵

I'm hiring a #postdoc 🥳 and applications are open 🤩 Candidates with interests in EITHER statistical methodology or microbial ecology / microbiome are welcome to apply. The position / projects will be tailored to the candidate 🌟📈🎤 Thank you for sharing widely! apply.interfolio.com/188571