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David Enard @denard.bsky.social · 1d

Is it a new test? I am not familair with it.

David Enard @denard.bsky.social · 1d

Indeed cases where the AA reversion is not the same nucleotide as the initial AA change. BTW I am preparing big mammal CDS alignments motably to look at reversions, you may again be interested, I learned my lesson trying to depart from Blat.

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David Enard @denard.bsky.social · 1d

Thank you!

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David Enard @denard.bsky.social · 1d

It does sound like we should look at similar signatures in alignments of mammals coding sequences.

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David Enard @denard.bsky.social · 1d

Do you think that the reverted amino acid changes were more likely to be advantageous under a previous, now gone selective pressure? In that case the claim would be the same?

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David Enard @denard.bsky.social · 1d

Super cool, thank you!

Reposted by David Enard

Tami Lieberman @contaminatedsci.bsky.social · 1d

We've made a related but different claim in bacteria:
elifesciences.org/articles/93146

Reversions mask the contribution of adaptive evolution in microbiomes

The timescale dependence of dN/dS in bacteria is better explained by adaptive than purifying dynamics, suggesting comparative genomics can underestimate past adaptation.

elifesciences.org

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David Enard @denard.bsky.social · 1d

We think this is definitely the case given what we see with virus-driven adaptation in host proteins that interact with viruses. The latter drive very strong selection. We do find signatures of compensatory protein stability evolution:
www.biorxiv.org/content/10.1...

Stability evolution as a major mechanism of human protein adaptation in response to viruses

Pathogens were a major driver of genetic adaptation during human evolution. Viruses in particular were a dominant driver of adaptation in the thousands of proteins that physically interact with viruse...

www.biorxiv.org

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David Enard @denard.bsky.social · 1d

2/2) For example if deleterious effect is related to a change in protein stability, many other amino acid substitutions will likely be able to compensate for it. But especially in large pops the "perfect" compensation should be recurrently available. That's all I have for now!

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David Enard @denard.bsky.social · 1d

1/2) That holds for transient selective pressures that make an otherwise deleterious mutation temporarily advantageous, but that's probably most selective pressures given enough evolutionary time. Remaining issue is if effects cannot be compensated by other substitutions.

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David Enard @denard.bsky.social · 1d

I am convinced that we have massively underestimated the impact of substitution reversions on the amount of molecular positive selection that we are able to see. Large populations will readily have reversing mutations readily available, and gene flow will also reintroduce ancestral alleles.

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David Enard @denard.bsky.social · 5d

Ryan Gutenkunst @ryangutenkunst.bsky.social · Sep 4

We all know hand-on learning is best. If you're a student interested in population genetics inference, compete in GHIST! ghi.st . You can even get started without installing any software using our webapps: ryangutenkunst-dadi-two-epoch.hf.space and ryangutenkunst-sweep-detection-dpi.hf.space .

A meme using the "Distracted Boyfriend" template showing a man in a blue plaid shirt (labeled "GRADUATE STUDENTS") looking back at a woman in a red dress (labeled "HANDS-ON GHIST COMPETITION EXPERIENCE") while walking with his girlfriend in light blue (labeled "THEORETICAL POP GEN COURSES"). The image satirizes graduate students being tempted by practical competition experience over theoretical population genetics coursework.

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Reposted by David Enard

Ryan Gutenkunst @ryangutenkunst.bsky.social · Aug 15

I built a Gradio app to illustrate how selective sweeps can be detected from population genetic data: ryangutenkunst-sweep-detection-dpi.hf.space . It can help with your first submissions to the GHIST sweep detection challenges! ghi.st #GHIST

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Reposted by David Enard

Ryan Gutenkunst @ryangutenkunst.bsky.social · Aug 25

The 2025 edition of the Genomic History Inference Strategies Tournament is live! ghi.st If you work in population genomics, join the competition to help the community learn which methods are best for demographic history inference and sweep detection.

Vince McMahon meme about competing in GHIST.

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Reposted by David Enard

Ryan Gutenkunst @ryangutenkunst.bsky.social · Aug 28

Did you know? This year's Genomic History Inference Strategies Tournament (GHIST) includes 4 challenges in detecting selective sweeps. Our field has many methods for doing this, but which will come out on top, especially when false positives matter? ghi.st #GHIST

Choosing button meme, in which the choice is between identifying a genomic region as a selective sweep versus it being a false positive. The chooser is competing in the GHIST multiple sweeps challenge.

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Reposted by David Enard

Daniel Bolnick @danielbolnick.bsky.social · 11d

Here’s a paper by an undergrad(!) that I’m very proud of:

academic.oup.com/evlett/artic...

What happens when a susceptible host founds a new population exposed to a parasite? In 50 years they go from highly infected to immune.

Validate User

academic.oup.com

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Reposted by David Enard

Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 13d

ARGs are good.
Inferring ARGs from real data hard.
Analyzing ARGs from real data hard.

...check your missing data; test your inference doesn't screw up with masked/missing data.

...check your polarization. SINGER prior for example doesn't work as expected if you give it a vcf with ref/alt

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David Enard @denard.bsky.social · 13d

Postdoc J. M. Moreno is very close to release Flex-sweep v2 to make users' life easier. v2 is entirely recoded, faster and uses much less RAM. Robustness is up thanks to adding Siepel's lab domain adaptive step.
Available soon at pypi.org/project/flex...
flexsweep.readthedocs.io/en/latest/

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David Enard @denard.bsky.social · Sep 2

Lab member Jesus Murga Moreno got a much faster and user-friendly version of Flex-sweep up and running. Among other improvements, it requires much less RAM thanks to a new version of discoal provided by Andy Kern:

github.com/jmurga/flexs...
flexsweep.readthedocs.io/en/latest/

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Reposted by David Enard

James McInerney @jomcinerney.bsky.social · Aug 29

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards.
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes

Background Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is wh...

www.biorxiv.org

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Reposted by David Enard

Daniel Bolnick @danielbolnick.bsky.social · Aug 29

In the earliest stages of adaptive introgression, beneficial immigration can drive genome-wide changes. In a new preprint www.biorxiv.org/content/10.1... colleagues & I document exceptionally rapid genomic introgression in a lake population of stickleback.

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David Enard @denard.bsky.social · Jul 5

Does anyone know if the current Alphafold EBI database is still made of Alphafold2 models, or has it been updated with Alphafold3? I cannot find the Alphafold version used to generate specific models.

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David Enard @denard.bsky.social · Jun 12

A simple place to start changing things is to stop systematically distributing conference awards among students from big famous labs.

Research on Research Institute (RoRI) @rorinstitute.bsky.social · Jun 12

🎯 Does early success in science funding shape the rest of your career?

New RoRI study says yes.

The ‘Matthew effect’ — early winners keep winning — holds across funders & countries.

📄 Read more: researchonresearch.org/largest-stud...

Largest study of its kind shows that the ‘Matthew effect’ in science funding holds true - Research on Research

New RoRI paper shows that researchers who win funding early in their career are more likely to get funded in the future

researchonresearch.org

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Reposted by David Enard

Yoav Gilad @ygilad.bsky.social · Jun 10

People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?"

(For the record, no one has ever asked me this, but it is a really good question!)

I think we know where they are.

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David Enard @denard.bsky.social · Jun 10

You might as well have written, "we sat HDCs at a terrace in Paris".

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