iiinova — where your digital self keeps evolving

Jesse Shapiro @bjesseshapiro.bsky.social · 06/10/2026

Minimoy, the cat we are cat-sitting for the year, is my sabbatical spirit animal

Photo of a sleeping black and brown cat curled up on a sofa cushion

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Jesse Shapiro @bjesseshapiro.bsky.social · 06/10/2026

Our village is celebrating the rainy season

Photo of a old stone building decorated with bright pink umbrellas strung across the square in front

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Jesse Shapiro @bjesseshapiro.bsky.social · 30/09/2026

Glyphosate-based herbicide exposure triggers genetic adaptation but not diversity collapse within bacterioplankton species (reposting with the article title and a gratuitous glam shot of the lake these bugs called home until we rudely plopped them into experimental ponds...)

Screenshot of the article title: Glyphosate-based herbicide exposure triggers genetic adaptation but not diversity collapse within bacterioplankton species

Photo of a beautiful blue sky with some clouds reflected in a lake. The surrounding hills are dappled with red and gold fall foliage.

Photo credit: Akhil Kholwadwala

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

19. Ours is one of a growing number of studies looking at evolution in the context of (semi) natural communities with known selective pressures. Still lots of open questions, but hopefully we can start to reach more general conclusions!

slide summarizing results of our work on eco-evolutionary effects of GBH selection, and listing other similar studies applying known selective pressures to semi-natural microbial commnities.

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

18. What about soft sweeps, in which targets of selection are shared by different lineages (strains)? It’s far from conclusive, but this explains many of our observations.

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

17. So what is going on? Genome-wide sweeps are not occurring in a classic sense, because polymorphism is retained. Gene-sweeps? Maybe, but dozens of concurrent sweeps would be required to explain the many genes under selection.

Sketches of genome-wide and gene-specific selective sweeps

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

16. Across all 7 MAGs, the targets of selection are enriched in amino acid metabolism (COG category E), in and around the AroA pathway known to be inhibited by GBH. Some other metabolism genes are enriched too.

Barplot of functional gene categories enriched in SNV frequency changes during GBH treatment relative to controls.

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

15. In some MAGs, we detect thousands of genes potentially under selection, too many to explain by gene-specific sweeps and more consistent with a rare strain rising in frequency in response to GBH (because average nucleotide identify [ANI] stays pretty low). In others, gene-sweeps are plausible.

table enumerating genes inferred to be under GBH-driven selection across 7 MAGs

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

14. To identify candidate genes under selection by GBH, we looked for large changes in SNV frequency in GBH but not control ponds. We could do this in 7 MAGs with sufficient coverage at both time points.

cartoon showing criteria to identify genes with large differences in SNV frequencies between GBH treatment and control ponds

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

13. But if we look at *polymorphic* SNVs (those that remain variable in the population, not fixing during the experiment), they are unaffected by GBH treatment. This is *inconsistent* with classic genome-wide sweeps, which predicts purging of polymorphisms.

boxplot showing that GBH does not purge polymorphism within MAGs

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

12. First, we find that GBH drives fixed SNVs (those that go to 100% frequency, replacing the nucleotide present in the reference genome from time 0). There is also a smaller but detectable effect of SNVs that fix over time due to drift, not treatment.

boxplots showing an increased in fixed substitutions with GBH treatment

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

11. Consistent with our previous experiments, GBH shifts the community from Beta to Alphaproteobacteria. But we really want to zoom in and look at genetic variation (SNVs) within MAGs (rough proxy for species).

Barplots showing Alphaproteobacteria increasing in relative abundance with GBH (Roundup) treatment

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

10. So we designed a pretty simple experiment: deeply sequence microbial communities before and 28 days after exposure to a Roundup (GBH) pulse.

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

9. In previous LEAP work, we found that the glyphosate-based herbicide (GBH) Roundup selects for MAGs (metagenome-assembled genomes, a proxy for bacterial species) that encode more efflux pumps. This explains much of the community-level response, but what about the population level, within species?

Slide showing a plot of MAG success being predicted by efflux pumps in their genome

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

8. Here we took an experimental approach by applying a known selective pressure to a semi-natural community in the Large Experimental Array of Ponds (LEAP) at the @mcgill.ca Gault Nature Reserve.

Slides showing the Large Experimental Array of Ponds

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

7. There is also evidence for both genome-wide and gene-specific sweeps in human gut bacteria. But in both cases, the selection driving these sweeps must be inferred and remains uncertain. Great work by @polzlab.bsky.social @nanditagarud.bsky.social @rwolff.bsky.social & co

Screen shots of recent studies showing genome-wide and gene-specific sweeps in human gut microbiomes

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

6. Putting gene ecology aside for the moment, do we observe sweeps in nature? Yes! Here’s an example (from @quendi.bsky.social & co) of a genome-wide sweep happening in a lake bacterium over 9 years. But was it driven by selection (and if so, what selective pressure?) or drift?

Heatmap of a genome-wide sweep observed by Bendall et al.

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

5. Of course, speciation is not guaranteed. There are models that could lead to ‘gene ecology’ where genes, not species, inhabit ecological niches.

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

4. If recombination is stronger, we can get gene-specific selective sweeps. Diversity is only purged locally near the targets of selection, and preserved genome-wide. If recombination becomes restricted between niches over time, we can get something resembling the Biological Species Concept.

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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026

3. If recombination is weak relative to selection, we expect genome-wide selective sweeps. Genetic diversity is purged genome-wide as linked variants hitchhike with the target of selection. If sweeps occur independently in different species, this leads to Fred Cohan’s Ecotype Species Concept.

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Jesse Shapiro @bjesseshapiro.bsky.social · 27/09/2026

Bittersweet watching these familiar streets from an ocean away! #UCI

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Jesse Shapiro @bjesseshapiro.bsky.social · 08/09/2026

Who needs a pickup truck?(Montpellier edition)

Photo of a person pedaling a bike with large front and back cargo platforms along a cobbled street

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Jesse Shapiro @bjesseshapiro.bsky.social · 05/09/2026

Fully immersing myself in French culture

Photo of my feet wearing Decathlon branded slides

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Jesse Shapiro @bjesseshapiro.bsky.social · 02/09/2026

Without saying your age, what was your favourite film that came out when you were 20 years old

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Jesse Shapiro @bjesseshapiro.bsky.social · 28/08/2026

In addition to the obvious fresh bread available everywhere, highlights of grocery shopping in France include: 1) tetrapacks of cheap gazpacho! So good. Going through about a litre a day. 2) UHT milk as a pantry item! Kids go through this so quickly. Fresh (refrigerated) milk is ridiculous.

Photo of a litre tetra pack of gazpacho beside a glass filled with gazpacho

Photo of an 8-pack of shelf-stable 1L milk bottles

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Jesse Shapiro @bjesseshapiro.bsky.social · 06/08/2026

Major career update: going back to being a postdoc and I am PSYCHED!

Screenshot of an email message indicating that, for HR purposes, I will be considered a postdoc during my sabbatical in Montpellier

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Jesse Shapiro @bjesseshapiro.bsky.social · 05/08/2026

Independent replication from my own hand (right) and foot (left) in a little family science project

Two Petri dishes with colonies growing on LB agar. The left dish, from a foot print, has more visibly fuzzy fungi than the right, from finger prints.

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Jesse Shapiro @bjesseshapiro.bsky.social · 04/08/2026

#MEEHubs2026 Montreal may have collectively lost the quiz but we are winning the poster session ;)

Photo of engaged, happy looking people gathered around posters in a futuristic blue corridor

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Jesse Shapiro @bjesseshapiro.bsky.social · 03/08/2026

I think Montreal hub got the best lunch! #MEEHubs2026

Photo of a plate with falafel, hummus, pita, veggies etc

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Jesse Shapiro @bjesseshapiro.bsky.social · 31/07/2026

Loving the mosaic sidewalk repair

Photo of a cracked sidewalk repaired with a colourful tile mosaic

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Jesse Shapiro @bjesseshapiro.bsky.social · 11/07/2026

Must find a way to play these. Where is my MD player?!

Photo of 3 minidiscs with handwritten labels. They are show recordings of The Weakerthans and Neko Case from the early 2000s.

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Jesse Shapiro @bjesseshapiro.bsky.social · 08/07/2026

Sabbatical year in France is HAPPENING !!

Slip of paper with text: “Vous venez d'obtenir un visa de long séjour valant titre de séjour vous permettant de séjourner en France, bienvenue !”

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Jesse Shapiro @bjesseshapiro.bsky.social · 24/06/2026

Love the #worldcup flag combos that appear in Canada but I doubt would be viable in their home countries…

Photo of a car flying mini flags of both Colombia and Brazil

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Jesse Shapiro @bjesseshapiro.bsky.social · 20/06/2026

Green roof at the local library is so cheerful on a rainy day

Photo of a rooftop covered in wildflowers and grasses. There are some buildings and an old church in the distance. It’s raining.

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Jesse Shapiro @bjesseshapiro.bsky.social · 05/06/2026

Re-upping for morning phage phriends. Hope you will find Brenna & Patrick's method useful! Here they are, with some other lab members, on a rock. They are rock stars.

A group of people standing in the woods on a sunny day on a large boulder, or on a wood ramp leading down from it.

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Jesse Shapiro @bjesseshapiro.bsky.social · 30/05/2026

Hard to stay sad about the Habs with these vibes! Let’s go Victoire! Championnes!!

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Jesse Shapiro @bjesseshapiro.bsky.social · 28/05/2026

The headline sounds silly but Jérôme is awesome and this is great news for science in Québec. Félicitations Jérôme, you rock!! montrealgazette.com/news/quebec-...