#eseb2025 — Public Fediverse posts

Fond memories are reflected in the photo recap of #eseb2025 available here https://eseb2025.com/eseb-2025-photo-recap/
Part of this photo gallery are also our PI @DenisMeuthen while asking a question to the presenter and our PhD student Nhamo Mutingwende during a scientific discussion. #EvolutionaryBiology #evolution #ecology @academicchatter

Our lab provided two more contributions to #eseb2025. Our PhD student Dominik Perisa presented a poster titled "Epigenomic profiles underlying induced defenses in a freshwater gastropod" while our PI @DenisMeuthen presented his work under the title "Antipredator phenotypic plasticity and evolutionary divergence in a freshwater snail". Both posters garnered a lot of interest from our colleagues and multiple fruitful discussions alongside possible collaborations emerged. #EvolutionaryBiology #evolution #ecology @academicchatter

After speeding through France at up to 300 km/h for a few hours, I am changing to a small regional train to take me the last 30 or so km to Basel.
As much as I enjoyed #ESEB2025, I also look forward to getting home and getting a good nights sleep 😴

The train journey along the Mediterranean between Perpignan and Montpellier is very scenic. I even saw Greater Flamingo’s feeding in the lagoons right beside the rail tracks.

After a 1 h stopover in Valence I get on another TGV, this time an older model, with the destination of the second leg being Mulhouse.

#ESEB2025

Since #ESEB2027 will be a hub meeting, which should reduce travel distances overall and thus be more environmentally friendly, I thought I’d get into the spirit early. My (not particularly impressive) train journey back home from #ESEB2025 starts with a TGV from Barcelona Sants to Valence, France.

Next ESEB meeting will have an innovative format, across four hubs. The aim is to make it easier to avoid plane travel, and to diversify the locations that can host a meeting #ESEB2025 #ESEB2027

RE: https://bsky.app/profile/did:plc:lk5b3r6ip3h4s7f4equw2jfx/post/3lwyguxo4bc2h

Incredibly moving session this morning for the EUEA awards at #ESEB2025. Thanks to the Equal Opportunity committee for helping us try to understand the enormous challenges that some of our colleagues are facing

von der Dunk: natural protein have less diversity of primary sequence than random sequences, but more diversity of 3D structures 🤔. de novo (young) proteins in yeast resemble random sequences -> evidence that properties of natural proteins have been selected.
How to evolve new protein folds? de novo -> low robustness; duplication -> low variation.
#ESEB2025

von der Dunk: natural protein have less diversity of primary sequence than random sequences, but more diversity of 3D structures 🤔. de novo (young) proteins in yeast resemble random sequences -> evidence that properties of natural proteins have been selected.
How to evolve new protein folds? de novo -> low robustness; duplication -> low variation.
#ESEB2025

Sam von der Dunk: we know that RNA structure is robust to mutation yet evolvable. What about protein structure? Take advantage of ESMfold https://doi.org/10.1126/science.ade2574
Natural proteins are robust to mutations, whereas random amino-acid sequences are not. Even disordered natural proteins are robust! #ESEB2025

Sam von der Dunk: we know that RNA structure is robust to mutation yet evolvable. What about protein structure? Take advantage of ESMfold https://doi.org/10.1126/science.ade2574
Natural proteins are robust to mutations, whereas random amino-acid sequences are not. Even disordered natural proteins are robust! #ESEB2025

Bornberg-Bauer: also convergence of de novo genes in slave-maker ants
https://doi.org/10.1101/2024.12.31.630940
#ESEB2025

Bornberg-Bauer: also convergence of de novo genes in slave-maker ants
https://doi.org/10.1101/2024.12.31.630940
#ESEB2025

Bornberg-Bauer: repeated relaxed selection and loss of odorant and gustatory receptors between slave-maker and “host” ants (3 pairs). Overall genome, slightly more expansions than contractions of gene families, but convergence in slavers is mostly in contractions. #ESEB2025

Bornberg-Bauer: repeated relaxed selection and loss of odorant and gustatory receptors between slave-maker and “host” ants (3 pairs). Overall genome, slightly more expansions than contractions of gene families, but convergence in slavers is mostly in contractions. #ESEB2025

Erich Bornberg-Bauer presenting results in ants, but tells us he found very similar patterns in termites (more love for termites needed in evolutionary genomics IMO). #ESEB2025

Erich Bornberg-Bauer presenting results in ants, but tells us he found very similar patterns in termites (more love for termites needed in evolutionary genomics IMO). #ESEB2025

The method is published so I can share it ;)
https://doi.org/10.1038/s42003-025-08651-2 #ESEB2025

The method is published so I can share it ;)
https://doi.org/10.1038/s42003-025-08651-2 #ESEB2025

Gemma Martínez Redondo very interesting topic “The march to land: unearthing how gene repertoire evolution triggered
terrestrialization across the Animal Tree of Life”, but asks not to post on social media, so… 🤫 #ESEB2025

Gemma Martínez Redondo very interesting topic “The march to land: unearthing how gene repertoire evolution triggered
terrestrialization across the Animal Tree of Life”, but asks not to post on social media, so… 🤫 #ESEB2025

Wacholder: very low rate of proteins entering the “conserved proteome” (meaning proteins under selection for their function if I understand well): <8/120k. #ESEB2025

Wacholder: very low rate of proteins entering the “conserved proteome” (meaning proteins under selection for their function if I understand well): <8/120k. #ESEB2025

Wacholder: a few unannotated transient ORFs have mutant phenotypes #ESEB2025
This and previous post correspond to https://doi.org/10.1016/j.cels.2023.04.002

Wacholder: a few unannotated transient ORFs have mutant phenotypes #ESEB2025
This and previous post correspond to https://doi.org/10.1016/j.cels.2023.04.002

Wacholder: unannotated yeast ORFs (19k of them!) tend to be short and lowly expressed, yet 1/3rd can be localised by microscopy. Do they have a function under selection? Check for reading frame conservation between species -> two classes of ORFs, corresponding well to annotations. Only 11 unannotated ORFs with conservation of reading frame, while 101 annotated ORFs are not conserved (“transient ORFs”) between yeasts. ≈1/2 of these annotated transient ORFs have mutant phenotypes. #ESEB2025

Wacholder: unannotated yeast ORFs (19k of them!) tend to be short and lowly expressed, yet 1/3rd can be localised by microscopy. Do they have a function under selection? Check for reading frame conservation between species -> two classes of ORFs, corresponding well to annotations. Only 11 unannotated ORFs with conservation of reading frame, while 101 annotated ORFs are not conserved (“transient ORFs”) between yeasts. ≈1/2 of these annotated transient ORFs have mutant phenotypes. #ESEB2025

Aaron Wacholder: ribosome profiling allows us to find translation outside of annotated coding sequences. Are they functional or just translation noise? #ESEB2025

Aaron Wacholder: ribosome profiling allows us to find translation outside of annotated coding sequences. Are they functional or just translation noise? #ESEB2025

Final words of the last #ESEB2025 plenary by @jmappes.bsky.social: "Science moves forward when we keep both our curiosity and our humility"

Johanna Mappes #ESEB2025

Johanna Mappes #ESEB2025

Mappes was expecting valkea gene to be pleiotropically linked to life-history, but data said otherwise. Moreover, melanin patterning is genetically independent of valkea. OTOH, the melanin locus associates with male behaviour. #ESEB2025

Mappes was expecting valkea gene to be pleiotropically linked to life-history, but data said otherwise. Moreover, melanin patterning is genetically independent of valkea. OTOH, the melanin locus associates with male behaviour. #ESEB2025

Mappes’s favorite model is the wood tiger moth Arctia plantaginis. Among males, yellow morphs protect better against predators but white morphs have more reproductive success.
No supergene, but white morphs have duplication of yellow-e gene, named in Finish valkea (poetic word for white) by non-Finish postdoc. #ESEB2025

Mappes’s favorite model is the wood tiger moth Arctia plantaginis. Among males, yellow morphs protect better against predators but white morphs have more reproductive success.
No supergene, but white morphs have duplication of yellow-e gene, named in Finish valkea (poetic word for white) by non-Finish postdoc. #ESEB2025

Last keynote #ESEB2025 Johanna Mappes: animal coloration has many roles. Aposematism: don’t eat me! Positive frequency-dependent selection is expected to eliminate variation in colour of toxic animals, yet we still see a lot of polymorphism and even distinct colour morphs.

Last keynote #ESEB2025 Johanna Mappes: animal coloration has many roles. Aposematism: don’t eat me! Positive frequency-dependent selection is expected to eliminate variation in colour of toxic animals, yet we still see a lot of polymorphism and even distinct colour morphs.

My small contribution to the popularization of evolutionary biology during the #ESEB2025 week, thanks to this article on the evolution of roses during the 19th in The Conversation France.

If you read French, here it is: https://theconversation.com/comment-le-croisement-des-roses-dorient-et-doccident-au-xix-siecle-a-totalement-change-nos-jardins-263157

If not, see our Genetics paper (& PCI Evol Biol recommendation): https://doi.org/10.1093/genetics/iyaf163 (and/or https://evolbiol.peercommunityin.org/articles/rec?id=793 )

For #ESEB2025 we're sharing just a few of the many open datasets published on Dryad through our partnership with the society. Next up is...

Data and R Script from: "The ancestor of sharks and rays laid eggs, but ancestral state reconstructions need empirically supported traits and transparent reporting" from researchers Daniel Hughes & Daniel Blackburn

DATA: bit.ly/4oQ78Pi
ARTICLE: bit.ly/3JnElkJ

#biology #evolutionarybiology #opendata #openaccess #shark #reproduction #genetics

Sadier: linking developmental trajectories with transcriptomes from dissected developing teeth, contrasting bats to mouse (model org). Conserved core of highly genes with expression conserved among bats and with mouse. Evolutionary divergent genes differ among bats and with mouse.
Specific gene expression patterns confirms heterochrony. Hello EDA! (classical tooth dev gene).
“When you eat a lot of sugar, you want to avoid cavities” (nectar eating bats)
#EvoDevo #ESEB2025

Sadier: linking developmental trajectories with transcriptomes from dissected developing teeth, contrasting bats to mouse (model org). Conserved core of highly genes with expression conserved among bats and with mouse. Evolutionary divergent genes differ among bats and with mouse.
Specific gene expression patterns confirms heterochrony. Hello EDA! (classical tooth dev gene).
“When you eat a lot of sugar, you want to avoid cavities” (nectar eating bats)
#EvoDevo #ESEB2025

Sadier: bat molars develop through two distinct developmental trajectories: most bats are along a common constrained axis of variation, moving along it by heterochrony, while short-faced bats break this constraint #ESEB2025 #EvoDevo

Sadier: bat molars develop through two distinct developmental trajectories: most bats are along a common constrained axis of variation, moving along it by heterochrony, while short-faced bats break this constraint #ESEB2025 #EvoDevo

With this the symposium on mechanisms of adaptation to changing conditions in microorganisms 🥵🦠🧬 is over. All talks were really interesting with great speakers.

I am also concluding my live posts. One day was more than enough for me, not sure where @marcrr gets the focus and energy to do this all week 😮‍💨

#ESEB2025

With this the symposium on mechanisms of adaptation to changing conditions in microorganisms 🥵🦠🧬 is over. All talks were really interesting with great speakers.

I am also concluding my live posts. One day was more than enough for me, not sure where @marcrr gets the focus and energy to do this all week 😮‍💨

#ESEB2025

Sadier: identifying conserved and variable traits of first lower molar in bats allows to identify convergence https://doi.org/10.1016/j.cub.2024.02.027 #ESEB2025

Sadier: identifying conserved and variable traits of first lower molar in bats allows to identify convergence https://doi.org/10.1016/j.cub.2024.02.027 #ESEB2025

Alexa Sadier: bat teeth allow us to study how constraints influence trait evolution and diversification. Teeth are very diverse despite strong developmental constraints et conserved patterning and regulatory genes. Bats cover most mammalian dietary niches and diverse crania-facial shapes (as discussed yesterday).
“We have the bats, we have the genomes, we have everything.”
#ESEB2025

Alexa Sadier: bat teeth allow us to study how constraints influence trait evolution and diversification. Teeth are very diverse despite strong developmental constraints et conserved patterning and regulatory genes. Bats cover most mammalian dietary niches and diverse crania-facial shapes (as discussed yesterday).
“We have the bats, we have the genomes, we have everything.”
#ESEB2025

Missimo Amicone from the University of Lausanne talks about resistance evolution in microbial communities. The frequency of evolutionary rescue from antimicrobials in a two-species system usually differs from the respective monocultures. In a polymicrobial UTI model, only three isolates lead to increased chance of rescue, with the direct metabolic interaction of the two partners likely explaining the effect.

#ESEB2025

David Liberles: 2 whole genome duplications in salmonids?
Method to evaluate duplicate gene retention: https://link.springer.com/article/10.1186/s12859-022-05042-w
Is retention independent between the two genome duplications? (Most of the literature says: not independent)
Unexpected result: some genes retained by first duplication are less likely to be retained by 2nd. Interpretation: retention by sub- or neofunctionalisation lowers probability of being further retained (less function space?).
#ESEB2025

Ricardo Léon-Sampedro from ETH Zurich @usyseth talks about invasion of E. coli into human gut microbiomes. While antibiotics were not necessary for successful invasion, they influenced how the species composition changed after invasion.

#ESEB2025

Russ Jasper from the University of Bern talks about local adaptation of the gut microbiome to the cecum and rectum. Despite the connectedness of the habitats and the high migration rates, he finds 10 SNPs across 20 species that indicate local adaptation. One particular region shows signs of high rates of horizontal gene transfer.

https://doi.org/10.1101/2025.06.06.658271

#ESEB2025

With such data Morales Garcia doesn’t need to restrict to orthologs, and also uses complete genome alignments for phylogeny. Yet Yangochiroptera remains difficult to resolve, maybe due to ancestral introgression. #ESEB2025

Next up is Nan Ye from Kiel University with a talk about heteroresistance, an intermediate phenotype between antimicrobial resistance and susceptibility. An evolution experiment revealed that under fluctuating conditions the frequency of heteroresistance increases because of it's overall fitness advantage.

#ESEB2025

Ariadna Esthela Morales Garcia: bats are super cool, but their phylogeny is hard to resolve. Now we have >100 full genomes, from Bat1k project. 🦇 #ESEB2025

Paps:
Classical phylogenomics with 14k genes: long branch attraction by default, can be removed (remove fast genes, minimise noise, or minimise paralogy).
Conclusion: Xenacoelomorpha as sister to all Bilateria
https://www.researchsquare.com/article/rs-5529390/v1
#ESEB2025

Jordi Paps: acoel flatworms to help distinguish the hypotheses of complex vs simple Urbilaterian. Problem: most deep animal “phylogenomics” is based on transcriptomics, which is biased. Instead, use only complete genomes (91 species) and incorporate genome-level processes into analysis.
Presence / absence of genes recovers excellent phylogeny, no apparent long branch attraction.
Duplication, transfers, losses: long branch attraction is rife by default; filtering data provides OK tree.
#ESEB2025

Mathilde Barthe proposes a revision of sloth species, and finds evidence of gene flow using @GaltierNicolas ’s Aphid method
Her work on armadillo: https://doi.org/10.1093/sysbio/syae027
#ESEB2025