Fabian van Beveren

Fungal symbioses: A multiplicity of fungi in the lichen union Increasing evidence suggests that lichens are not just a partnership between one fungus and one alga or cyanobacterium but may contain multiple intera…

Thrilled to see this published! 😄
Our dispatch examines potential additional fungal symbionts in lichen partnerships and the key challenges in unraveling their biology.

Thanks for involving me in this @talbotlabtsl.bsky.social

@currentbiology.bsky.social

www.sciencedirect.com/science/arti...

Diversity, ecology, cell biology and evolution of the Asgard archaea - Nature Reviews Microbiology The Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of th...

Just over ten years after the discovery of the first Asgard archaeal genomes, we revisit the rapid expansion of this remarkable archaeal lineage. From diverse genomes and metabolisms to eukaryotic signature proteins and the first cultured representatives.
www.nature.com/articles/s41...

Finally out in @natmicrobiol.nature.com: Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling. Great work by @stephkoe.bsky.social @kassipan.bsky.social @jvhooff.bsky.social

www.nature.com/articles/s41...

1/ ✨ New preprint alert ✨

It is my pleasure to share:
"Stepwise evolution of the developmental and symbiotic functions of DELLA in land plants"

Here we investigated the role of the single GRAS transcription factor DELLA in #MyMarchantia

doi.org/10.64898/202...

#PlantScience
A thread...

Finally out in @nature.com: a new piece of the puzzle of how complex life evolved. Lead by @archaeal.bsky.social & @katyappler.bsky.social. Great collab with @greening.bsky.social and @kassipan.bsky.social. More pieces to follow soon! www.nature.com/articles/s41...

Two more weeks to apply - come join us () in The Netherlands as a postdoctoral researcher on large-scale metagenomic exploration of new lineages!

1/9 Our latest paper on immunity mechanisms in Marchantia just out @pnas.org ! 🔽

Close collaboration between our former PhD students @karimaelm.bsky.social and @chloe-beaulieu.bsky.social !

and the old gard @jacquet-chris.bsky.social @maximebonhomme.bsky.social

www.pnas.org/doi/10.1073/...

dplyr 1.2.0 dplyr 1.2.0 fills in some important gaps in dplyr's API: we've added a new complement to `filter()` focused on dropping rows, and we've expanded the `case_when()` family with three new recoding and re...

dplyr 1.2.0 is out now and we are SO excited!

- `filter_out()` for dropping rows

- `recode_values()`, `replace_values()`, and `replace_when()` that join `case_when()` as a complete family of recoding/replacing tools

These are huge quality of life wins for #rstats!

tidyverse.org/blog/2026/02...

A novel pathosystem between Aeschynomene evenia and Aphanomyces euteiches reveals new immune components in quantitative legume root-rot resistance. Legumes are pivotal for sustainable agriculture, yet their productivity is hindered by soilborne pathogens such as Aphanomyces euteiches . This study introduces Aeschynomene evenia as a novel model to...

🚨 New preprint alert! 🚨
Excited to share my first preprint from my PhD! 🎉
We introduce a novel Aeschynomene evenia – Aphanomyces euteiches pathosystem to explore links between quantitative resistance and symbiosis in legumes. 🌱🔬
🧾 www.biorxiv.org/cgi/content/...

🧵 Thread:

1/9

Come join our group in the beautiful (currently very snowy) Wageningen!

A Cell So Minimal That It Challenges Definitions of Life | Quanta Magazine The newly described microbe represents a world of parasitic, intercellular biodiversity only beginning to be revealed by genome sequencing.

A newly discovered archaeal cell has a tiny genome and can’t metabolize biomolecules. It’s upending biologists’ definition of a living thing. “These types of organisms have been found before, but not as extreme as this,” said microbiologist Thijs Ettema.

Huge honor to receive this price! Glad to see the lichen research rewarded with such a distinction
Thanks @pierremarcdelaux.bsky.social and @kellerjeanphd.bsky.social for your SUPERvision ✨

Merci @academiesciences.bsky.social pour cette opportunité et cette belle cérémonie!

Amazing!! Congratulations :)

Postdoc (m/f/d) in Endosymbiosis Research

📢Postdoc position available!🧪🧫🧬
Our group is seeking a motivated researcher to investigate the molecular mechanisms driving host–endosymbiont interactions.
Full details & application: karriere.hhu.de//index.php?a....
Please help us get the word out!

Diversity and spread of cytoplasmic incompatibility genes among maternally inherited symbionts Author summary Cytoplasmic incompatibility (CI) is a reproductive strategy used by certain bacteria to promote their spread within arthropod populations. These bacteria, inherited through the mother, ...

Diversity and spread of #cytoplasmicIncompatibility genes among maternally inherited #symbionts

#SymbioSky

doi.org/10.1371/jour...

Mechanisms, Detection, and Impact of Horizontal Gene Transfer in Plant Functional Evolution Abstract. Horizontal gene transfers (HGT) have been observed across the tree of life. While their adaptive importance in bacteria is conspicuous, the occur

So excited to see our review on how to detect horizontal gene transfers and their impact on plant functional evolution finally published in @theplantcell.bsky.social!
Great teamwork between @lrsv-toulouse.bsky.social and LGDP-Perpignan 😎🥳🌱
academic.oup.com/plcell/advan...

New paper is out! We have studied the cute tiny Discocelia plataet sp. n. to obtain the first molecular data of the order Discocelida and clarify its cell structure. All this for a better understanding of the evolution of Cercozoa.

onlinelibrary.wiley.com/doi/epdf/10....

I gave a symposium talk at the European Society for Evolutionary Biology 2025 (#eseb2025) meeting last week and this was my title slide showcasing how I was speaking as an independent scientist because @dalhousieu.bsky.social @dalhousie.bsky.social has locked us out.

WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...

1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...

Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.

The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky

String manipulation is a critical daily task for bioinformaticians.
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats

No, AlphaFold has not completely solved protein folding Biology is hard. Yes, even for AI.

AlphaFold is great, but contrary to public opinion it has not completely solved the protein folding problem. Much work remains to be done.
clauswilke.substack.com/p/no-alphafo...

Microbe with bizarrely tiny genome may be evolving into a virus With DNA focused almost entirely on replication, newly discovered organism blurs the line between cells and viruses

𝗠𝗶𝗰𝗿𝗼𝗯𝗲 𝘄𝗶𝘁𝗵 𝗯𝗶𝘇𝗮𝗿𝗿𝗲𝗹𝘆 𝘁𝗶𝗻𝘆 𝗴𝗲𝗻𝗼𝗺𝗲 𝗺𝗮𝘆 𝗯𝗲 𝗲𝘃𝗼𝗹𝘃𝗶𝗻𝗴 𝗶𝗻𝘁𝗼 𝗮 𝘃𝗶𝗿𝘂𝘀
or maybe not. a 🧵

roland @environmicrobio.bsky.social‬ ‪and Krzysztof @ktjurdzinski.bsky.social‬ already commented, please also read their posts.
www.science.org/content/arti...
#MicroSky #SymbioSky #ProtistsOnSky

New vacancy in my team!

PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.

Please repost and share with talented MSc students in #evobio, bioinformatics or related :)

www.uu.nl/en/organisat...

#MEvoSky #MicroSky

Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls - Nature Plants New fern transcriptomes reveal repeated whole-genome duplications, unique gene families and distinct lignocellulosic evolution, providing a comprehensive database that underscores the ancient divergen...

A fantastic resource for fern biology @natplants.nature.com 🔽!

www.nature.com/articles/s41...

Taking about ferns, are you interested by their immune system? Have a look at our recent preprint by @baptistebio.bsky.social @jacquet-chris.bsky.social 🔽

www.biorxiv.org/content/10.1...

Sounds very cool, excited to have a look!

Angomonas deanei with flourescent-labeled nucleus and endosymbiont. ETP9 localizes at the endosymbiont division site.

Out today: Exciting intermediate between endosymbiont and organelle identified! Endosymbionts in Angomonas deanei lost nearly all bacterial cell division genes. Instead, we identified a host-encoded protein, ETP9, that became specialized for endosymbiont division. 1/2
www.science.org/doi/10.1126/...

Exploring fern pathosystems and immune receptors to bridge gaps in plant immunity Land plants include angiosperms, bryophytes, lycophytes and ferns, each of which may deploy distinct strategies to resist pathogens. Here, we investigate fern-pathogen interactions by characterizing n...

🔗 Preprint alert: www.biorxiv.org/content/10.1...

🧵 New insights into plant immunity: using ferns to understand evolution! 🌱✨🌿

Excited to share my first (but not last) published research at @lrsv-toulouse.bsky.social. A THREAD … [1/9]

Similar to these ECM plants, I also adapted to new symbiotic partners at the @lrsv-toulouse.bsky.social and I’m happy we’ve been able to do cool science together! 🙌

In our study, the included ECM-only species have retained most of these genes, but what role they play in different ECM lineages remains an open question!

For the full story, see our letter in @newphyt.bsky.social!

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