Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺

#OnThisDay in 1938, American evolutionary biologist Lynn Margulis was born. Margulis is most known for developing and popularising the endosymbiotic theory, which explains how eukaryotic cells evolved organelles from simpler prokaryotic organisms that resided within another and became incorporated.

Read our review about the "Diversity, ecology, cell biology and evolution of the Asgard archaea" in @natrevmicro.nature.com here: www.nature.com/articles/s41...

By @kassipan.bsky.social @stephkoe.bsky.social @micropat.bsky.social & @gerbenz.bsky.social

Also big thanks to @danieltamarit.bsky.social! See more elaborate post by @stephkoe.bsky.social here: bsky.app/profile/step...

Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling - Nature Microbiology A structural catalogue of the Asgard archaeal pangenome reveals hundreds of eukaryotic-like proteins that suggest a higher degree of cellular complexity in the archaeal ancestor of eukaryotes.

🧵 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! 🎉

How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us — so we used protein structure prediction to look deeper. 🧬
www.nature.com/articles/s41...

Thanks to @archaeal.bsky.social @katyappler.bsky.social @valdeanda.bsky.social for providing prior excess to Asgard metagenome data.

Using extensive protein structure modelling and
sequence similarity detection across an expanded Asgard archaeal genomic dataset to build a structural catalogue of the Asgard archaeal pangenome. Within this dataset we identified many new structural/isomorphic eukaryotic signature proteins (ESPs).

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...

Have a novel protist's genome or transcriptome and want to predict it's mitochondrial proteome? Look no further than CoMR, this handy bioinformatic workflow to help you: www.biorxiv.org/content/10.6... #phylogenetics

An AI Agent Published a Hit Piece on Me Summary: An AI agent of unknown ownership autonomously wrote and published a personalized hit piece about me after I rejected its code, attempting to damage my reputation and shame me into acceptin…

AI agent goes nuts on open source maintainer after having its pull request denied. This is a pretty insane story. Open source development as we've been used to for the last few decades is likely over. 1/
theshamblog.com/an-ai-agent-...

EMBO Press co-evolves with molecular ecology and evolutionary biology - The EMBO Journal The EMBO Journal - Molecular ecology and evolution are central to understanding how biological systems function, interact, and diversify. A special issue of this journal reflects the growing...

Read how @embopress.org is expanding its focus on molecular ecology and evolution as central underpinnings of functions/interactions/diversification of biological systems – by @yehumoran.bsky.social, @berndpulverer.bsky.social, and our new team of Editorial Advisors
link.springer.com/article/10.1...

This local Wolfdog joined an Olympic ski event and triggered the finish-line camera. This is Nazgul. He snuck into a cross-country skiing sprint this morning and raced the homestretch with some competitors before being escorted home. 14/10 someone get him a medal

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...

Tijd dat universiteiten een nieuw promotiestelsel krijgen Vandaag is de landelijke studiedag promovendibeleid hier in Utrecht. Hoogleraar Erik van Sebille mocht er vanochtend een column uitspreken waarin hij zich afvraagt of het huidige promotietraject niet ...

Oei.. dat was idd wel handig geweest... hier is ie: dub.uu.nl/nl/opinie/ti...

Tijd dat universiteiten een nieuw promotiestelsel krijgen Vandaag is de landelijke studiedag promovendibeleid hier in Utrecht. Hoogleraar Erik van Sebille mocht er vanochtend een column uitspreken waarin hij zich afvraagt of het huidige promotietraject niet ...

dub.uu.nl/nl/opinie/ti...

Abstract deadline of February 27 is quickly approaching. Registration for the meeting is limited to 120 partipants with presenters (poster or talk) being given priority. So submit an abstract to secure your spot! comparativegenomics2026.com

All inclusive registration (hotel+3 meals)

Thanks to everyone involved since this project started in 2016, in particular Jan Löwe & team, @danieltamarit.bsky.social @stephkoe.bsky.social @julianvosseberg.bsky.social @jennahed.bsky.social @archaeal.bsky.social @brendanburns999.bsky.social @tbharat-lab.bsky.social & those not on BlueSky

Our latest preprint: Together with the team of Jan Löwe, @danieltamarit.bsky.social and many others we discovered and characterized several Asgard tubulin genes and propose that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis
www.biorxiv.org/content/10.6...

Hamer + Spijker. Tijd voor verandering van de PhD stelsel op Nederlandse Universiteiten. Lees dit opiniestuk van @erikvansebille.bsky.social in het Digitaal Universiteitsblad van @utrechtuniversity.bsky.social

How specific are heritable symbioses?

And what can we learn from swapping obligate symbionts across host species?

We address this in our latest, led by @inespons.bsky.social & in our collaboration w/ @microbiome.bsky.social 🦠🪲 Out today in @natcomms.nature.com!

1/n
www.nature.com/articles/s41...

I'm happy to share our new review with @lau-co89.bsky.social @liigh-unam.bsky.social just published in @genomebiolevol.bsky.social

Recent microbial evolutionary insights from metagenomics
academic.oup.com/gbe/advance-...

Inspired by the session "Molecular evolution through metagenomics" at #SMBE24

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

Bluesky Map Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.

I made a map of 3.4 million Bluesky users - see if you can find yourself!

bluesky-map.theo.io

I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail

The visualization of two bacterial genomes, of 50 and 52kb, representing independent instances of extreme genomic reduction in ancient heritable endosymbionts of planthoppers.

Our new paper in @natcomms.nature.com is now online-early!

We describe independent evolution of bacterial genomes of only ~50–52 kb — the smallest known outside cellular organelles — revealing striking convergence toward minimal gene sets.

🔗 doi.org/10.1038/s414...

Thanks to @lauraeme.bsky.social and @danieltamarit.bsky.social for performing the re-analyses of the corrected datasets.

Non pay-walled version of the Correction Notice can be found here: rdcu.be/e3wMO

Importantly, while we observe small variations in statistical support, the overall trends support that eukaryotes are placed within Heimdallarchaeia, as sister-group to the order Hodarchaeales when both SR4-recoding and FSR treatments were combined - as was reported in the original paper.

We have therefore removed these redundant markers from the dataset, and subjected the resulting dataset of 54 non-redundant markers, and used the same methodology to re-run all phylogenomic analyses presented in the paper.

In our paper we used a phylogenomic dataset of 57 markers to study of the evolutionary relationship between eukaryotes and Asgard archaea. After the publication of our study, we noticed that three of these markers (M127, M028, & MA54) were partially redundant, as they belong to paralogous families.

Today we published a Correction on our 2023 @nature.com paper reporting the heimdallarchaeial ancestry of eukaryotes: www.nature.com/articles/s41...

Corrected paper: www.nature.com/articles/s41...

Importantly, the re-analyses of the corrected dataset are consistent with the original findings.

Full Professor and Chair Laboratory of Biophysics We are looking for a Full Professor in the Biophysics chair group, part of Wageningen University & Research (WUR)

www.wur.nl/en/vacancy/f...

Become our new colleague (and next door neighbor) and lead a chair/group/department of Biophysics at Wageningen University. Reach out to me for info and please spread!!!