academic.oup.com/mbe/advance-...

Happy to share this one. We investigated the #phylogenetic placement and #genome_evolution of Pangui/Njordarchaea-unique #Asgardarchaea that might have undergone genome reduction...

Check out this beautiful work led by @stephkoe.bsky.social, with great teamwork from @danieltamarit.bsky.social and @ettema.bsky.social :
💻 github.com/stephkoest/w...
📄 doi.org/10.1101/2025.07.14.663642

🧂The placement of halophilic lineages was restored — Methanonatronarchaeia emerged outside Halobacteria, supporting independent origins of halophily
(in agreement with targeted analyses: doi.org/10.1038/s415... &
doi.org/10.1038/s415...)

🧩 Phyla representing the clades Acherontia and Stygia (Methanobacteriota_B + Hadarchaeota) shifted to sister TACK + Asgardarchaeota — consistent with site-heterogeneous models (doi.org/10.1186/s128...).

Among the topological improvements:

🔥Thermophilic clades (e.g. JANJXX01, DRAE01, Korarchaeia) were repositioned in line with recent phylogenomic studies (doi.org/10.1038/s415... &
doi.org/10.1101/2025...).

→ The number of biased taxa dropped from 95.1% to just 2.3%
→ Pruning automatically stopped once further trimming risked loss of phylogenetic signal

Discrepancy between observed and expected amino acid frequencies in taxa:

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

Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes.

🔗: doi.org/10.1016/j.ce...

#Genomics #Evolution #CellBiology #LECA

Our review on how thermophilic carbon monoxide(!)-eating microbes can aid the transition to renewable carbon-based products.

#Asgard,#phylogeny
1/ 🧵 Does MAGs contamination affect the placement of Njord as suggested by Zhang et al, 2025? www.nature.com/articles/s41...
Our updated analysis suggests instead... www.biorxiv.org/content/10.1...

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

Excited to share our recent work on the evolution of ectomycorrhizal plants! 🌳 🧬 🖥️
doi.org/10.1111/nph.70054

With: Yvet Boele, @puginiercamille.bsky.social, @mbianc.bsky.social, Cyril Libourel, @maximebonhomme.bsky.social, @kellerjeanphd.bsky.social, @pierremarcdelaux.bsky.social

A thread: (1/5)

Exciting news! I'm looking for a computational biologist to join my lab at Wageningen University & Research! It's a 3-year postdoc position on Holomycota genome architecture and evolution. Spread the word! www.wur.nl/en/vacancy/p...

Not new here but will become more active at @bsky.app (I am no longer active on X)

Follow me to hear more about the wonderful world of microbes (evolution, archaea, symbiosis, new microbes, ...). Expect occasional rants about academia, 🇳🇱 politics, life, etc.

My research group: go.bsky.app/MzZPftE