DEEMteam_Orsay

Call for a group leader in Evolutionary Biology The IGFL @igflyon.bsky.social in Lyon, France, is recruiting a group leader in Evolutionary Biology. An exciting place for exploring the interfaces of evolution with physiology and development. #EvolBiol #ecoevo #evodevo tinyurl.com/evolbiol

We are updating our Expansion Microscopy (U-ExM) website with : - Protocols tips to help you get started - Examples of applications across different biological systems. - work in progress - an antibody database 👉 mocel.unige.ch/research-gro...

How do redox conditions in an Asgard archaea-rich environment determine their vertical distribution? Find out in our latest paper about the amazing Catherine crater lake microbial mat: www.nature.com/articles/s41...

Now published :) doi.org/10.1093/bib/... and available here github.com/theLabUpstai...

Databases may contain lots of misannotated 16S rRNA sequences, which can hinder accurate taxonomic assignment in metabarcoding and metagenomic analyses. We have addressed this issue for Asgard archaea and generated a curated set of high-quality 16S rRNA sequences: academic.oup.com/ismecommun/a...

My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore.

Ana Gutiérrez-Preciado talking about the microbial communities inhabiting the colorful, arsenic-rich extreme Amuyo Lagoons in northern Chile. #ISSOL2026 #Origins2026

Puri talking about the origin of eukaryotes at the Origins 2026 meeting of the International Society for the Study of the Origins of Life in Paris #ISSOL #Origins2026

Talks and posters by DEEM team members at #SMBE2026: Archaea, eukaryotes, and phylogeny methods.

A few hours before the kickoff of #SMBE2026, visiting Grundtvig's Church, a rare example of Expressionist architecture in Copenhagen.

In our latest paper with @kristina-prokina.bsky.social, we describe many new species of Developea, a poorly-known group of Stramenopiles: www.sciencedirect.com/science/arti...

We have contributed to two recent opinion papers, one on the overwhelming burden of unnecessary bureaucracy in science and the other on the role that professional academies can play in addressing current societal challenges: shorturl.at/iy5JM shorturl.at/gd2X7

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

Our thoughts on the recent article by Edu Ocaña-Pallares on the evolution of osmotrophic eukaryotes, just published in NEE: Reversal to osmotrophy in eukaryotes www.nature.com/articles/s41... www.nature.com/articles/s41...

1/ Our new paper in Systematic Biology "Modeling Site-and-Branch-Heterogeneity with GFmix" led by @cgpmcc.bsky.social describes improved ways to model compositional heterogeneity across both sites and branches—an important source of error in deep phylogenomics. doi.org/10.1093/sysb...

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

In our latest study, we show that HGT of the ccyA gene from cyanobacteria enables some methanotrophic Methylococcaceae gammaproteobacteria to synthesize intracellular amorphous calcium carbonate (iACC) inclusions. enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

With @animalculum.bsky.social, we have studied the phylogeny of cryptophyte nucleomorphs within an enriched dataset of red algae. Surprisingly, they seem to be related to Cyanidiophytina. The origin of red secondary plastids remains an open question! nph.onlinelibrary.wiley.com/doi/10.1111/...

Latest output of the European Academy of Microbiology Task Force on Predatory Publishing Practices, initiated and steered by Stipan Jonjić and Ceren Karahan: Fragile Research Systems, Brain Drain, and Predatory Publishing in Under-resourced Countries url: academic.oup.com/microlife/ar...

We have just published a short note on archaeal phylogeny: complex mixture models support a deep placement of Methanonatronarchaeia within Euryarchaea and indicate that three recently described groups (Halorutilales, Afararchaeaceae, and Ordosarchaeia) are actually the same. shorturl.at/5GMpU

Redox distribution of Asgard archaea and co-occurring taxa in microbial mats from an early Proterozoic ecosystem analog | bioRxiv https://www.biorxiv.org/content/10.64898/2026.03.20.713109v1?rss=1

So you are using IQ-TREE to estimate a tree for "deep time" phylogenetics using amino acid alignments. There is a lot of confusion about how to test model fit. Here are some suggestions.

Living patescibacterial (CPR) cells are a rare sight! Meet Strigamonas methylophilicida, a parasite of methylotrophic proteobacteria we just described in our latest paper: doi.org/10.1128/mbio...

Interested in microbial proteins and their diversity? 🖥️🧬🦠 We have recently released the Amino Acid Sequence Toolkit (AASTK). AASTK is designed to work with the GlobDB to create and work with datasets of protein sequences. AASTK currently consists of 4 tools: - CASM - PASR - CUGO - Meta 1/

I am happy to share the unfinished but nevertheless fascinating autobiography of the late Thomas Cavalier-Smith, written in 2020, shortly before Tom passed away in 2021. I thank Ema Cavalier-Smith for sharing the text with me. I recently finished curating […] [Original post on biologists.social]

Before he passed away in 2021, Tom Cavalier-Smith had drafted parts of his autobiography. It's now 'published' because Gáspár Jékely put a lot of effort in! Please enjoy and share: doi.org/10.5281/zeno...

OrthoSNAP v1.6.0 is out. If you process large phylogenomic datasets, this release is built for your workflow. (1/3)

We are happy to welcome Xianzhe Gong to the team! His expertise in microbial metabolism and related fields will help us better characterize our collection of MAGs and cultured organisms from many different environments.

Playing with a new toy to study our favorite microbial mats.

Puri talking at the "Cell biology of eukaryogenesis" meeting organized by the @sbcf.bsky.social

First sampling of the year in a sunlit Parisian forest.

2026 kicks off with new faces in the lab! We’re excited to welcome Dina Boukheloua, Eliott Tempez, and Pierre van Ettro, who will be working on endosymbionts in protists, archaeal genome evolution, and aquatic amoeba diversity. Welcome to the team!

With our old friends Sergey, Luis and Guifré, we have published a minireview in @currentbiology.bsky.social about aphelids, the sister group to fungi, including why we think they are not fungi but, nevertheless, key to understand early fungal evolution. authors.elsevier.com/a/1mH793QW8S...

Near the end of the year, we are excited to welcome three new members to the team: Inés Ochoa (PhD student), and Charley McCarthy and Eva Zanditenas (postdocs). They will work on different projects using experimental and bioinformatics approaches.

Microbial eukaryotes keep challenging assumptions about eukaryotic cell and genome biology. Our upcoming workshop explores the frontier of protist genomics and how it shapes cell biology, ecology and evolution. Please save the date! Talks, posters and ECR events Websites and details coming soon

SMBE2026 Symposium 12 | Reconstructing the deep Tree of Life: challenges and new approaches 📨 Abstract submission smbe2026.org/abstracts 📋 Programme details smbe2026.org/programme #SMBE2026

Those interested in performing maximum likelihood phylogenomic analysis on data sets made up of eukaryotic nuclear genes using site heterogeneous mixture models like C60, I suggest you use the ELM model in IQ-TREE instead of the LG model /1

Discussing the origin and evolution of life in an ancient church during the meeting of the French Astrobiology Society

According to the microbial ecologist Puri López-García, pictured here at a salt flat in the Chilean Andes, some 25% to 50% of all bacterial cells may be parasites of other cells.

Bernabeu, @microbiobits.bsky.social and @tonigabaldon.bsky.social use simulations to test for the robustness of inferred relative timings of gene transfers in the lineage leading to the ancestor of eukaryotes 🔗 doi.org/10.1093/gbe/evaf190 #genome #evolution

Dive into our November issue featuring: 🪆nested archaeal symbioses 🌱microbiota driven drought responses in plants 🏗️ BAM complex in Bacteroidota 💨microbial fermentative growth in the gut 🍸hospital-specific phage therapy cocktail and much more..! www.nature.com/nmicrobiol/v...

This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com rdcu.be/eLtCH

How did life begin, and why does it matter? Scientists are tracing early microbial life–from LUCA to multicellularity–to unlock insights for biotech, climate science and even space exploration. Read the article: asm.org/articles/202...

Mesquite 4.02 update released! It fixes a few bugs and adds Codon Alignment and various other improvements. Also, much faster with genomics files with 1000s of loci. www.mesquiteproject.org 🧪 #evolbio @bembidion.bsky.social

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years. academic.oup.com/nar/advance-...

Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions Out now in Nature Microbiology, by Yifan Zhou, Mart Krupovic & colleagues. @mkrupovic.bsky.social @yifanzhou.bsky.social @deemteam.bsky.social www.nature.com/articles/s41...

A nice N&V article by Mike Dyall-Smith on our recent paper ( www.nature.com/articles/s41... ): www.nature.com/articles/s41...

Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov Free access link: rdcu.be/eLtCH 🧵 by @yifanzhou.bsky.social 👇

A proposal for journal accreditation systems to counter predatory practices. If funding agencies enforced these accreditations, predatory journals would quickly vanish. doi.org/10.1093/fems...

Ponce-Toledo et al. confirm the presence, homology, and monophyletic origin of the SELMA protein complex in Cryptophyta, Alveolata, Stramenopiles, and Haptophyta, shedding light on the evolution of photosynthetic eukaryotes. 🔗 doi.org/10.1093/molbev/msaf167 #evobio #molbio