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Molecular Biology and Evolution @molbioevol.bsky.social · Sep 8

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

Molecular Phylogeny of the SELMA Translocation Machinery Recounts the Evolution of Complex Photosynthetic Eukaryotes

Abstract. Photosynthetic eukaryotes and their relatives are the result of an intricate evolutionary history involving a series of plastid acquisitions thro

doi.org

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DEEMteam_Orsay @deemteam.bsky.social · Aug 31

Enjoying the mountains that forams built for us (with some help from plate tectonics) long ago.

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DEEMteam_Orsay @deemteam.bsky.social · Aug 26

Thank you very much for teaching her this amazing technique!

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Kristina Prokina @kristina-prokina.bsky.social · Aug 26

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....

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Michael Kuhn @biocs.bsky.social · Aug 15

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7

#microsky

Metalog

Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.

metalog.embl.de

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DEEMteam_Orsay @deemteam.bsky.social · Aug 14

Congratulations!

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Andrew Roger @andrewjroger.bsky.social · Aug 12

Our paper describing our new improved GFmix models for phylogenetic inference that capture site-and-branch heterogeneity in amino acid composition.
www.biorxiv.org/content/10.1...

Modeling site-and-branch-heterogeneity with GFmix

Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino acid sequences may be heterogeneous across both sites an...

www.biorxiv.org

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DEEMteam_Orsay @deemteam.bsky.social · Aug 7

In our ongoing saga of description of new protists, we are happy to introduce Multisulcus malaysiensis, a deep-branching heterolobosean that forms highly unusual multiflagellated cells with multiple ventral grooves. Great work by @kristina-prokina.bsky.social

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

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DEEMteam_Orsay @deemteam.bsky.social · Aug 4

Gloeomargarita lithophora, it has many interesting metabolic and evolutionary stories to tell.

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DEEMteam_Orsay @deemteam.bsky.social · Jul 27

This could have been avoided if Science had requested a second round of reviews when the deluge of criticisms arrived following the paper’s pre-publication. Publishing it along with all the criticisms, and then retracting it now -and only this paper- after so many years, seems odd.

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Matthew Cobb @matthewcobb.bsky.social · Jun 26

Just learned that Frank Stahl (of the Meselson and Stahl DNA replication experiment ("the most beautiful experiment in biology") died at the beginning of April, to no fanfare. Here's a lovely video of them reminiscing: www.youtube.com/watch?v=7-tn...

The Most Beautiful Experiment: Meselson and Stahl

YouTube video by Science Communication Lab

www.youtube.com

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Ben J Woodcroft @benjwoodcroft.bsky.social · Jul 16

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

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DEEMteam_Orsay @deemteam.bsky.social · Jul 23

Check out our paper to explore how the evolutionary history of SELMA supports or challenges various hypotheses on the origin of red complex plastids.

academic.oup.com/mbe/article/...

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DEEMteam_Orsay @deemteam.bsky.social · Jul 23

🚨 Fresh off the press! We have just published our paper on the evolution of the SELMA translocon of red secondary plastids‬. We analyze the phylogeny of each individual protein and the implications for the evolutionary history of the entire complex.

academic.oup.com/mbe/article/...

Molecular phylogeny of the SELMA translocation machinery recounts the evolution of complex photosynthetic eukaryotes

Abstract. Photosynthetic eukaryotes and their relatives are the result of an intricate evolutionary history involving a series of plastid acquisitions thro

academic.oup.com

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DEEMteam_Orsay @deemteam.bsky.social · Jul 15

Some ceramic protists from our talented friend Anabel López-Archilla. Do you recognize them?

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Université Paris-Saclay @univparissaclay.bsky.social · Jul 10

Partez à la quête des origines de la vie avec Puri Lopez-Garcia, naturaliste du monde microbien !
Puri López-García est chercheuse en biologie et directrice de recherche @cnrs.fr au laboratoire Écologie, société et évolution (ESE - Univ. Paris-Saclay/CNRS/AgroParisTech).

🔗 tinyurl.com/2cm7zn27

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DEEMteam_Orsay @deemteam.bsky.social · Jul 9

Joachim Hämmerling experiments in the 50’s using giant unicellular algae (Acetabularia) to demonstrate that the genetic information is contained in the nucleus.

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

Nucleo-cytoplasmic Relationships in the Development of Acetabularia

The Acetabulariae are green marine algae of subtropical and tropical waters (class Siphonocladales, family Dasycladaceae, subfamily Acetabulariae). Th…

www.sciencedirect.com

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Nature Reviews Earth & Environment @natrevearthenviron.nature.com · Jul 3

New online! Using anaerobic cultivation chambers to decipher geomicrobiological processes

Using anaerobic cultivation chambers to decipher geomicrobiological processes

Nature Reviews Earth & Environment, Published online: 03 July 2025; doi:10.1038/s43017-025-00700-yLewen Liang explains how anaerobic cultivation chambers can be used to decipher geomicrobiological processes underlying key biogeochemical cycles.

www.nature.com

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DEEMteam_Orsay @deemteam.bsky.social · Jul 1

We are very happy to welcome Benjy Sedano @bencyano7.bsky.social , our new PhD student who will be working with some of our favorite cyanobacteria!

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DEEMteam_Orsay @deemteam.bsky.social · Jun 30

Very nice, though it’s a bit weird to see this horizontal version of a sequencing gel.

DEEMteam_Orsay @deemteam.bsky.social · Jun 28

Welcome to France!

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DEEMteam_Orsay @deemteam.bsky.social · Jun 26

The "most beautiful" but also the most intelligent experiment in biology.

Matthew Cobb @matthewcobb.bsky.social · Jun 26

Just learned that Frank Stahl (of the Meselson and Stahl DNA replication experiment ("the most beautiful experiment in biology") died at the beginning of April, to no fanfare. Here's a lovely video of them reminiscing: www.youtube.com/watch?v=7-tn...

The Most Beautiful Experiment: Meselson and Stahl

YouTube video by Science Communication Lab

www.youtube.com

1 1 2

Laura Eme @lauraeme.bsky.social · Jun 22

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

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DEEMteam_Orsay @deemteam.bsky.social · Jun 20

A N&V by Blair Paul and Biagio DiSalvo summarizes the main points of our paper:

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

Retracing a tangled tree of archaeal evolution - Nature Microbiology

Updated phylogenetic analyses yield a more nuanced view of the evolution of the DPANN archaea, a diverse superphylum of enigmatic and symbiotic microorganisms with a debated placement on the tree of l...

www.nature.com

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Nature Microbiology @natmicrobiol.nature.com · Jun 18

#NewResearch

🚨Out Now

Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors, by @bbaker24.bsky.social @deemteam.bsky.social and team

#MicroSky #Archaea 🦠

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

Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors - Nature Microbiology

Phylogenetic reconstructions with conserved protein markers from the 11 known DPANN phyla reveal their monophyletic placement within the Euryarchaeota.

www.nature.com

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DEEMteam_Orsay @deemteam.bsky.social · Jun 17

Finally, using a model that accounts for the sequence compositional, we found that DPANN most likely branch within Euryarchaeota. Interestingly, DPANN share more protein-coding genes with eurys than with other archaea. Therefore, they appear to constitute a highly derived lineage of Euryarchaeota.

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DEEMteam_Orsay @deemteam.bsky.social · Jun 17

We also found that ribosomal proteins, commonly used to reconstruct the phylogeny of archaea, are extremely biased in their amino acid composition compared to that of the complete proteomes, calling into question the suitability of using them as phylogenetic markers.

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DEEMteam_Orsay @deemteam.bsky.social · Jun 17

Using various approaches to overcome sequence compositional bias and the high evolutionary rates of DPANN, we found strong support for their monophyly. Altiarchaeota, which may contain free-living species, forms the first branch to diverge within DPANN.

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DEEMteam_Orsay @deemteam.bsky.social · Jun 16

Some of us have participated in writing the "Early Microbial Life: Our Past, Present, and Future" report, a comprehensive summary of knowledge on early life, from its origins to the emergence of complex multicellular lineages:

asm.org/reports/earl...

Early Microbial Life: Our Past, Present, and Future

The Academy report, funded by a grant from the Gordon and Betty Moore Foundation, examines the origins and trajectory of early microbial life to inform and inspire future research.

asm.org

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Wayne Maddison @waynemaddison.bsky.social · Jun 8

Mesquite 4.beta2 released! Much faster reading of files with thousands of matrices. New features since 4.beta include Trace All Changes (known from MacClade) and Import GenBank Numbers. www.mesquiteproject.org & discuss at groups.google.com/g/mesquite-p...
‪@bembidion.bsky.social ‬🧪 #evolbio

Two icons of the Mesquite program, with leaves of the mesquite tree against a black background (first icon) and against the blue sky and sun (second icon).

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