🚨New PrePrint🚨
I am excited to share this comparative analysis of transposable elements in medusozoa genomes led by graduate student Ayanna Mays 🧬🧪

www.biorxiv.org/content/10.6...

See the intricate worlds of parasites and algae — March’s best science images The month’s sharpest science shots, selected by Nature’s photo team.

Our ExM Atlas of eukaryotes is moving along with more and more images coming in - some featured in nature last month!
Culture we’re provided by @ccapoban.bsky.social & Julius Lukeš during visits last year

www.nature.com/immersive/d4...

TAD boundaries and gene activity are uncoupled Single-cell analysis fails to find a functional link between the organization of chromatin domain organization and gene activity.

"We find that while TAD boundaries pair more frequently than non-boundary regions, these interactions are infrequent and are uncorrelated with transcriptional activity of genes within the TAD"

elifesciences.org/articles/110...

Coexistence of Photosynthetic Marine Microorganisms, Viruses and Grazers: Towards Integration in Ocean Ecosystem Models Our study explores coexistence regimes of a virus and a zooplankton with a single phytoplankton for different model structures (left panel). The inclusion of an infected class and a resistant class i...

Coexistence of Photosynthetic Marine Microorganisms, Viruses and Grazers: Towards Integration in Ocean Ecosystem Models enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga).
🔗 DOI: www.biorxiv.org/content/10.6...

Somehow this paper has been largely ignored, but the basic idea has been presented by others as novel, or the idea gets misattributed to someone else. If you're interested in #diatom sex and its evolutionary importance, read and cite this paper.
www.jstor.org/stable/2460887

"men continued to publish the same number of papers after becoming fathers, women experienced a significant drop in research output (mothers had 31% fewer publications than did fathers 8 years after the birth of their first child)"

Evolution of a distinct chromatin regulatory landscape in brown algae - Nature Ecology & Evolution Chromatin plays a central role in gene regulation, but chromatin systems are only known for a few model species. This study analyses chromatin regulatory landscapes in brown algal lineages to elucidat...

Chromatin plays a central role in gene regulation, but chromatin systems are only known for a few model species. This study analyses chromatin regulatory landscapes in brown algal lineages to elucidate their structural organization and evolution 🧪 www.nature.com/articles/s41...

Spatial Proteomics Workshop for Protists

(see more in thread below)

Registration
Early Bird Monday 22nd June 2026.
Regular Monday 10th August 2026.
There will be a conference dinner on day 1. To register visit protistology.org.uk/autumn-meeti...

In our new pre-print, we established massive single-cell RNA-sequencing for diatoms to investigate key cell fate transitions. Notably, we discovered that the diploid-to-haploid transition is regulated by Myb TFs, a process that is actively ongoing across the Global Ocean! 🌊

Very excited to present our new project #BYGENEX, an @ERC_Research Advanced Grant! During the next five years we will be studying the genetic mechanisms that govern the phagocytosis of bacteria by protists @icmcsic.bsky.social

Extensive array of endogenous giant viral elements in a polar alga shows dynamic transcriptional response to abiotic stress Schultz et al. show that polar algae harbor extensive endogenous giant virus elements that are transcriptionally active, stress responsive, and integrated into host regulatory networks, highlighting v...

Excited to share our lab's new paper in Current Biology featuring MS student Sydney Schultz's work. We show that a polar alga carries large amount of giant viral DNA in its genome, and many of the viral genes respond to stress - with implications for host adaptation.

www.cell.com/current-biol...

Hi all. I am very excited that after 6 years I finally got my phylogenetic comparative methods book and online exercises online. Feel free to use and share. The book is here: nhcooper123.github.io/pcm-primer/. Note that it is not finished, we had to abandon it before the sunk costs fallacy broke us

Aerobic sister lineage of breviates has gene-rich mitochondrial genomes Cho et al. describe a novel, aerobic sister lineage of Breviatea using flow cytometric single-cell sorting and genome amplification. The new lineage harbors gene-rich mitochondrial genomes, unlike Bre...

Aerobic sister lineage of breviates has gene-rich mitochondrial genomes
#microbiology #eukaryotes #mitochondria #protists #MicroSky #ProtistsOnSky
@cellpress.bsky.social
www.cell.com/current-biol...

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.

Our SPECIAL ISSUE on MOLECULAR EVOLUTION & ECOLOGY is out!
Editorial: @yehumoran.bsky.social, @berndpulverer.bsky.social et al
Reviews on Asgard archaea, epimutations, giant-virus/host dynamics, smartphone analogy for animal origins…
…& many related primary articles
link.springer.com/journal/4431...

Happy to open a new BlueSky account to discuss the #diversity and #evolution of #protists. 🧬🔬
Stay tuned!

A phylogenetic classification of diatoms (Bacillariophyta) Diatoms are known for their extraordinary species richness, cornerstone roles in aquatic ecosystems, and immense contributions to the global cycling of carbon, oxygen, and silica. For nearly 2 centur....

Our phylogenetic classification of >400 diatom genera is now published in Journal of Phycology.
onlinelibrary.wiley.com/doi/10.1111/...

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...

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

We are very excited to share a new resource from our team: spatial subcellular proteome maps in plants! We developed an MS-based method that registers localizations of about 8000 proteins in Arabidopsis roots in a single experiment.

(1/9)
www.biorxiv.org/cgi/content/...

We’ve extended the deadline!

Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating).

A brief 🧵 (carried over from the old place)

Huge news 🌍🧬
The Protist 10,000 Genomes Project is joining the Earth BioGenome Project.
Protists may represent the majority of eukaryotic diversity — yet only a tiny fraction have reference genomes.
Time to change that. 🚀✨
Learn more 👉 ngdc.cncb.ac.cn/p10k/
#EBP #Protists #Genomics #TreeOfLife

Spectacular study revealing multiple ways by which Choanoeca flexa forms monolayers! Congratulations to @thibautbrunet.bsky.social Núria Ros-Rocher @pasteur.fr and all partners involved 👏👏👏

This looks so cool! 😍

MicroSEA (Microbial Sea Eukaryotes) course is a one-week, field-based summer school to train early-career researchers in the diversity, ecology, and single-cell biology of marine protists. MicroSEA course integrates lectures, field sampling, and lab-based practicals in advanced techniques, such as flow cytometry, microscopy, culturing, and molecular analysis. The main objectives of MicroSEA course are: Fostering a deep understanding of marine protist diversity, ecology and biology; Providing hands-on training in advanced single-cell methods that are not commonly available in university programs; Building participants' confidence in designing and conducting research projects from field to data analysis; Promoting international collaborations and peer networking among students and speakers/trainers. The course will take place at the Station Biologique de Roscoff - SBR (France) - 7th to 12th of June, 2026 (arrival on the 6th, departure on the 13th). 20 participants will be selected, including 10 from EuroMarine member institutes. https://opbc.sciencesconf.org/

Protist lovers: Please apply for a week of rhapsody! Learn by doing:

MicroSEA (Microbial Sea Eukaryotes) course is a one-week, field-based summer school to train early-career researchers in the diversity, ecology, and single-cell biology of marine protists. opbc.sciencesconf.org

#protistsonsky

Phylogenomic tree of Cercozoa based on single-cell transcriptomes from 100 uncultured cells - BMC Biology Background Cercozoa are single-celled eukaryotes (protists) and are part of the supergroup Rhizaria. Cercozoans have vastly different morphologies and are defined by their phylogenetic affinity. While...

Great to see this paper in all its glory online: link.springer.com/article/10.1...

A huge effort from Gordon and the team at @pjkeelinglab.bsky.social!

Phylogenomic tree of Cercozoa based on single-cell transcriptomes from 100 uncultured cells

@ubcbotany.bsky.social @science.ubc.ca

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

Explore how genetics, evolution and ecology intertwine at EMBO Workshop "Evolving together: From genomics to biological interactions" in #Taipei, TW, 24–27 Apr 2026.

Abstract submission/Registration by 20 Jan/28 Feb

https://meetings.embo.org/event/26-bio-interactions
#EMBOEvoGenBio #EMBOevents 🧪