~100 fish drawn in amateurish black and white doodles - mainly eels, catfish, and carpy things

~100 fishes drawn in amateurish black and white doodles. Lots of deep sea weirdos on this one, as well as gobies and cods and their ilk

About a hundred fishes drawn in amateurish black and white doodles. This has a lot of flatfish, as well as many spiny-finned fish

About 40 amateurish black and white fishes, bringing us up to #400z this is mostly very normal looking fishes, but there are some oddballs

Last really big milestone crossed in the Big Dumb Fish Project - Fish #400 ticked off the list! Theres some mismatches between the source I’m using and current taxonomy so I’ve still got “Pataecidae” as a group - very cool fish though so can’t really be mad, he reminds me of a Bosozuko biker.

Convergent genome streamlining accompanies independent miniaturization in the world's smallest fishes www.biorxiv.org/content/10.64898/2026.04...

Having a hard time keeping up with the fast-moving field of origin of eukaryotes/Asgards archaea? Our new perspective article can help, we review the status of research over the last decade and where it's going.

The archaeal roots of eukaryotic life

www.pnas.org/doi/10.1073/...

Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes

www.science.org/doi/10.1126/...

Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration!

Linking below previous thread on our findings

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...

When you zoom out from individual genes to consider the context of whole chromosomes across animal diversity, animal evolution takes on a different look. Oleg Simakov and I published a review in @annualreviews.bsky.social on topological approaches in comparative genomics. 🧬 doi.org/10.1146/annu...

Structure-guided discovery of protein functions in plants Protein structure-based searches enable the functional annotation of many plant proteins for which sequence-based methods fall short.

We also conducted comparative structural genomics and found that protein structure serves as a critical bridge between sequence and functional annotation in plants @theplantcell.bsky.social . academic.oup.com/plcell/advan...

3/10 We discovered that sing different types of commonly used genome-wide markers, such as UCEs and BUSCO genes, produce fundamentally different hypotheses about shark and ray evolution! Depending on the type used, sharks are NOT necessarily their own clade!

Structural alphabets approach performance of structural alignment in remote homology detection www.biorxiv.org/content/10.64898/2026.01...

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...

Proud to be part of this work. This is the project with the largest species sampling I’ve been involved in so far. We built a massive insect phylogeny, explored protein structures across the insect tree of life, and uncovered exciting insights into immune protein evolution!

Very happy to see this paper live - the result of a delightful collaboration with delightful collaborators. Population Genomics of Endangered Lenoks (Brachymystax spp.) in China Reveals the Presence of Cryptic Species academic.oup.com/sysbio/advan....

Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations www.biorxiv.org/content/10.64898/2026.01...

Our eLetter github.com/caseywdunn/s... responding to a recent Science paper was just posted. The paper found more genes with consistent support for sponge-sister than ctenophore-sister. We found several technical issues that, when corrected, reverse the conclusions and recover ctenophore-sister.

Evolutionary rates provide genomic insights into convergent and lineage-specific evolution in carnivorous plants www.biorxiv.org/content/10.64898/2025.12...

PhytClust: efficient and optimal node clustering in phylogenetic trees www.biorxiv.org/content/10.64898/2025.12...

An RNA splicing system that excises DNA transposons from animal mRNAs - Nature A new type of mRNA splicing mechanism discovered in Caenorhabditis elegans that detects and removes inverted repeats also occurs in human cells, thereby providing another strategy to protect against t...

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

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...

🚀 Big news in genome annotation! The latest Nature Methods paper presents Helixer. Developed as part of the @denbi.bsky.social infrastructure, Helixer makes high-quality genome annotations more accessible and efficient for the community.
🔗 nature.com/articles/s41592-025-02939-1

Ticks on an Eel: Museum Specimen is a First of its Kind Two ticks found on an 1873 electric eel specimen mark the first recorded case of ticks parasitizing a fish—but only documented just this year.

Forget Snakes on a Plane; how about Ticks on an Eel? cc @greenleejw.bsky.social entomologytoday.org/2025/12/03/t...

Systematic discovery of TIR-based immune signaling systems in bacteria Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immuni...

I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life.

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

Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex archaea that already possessed an elaborated cytoskeleton, membrane trafficking, endomembrane, phagocytotic machinery and a nucleus.

Nature research paper: Dated gene duplications elucidate the evolutionary assembly of eukaryotes

go.nature.com/4azJDF8

The origins and molecular evolution of sperm www.biorxiv.org/content/10.1101/2025.11....

LoL-align: sensitive and fast probabilistic protein structure alignment www.biorxiv.org/content/10.1101/2025.11....

An archaeal genetic code with all TAG codons as pyrrolysine Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...

An archaeal genetic code with all TAG codons as pyrrolysine www.science.org/doi/abs/10.1... #jcampubs

Convergent genome evolution shaped the emergence of terrestrial animals - Nature Comparisons of 154 genomes from 21 animal phyla and outgroups have been used to reconstruct ancestral adaptation to life on land across 11 distinct terrestrialization events, revealing strong evidence for convergent genomic evolution across the animal kingdom and recurring periods of terrestrial colonization.

Nature research paper: Convergent genome evolution shaped the emergence of terrestrial animals

go.nature.com/4i0i61w

Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...

#Archaea, #DPANN, #phylogenetic_reconciliation
New preprint online!
www.biorxiv.org/content/10.1...

Insertion of an invading retrovirus regulates a novel color trait in swordtail fish For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...

I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A

Cover of book titled The Tree of Life: solving science's greatest puzzle.

My book 'The Tree of Life' is published in the USA and Canada today.

Available as book, on kindle and as audio.

I would be really grateful for reposts.

www.amazon.com/Tree-Life-So...
www.amazon.ca/Tree-Life-So...

Diagram showing the inferred evolutionary relationships among major bird groups. A grid to the right shows whether certain major groupings were supported by different analytical approaches.

Efficient inference of large phylogenetic trees as applied to birds: academic.oup.com/sysbio/advan... 🧪🪶 (📷Zhao et al.)

A global coral phylogeny reveals resilience and vulnerability through deep time - Nature The most recent common ancestor of the stony coral Scleractinia dates to about 460 million years ago and was probably a solitary, heterotrophic and free-living organism.

New Nature paper!

Vaga et al. (2025) reconstruct a time-calibrated phylogeny of stony (scleractinian) corals, which suggests that some could be resilient to climate change.

Congrats @claudiavaga.bsky.social

Link to paper: doi.org/10.1038/s415...