Evolutionarily conserved behavioral plasticity enables context-dependent mating in C. elegans www.cell.com/current-biol...

The Hallmarks of Cancer Enter the Multiverse www.cell.com/cell/fulltex...

I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵 www.nature.com/articles/s41...

For historical and conceptual context of understanding the genome as a dynamic reactive system, may I suggest our paper in @biologicaltheory.bsky.social link.springer.com/article/10.1...

Chromosome-scale #genomes from newly sequenced spiders & the whip scorpion, the genetic basis of spinneret emergence in spiders & the complex history & functional importance of arachnid genome #evolution www.science.org/doi/10.1126/... #biodiversity #genomics

#DBfeature Bones, brains, and bias—neural crest cell contribution to craniofacial structure Active Learning Assignments for craniofacial perception & normal phenotypic variation by Jeffrey Carmichael, Diane Darland et al www.sciencedirect.com/science/arti...

How does gene regulation shape brain evolution? Our new preprint dives into this question in the context of mammalian cerebellum development! rb.gy/dbcxjz Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social

The Caenorhabditis Genetics Center Curated Special Collections: a guide to protein degradation systems academic.oup.com/genetics/adv...

Calling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results. www.biorxiv.org/content/10.6... github.com/lauriebelch/... (1/10)

Are stick insects unique in their ability to transition to parthenogenesis? Our new review in @journal-evo.bsky.social covers intraspecific and hybrid origins, cytological mechanisms, and co-occurence of female-only and sexual populations, with comparisons to other taxa. doi.org/10.1093/evol...

Check out our new review in Nature Reviews Genetics on de novo emerged genes and proteins. How they emerge, are lost and persist - and how de novo emerged proteins relate to randomized proteins! @bornberglab.bsky.social www.nature.com/articles/s41...

Check out our new paper, out in the current issue of Proc B! In this work, we investigate the long-term persistence of the Drosophila pseudoobscura SR chromosome without suppression. We reconstruct its evolutionary history, showing that it has a history of suppression and escape from suppression.

Meiotic drive has long been considered as a genetic curiosity. Genomic "footprints" suggest otherwise. Check out our new review doi.org/10.1093/molb..., a cross-taxa synthesis arguing that recurrent drive is a pervasive and underappreciated force in genome evolution.

Finally had a chance to read this beautiful paper from Susan Mackem's lab. It's interesting that even well-established paradigms, like Sonic Hedgehog's role as a traditional morphogen in limb development, can be proven wrong over time. www.sciencedirect.com/science/arti...

Do contest-related traits evolve faster? A test of the exaggerated evolution hypothesis in a clade of Neotropical arachnids royalsocietypublishing.org/rsbl/article... | #BiologyLetters #Evolution

gonna do the old science twitter thing and post my reading here this year

New paper with @smishra677.bsky.social! How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process. 1/ www.biorxiv.org/content/10.6...

PEQG! My favorite conference ever*. Single session, fantastic talks, great discussions. Only once every 2 years. And in the best conference location too! Abstract deadline coming up Feb 5! *Disclosure: I am required to say it's the best conference because it is and I told my mom I wouldn't lie.

OUT NOW! Parasex generates highly recombinant progeny in Candida albicans with increased virulence By Robert Fillinger, Scott Filler, Anna Selmecki, Richard Bennett, Matthew Anderson & colleagues. #microsky @annaselmecki.bsky.social www.nature.com/articles/s41...

✨ Latest exciting story of the group in @nature.com. Here, we go beyond SNPs and built a species-wide atlas of genetic variants in yeast. With >1,000 near T2T genomes, we show how large genomic variations affect trait diversity. www.nature.com/articles/s41...

An extensive ER network develops in the olfactory hair cells of Drosophila. Inagaki et al. @riken-bdr.bsky.social report that the transmembrane protein Gore-tex controls a novel ER to the plasma membrane trafficking pathway essential for the cuticular nanopore formation. rupress.org/jcb/article/...

A protein language model unveils the E. coli pangenome functional landscape regulating host proteostasis www.biorxiv.org/content/10.6...

! Haldane’s law works through X:Autosome incompatibility in Caenorhabditis briggsae/C. nigoni hybrids www.nature.com/articles/s41...

! More heroic work from Zhongying Zhao's group Sequential evolution of antidote and toxin links genetic incompatibility with immune responses www.biorxiv.org/content/10.6...

The tutorial for how to assemble organellar genomes from nuclear-targeted long reads is ready to be used. Please check it out bioinformaticsworkbook.org/dataAnalysis... #Genome #genomics #assembly #bioinformatics #chloroplast #mitochondria

Crystal structures of Caenorhabditis elegans PUF-3 depict plasticity of RNA recognition that enables germline gene regulation academic.oup.com/nar/article/...

Interesting new multi-population aDNA selection scan from Colbran, Terhorst, Mathieson. Loci that are estimated to be under selection in one population also show enrichment in other populations, consistent with parallel or pre-split selection. www.biorxiv.org/content/10.6...

Epimutations: raw material for evolution? doi.org/10.1038/s443...

What a breakthrough! Such a puzzle for 30 years, this is real progress! I wonder how general this mechanism of repression is for other systems where highly-selective expression is needed. www.biorxiv.org/content/10.6...

New work from @miyapan.bsky.social and our team, bringing ant, bee, and wasp labs together. @chuanxinyu.bsky.social shows that the ANTSR locus we discovered in ants has determined sex for 150+ My across bees and stinging wasps 🐜🐝, despite virtually no sequence conservation 😮 doi.org/10.1073/pnas...

How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n

Systematic identification of oscillatory gene expression in single cell types www.biorxiv.org/content/10.1...

Haller, Ralph & Messer present SLiM 5, a major extension of the SLiM simulation framework for simulating multiple chromosomes, enabling a heightened level of realism for full-genome simulations. 🔗 doi.org/10.1093/molbev/msaf313 #evobio #molbio #compbio

Another YouTube Tutorial – This one on Proximity Labeling and connected to our recent EMBO J. paper (PMID: 41381733). This is a recording of a talk at the IDeA National Resource for Quantitative Proteomics in Little Rock AR. One of the top facilities in the country! www.youtube.com/watch?v=0T9P...

Congrats Simon Han & @brugmannlab.bsky.social on your publication @cincyresearch.bsky.social A dual role for GLI3 signaling in neural crest development journals.biologists.com/dev/article/...

Greetings! I decided to make a YouTube video of my AlphaFold workshop that I've given a few times in the past year. Caveats aside, people seem to find this useful for thinking about how to model protein interactions and how to interpret various AF outputs 1/2 www.youtube.com/watch?v=u63o...

Mutational Biases and Selection in Mitochondrial Genomes: Insights from a Comparative Analysis of Natural and Laboratory Populations of Caenorhabditis elegans academic.oup.com/g3journal/ad...

How to measure, analyze, and interpret age-related changes in Caenorhabditis elegans: lessons for mechanistic and evolutionary theories of aging www.sciencedirect.com/science/arti...

Hybridization and introgression between two fig trees with contrasting ecological preferences link.springer.com/article/10.1...

Somatic and germline mutational processes across the tree of life https://www.biorxiv.org/content/10.64898/2025.12.28.691837v1

This story is absolutely wild. Did you know that avocados change sex over the course of a day? And that it's controlled by a single ancient balanced polymorphism? This is flat our crazy

Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social

Within a pitcher plant, bacteria break down prey to feed the plant. As the leaf ages, bacteria become less diverse, but more efficient at degrading insects. It appears that species that are strong degraders are weak competitors. Read now ahead of print! www.journals.uchicago.edu/doi/10.1086/...

Biologists who teach: in what order do you teach the four forces of evolution? Genetic drift first or selection first? And I'm still struggling to smoothly fit in HWE so that its utility is emphasized (students focus so much on how likely it is that assumptions are violated). #iteachbio 🧪 #Evolution

Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social, @natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n

Interesting article on the evolution of views of Stephen Jay Gould in relation to punctuated equilibria. www.cambridge.org/core/journal... 🧪 #Paleobio #EvoBio

Excited to share the final version of our study on Nematostella cell type regulatory programs. Part of our @erc.europa.eu StG project, this was a challenging 5-year effort extraodinarily led by @aelek.bsky.social and @martaig.bsky.social. www.nature.com/articles/s41...

Happy to announce the publication of our foray into studying what happens to the transcriptomes of nuclei when cells fuse to form a syncytium. More to follow in the coming few years. One really wonderful thing about the Company of Biologists is that's it's free to publish there for my university!

All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.

"Range extender mediates long-distance enhancer activity" by @evgenykvon.bsky.social 's team, led by @gracebower.bsky.social is one of my papers of the year. Discovery of a new class of cis-regulatory elements that modulate the regulatory activity and reach of enhancers. doi.org/10.1038/s415...