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Gavin Woodruff

@weirdworms.bsky.social
764 followers 1.2K following 361 posts

Development, evolution, worms, gene name etymology. I log interesting papers, questions, and ideas.

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Gavin Woodruff @weirdworms.bsky.social · 31/08/2026
Transposable Elements and the Impact of Genomic Autoimmunity www.annualreviews.org/content/jour...
annualreviews.org
Transposable Elements and the Impact of Genomic Autoimmunity
Transposable elements (TEs), originally characterized in maize, are ubiquitous features of eukaryotes and replicate within genomes independent of the host replication cycle. This replicative advantage...
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Gavin Woodruff @weirdworms.bsky.social · 31/08/2026
Regulatory architecture controlling terminal differentiation of an interoceptive paraneuron in Caenorhabditis elegans journals.biologists.com/dev/article/...
journals.biologists.com
Regulatory architecture controlling terminal differentiation of an interoceptive paraneuron in Caenorhabditis elegans
Summary: The similarity of the regulatory architecture of neurons and paraneurons revealed using cell identity markers to characterize the neuronal features of Caenorhabditis elegans uv1 paraneurons i...
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Gavin Woodruff @weirdworms.bsky.social · 31/08/2026
Breaching the Weismann Barrier – a role of vitellogenin yolk proteins in nematode non-Mendelian inheritance www.frontiersin.org/journals/eco...
frontiersin.org
Frontiers | Breaching the Weismann Barrier – a role of vitellogenin yolk proteins in nematode non-Mendelian inheritance
August Weismann from Freiburg, Germany played an essential role in the general acceptance of Charles Darwin´s theory of evolution. He argued against the inhe...
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Gavin Woodruff @weirdworms.bsky.social · 31/08/2026
Genomic predisposition is associated with the direction of sex chromosome evolution www.science.org/doi/abs/10.1...
science.org
Genomic predisposition is associated with the direction of sex chromosome evolution
Sex chromosome evolution is among the most dynamic genomic innovations in vertebrates, yet why some lineages evolve XY while others evolve ZW remains unclear. Using chromosome-level genomes from 19 ge...
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Gavin Woodruff @weirdworms.bsky.social · 31/08/2026
25 Years Since the First Microsporidian Genome Assembly, Insights on How Genomics Has Shaped Our Understanding of Parasites with the Smallest Eukaryotic Genomes www.annualreviews.org/content/jour...
annualreviews.org
25 Years Since the First Microsporidian Genome Assembly, Insights on How Genomics Has Shaped Our Understanding of Parasites with the Smallest Eukaryotic Genomes
Microsporidia are fungal intracellular parasites of animals and are a threat to human health and food security. In 2001, they became the first eukaryotic parasites to have their genome fully sequenced...
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Gavin Woodruff @weirdworms.bsky.social · 31/08/2026
The Caenorhabditis elegans microbiome impacts microsporidia infection through nutrient limitation and spore inactivation www.nature.com/articles/s41...
nature.com
The Caenorhabditis elegans microbiome impacts microsporidia infection through nutrient limitation and spore inactivation - Nature Communications
Here, the authors show that gut bacteria can protect nematodes from microsporidia via altering host fatty acids the parasites need to grow, and secreting molecules that inactivate parasite spores, rev...
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Nature Communications @natcomms.nature.com · 02/08/2026
#Adaptation is assumed to proceed by survival of the fittest. The study shows that #mutation bias can drive adaptation via survival of the likeliest, steering bacteria along divergent paths to resistance with major consequences for control strategies. www.nature.com/articles/s41...
nature.com
Mutation-biased adaptation is consequential even in large bacterial populations - Nature Communications
Adaptation is assumed to proceed by survival of the fittest. The study shows that mutation bias can drive adaptation via survival of the likeliest, steering bacteria along divergent paths to resistanc...
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Arvid Ågren @arvidagren.bsky.social · 24/08/2026
From his review of John Dupre’s edited volume The Latest on the Best (MIT 1987). Krebs, J. 1988. Making the most of models. Nature 331, 126–127. doi.org/10.1038/3311...
doi.org
Making the most of models - Nature
Nature - Making the most of models
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Gavin Woodruff @weirdworms.bsky.social · 23/08/2026
Replicated evolution and environmental reversal reveal strong correlated response in a polyphenism doi.org/10.1093/evol...
doi.org
Replicated evolution and environmental reversal reveal strong correlated response in a polyphenism
Abstract. Environmental heterogeneity can favor phenotypic plasticity, but whether evolutionary responses in one environment predict trait expression after
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Tobias Warnecke @tobiaswarnecke.bsky.social · 22/08/2026
Who needs chromatin anyway...? NOT THIS GUY! www.biorxiv.org/content/10.6... 1/n
biorxiv.org
Chromatin is dispensable for bacterial life
Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...
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Gavin Woodruff @weirdworms.bsky.social · 21/08/2026
Species-specific barriers restrict virus spillover potential across the Caenorhabditis genus journals.plos.org/plosbiology/...
journals.plos.org
Species-specific barriers restrict virus spillover potential across the Caenorhabditis genus
Why do most cross-species virus jumps fail? Using Orsay virus across multiple Caenorhabditis species, this study reveals how mismatches in replication, genome balance, and transmission create layered ...
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Arvid Ågren @arvidagren.bsky.social · 18/08/2026
New paper with Nick Davies and Kevin Foster in @natcomms.nature.com. We show that often neither selection against transposons’ deleterious effects nor exploitation by parasitic elements is sufficient to keep them in control. Only active host suppression does. www.nature.com/articles/s41...
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Evolution Letters @evolletters.bsky.social · 10/08/2026
Big evolutionary events can fool phylogenetic analyses. A new approach combines phylogenetic regression with eigenvectors to reduce false positives and better account for the history written in genomes. doi.org/10.1093/evle...
doi.org
Characterizing and mitigating confounding by unreplicated evolutionary events in phylogenetic regression
Abstract. When researchers want to test for a direct effect of one attribute on another using interspecific data, they need to account for the confounding
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Gavin Woodruff @weirdworms.bsky.social · 17/08/2026
Ecologically relevant low oxygen levels reduce unfertilized oocyte output in Caenorhabditis elegans www.micropublication.org/journals/bio...
micropublication.org
Ecologically relevant low oxygen levels reduce unfertilized oocyte output in Caenorhabditis elegans | microPublication
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Gavin Woodruff @weirdworms.bsky.social · 14/08/2026
Population structure and punctuated genomic hyper-diversity in Caenorhabditis briggsae doi.org/10.1093/molb...
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Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 13/08/2026
WOAH 👀🧪 "we show that eukaryotic chromosomes are ionic hydrogels and that the chromosomal material is a two-state system, with interconversion between condensed and decondensed states through a volume phase transition, analogous to a liquid-gas transition" www.science.org/doi/10.1126/...
science.org
The eukaryote chromosome, a two-state system with interconversion by a volume phase transition
The formation of metaphase chromosomes requires the activity of condensins, DNA translocases that reduce chromosomal length through the process of loop extrusion. Reduction of length, however, does no...
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Gavin Woodruff @weirdworms.bsky.social · 10/08/2026
Apical spectrin organizes cortical actin filament bundles to pattern C. elegans cuticle ridges journals.plos.org/plosgenetics...
journals.plos.org
Apical spectrin organizes cortical actin filament bundles to pattern C. elegans cuticle ridges
Author summary The external surfaces of many organisms are decorated with regularly spaced protruding structures such as hairs, bristles, scales, and ridges. These structures play important roles in s...
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Gavin Woodruff @weirdworms.bsky.social · 10/08/2026
The rights and wrongs of rescaling in population genetics simulations journals.plos.org/plosgenetics...
journals.plos.org
The rights and wrongs of rescaling in population genetics simulations
Author summary Large-scale datasets of multiple genome sequences from a single species are increasingly available. Computer simulations of complex population genetic models are essential for making se...
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Adam Phillippy @aphillippy.bsky.social · 06/08/2026
For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]
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Crystal Rogers, PhD @rogerslabucd.bsky.social · 03/08/2026
Yay! Just saw that we got the cover of the August 1 MBoC! Woot! 🎉 Please check out our paper if you are interested in it the tubulin code or early development. www.molbiolcell.org/doi/10.1091/...
Cover of the August 1 MBoC journal- image from the Rogers Lab at UC Davis
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Dr. Ahna Skop @ahnaskop.bsky.social · 04/08/2026
Super excited my new review on midbody remnants (MBRs) is out: "Condensates on the Move: Midbody Remnants as Large, Translation‐Competent Extracellular Vesicles" #extracellularvesicles #midbody #mitosis #condensates #translation #proteinsynthesis onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
Condensates on the Move: Midbody Remnants as Large, Translation‐Competent Extracellular Vesicles
Mitotic cells produce three EV types: exosomes and microvesicles (green/blue) delivering pre-formed molecules, and midbody remnants (magenta) containing functional ribosomes and translation machinery...
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C. Brandon Ogbunu @cbo.bsky.social · 04/08/2026
🚨NEW PAPER 🚨 "Deconstructing empirical fitness seascapes across scales of granularity" published in #G3 (@genetics-gsa.bsky.social) 1/2 The fitness landscape has been among the most influential instruments in evolutionary theory for nearly a century. But we often treat them as fixed and static.
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Kurianlab @kurianlab.bsky.social · 30/07/2026
www.nature.com/articles/s41... how cool!
nature.com
Intestinal stem cells count self-renewal divisions to switch multipotency - Nature
In Drosophila, cell fate switching in adult intestinal stem cells is determined through an epigenetic mechanism in which these cells count divisions, switching from producing enterocytes to producing ...
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Jeff Groh @jeffgroh.bsky.social · 28/07/2026
Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...
pnas.org
Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS
In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...
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Gavin Woodruff @weirdworms.bsky.social · 13/07/2026
A Fluorescent Dauer Marker in Caenorhabditis inopinata Enables Comparative Analysis of Dauer-Inducing Mechanisms www.biorxiv.org/content/10.6...
biorxiv.org
A Fluorescent Dauer Marker in Caenorhabditis inopinata Enables Comparative Analysis of Dauer-Inducing Mechanisms
Dauer larvae are a dormant developmental stage in nematodes that is induced by a range of environmental cues. The molecular mechanisms that transduce these cues to regulate dauer entry have been well ...
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Nicholas Bellono @nbellono.bsky.social · 09/07/2026
How did octopuses evolve novel traits? Rishav Mitra, Richard Han, Trey Scott, et al serendipitously discover a unique ribosome adaptation that increases the accuracy of protein synthesis and evolved alongside their elaborate nervous systems vs deep sea relatives. www.biorxiv.org/content/10.6...
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Gavin Woodruff @weirdworms.bsky.social · 03/07/2026
Caenorhabditis becei recombinant inbred lines (beRILs) reveal the scope of heritable variation within a gonochoristic nematode population www.biorxiv.org/content/10.6...
biorxiv.org
Caenorhabditis becei recombinant inbred lines (beRILs) reveal the scope of heritable variation within a gonochoristic nematode population
Caenorhabditis nematodes are a powerful model clade for evolutionary genetics. Isogenic lines and panels of recombinant inbred lines (RILs) are among the most essential tools for genetic studies in th...
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Chris Bertram @crookedfootball.bsky.social · 02/07/2026
Reading Runciman’s sneery review of one of the best books I’ve read in the past few years has further lowered my opinion of Runciman
lrb.co.uk
David Runciman · Trivial Pursuits: Gamification
What makes a game liberating to play is also what makes it stifling and oppressive: in both cases it’s because the...
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Max Heiman @heiman.bsky.social · 01/07/2026
Clever approach from @astavoe.bsky.social for those pesky lines that were integrated with Rol -- edit them back to nonRol! I wonder what else we could build from all the existing integrated arrays. Switch colors?
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Oscar @oscarw.bsky.social · 16/06/2026
Just came across this remarkable interview with Marjorie Grene at age 94: www.thebeliever.net/an-interview... Two of my favourite bits, when Grene is asked about Rorty and about Lakatos: Rorty is just witty, but doesn't have a philosophy and Grene is quick to say that she did not kill Lakatos!
BLVR: That reminds me, I forgot to ask about Richard Rorty. You’re friends with him, though you don’t agree with his philosophy?

MG: We are friends, but you can’t agree with his philosophy. It doesn’t exist! He’s a wit! He should’ve lived in the eighteenth century. He just makes clever remarks that don’t mean anything. The thing about Philosophy and the Mirror of Nature is based on a total misinterpretation of Kant. It’s totally wrong about Kant, and I’m sort of a Kant person.BLVR: You know, I forgot to ask about philosopher of science Imre Lakatos—

MG: I didn’t kill him!!

BLVR: Why does everyone say you had a part in it?

MG: Because once he helped me out of a taxi in London and he hit his head on the door. And I didn’t kill him! He died soon, and I don’t know if it was the head bump. But it wasn’t because of me! [Laughing heartily]
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Charlotte Fare @charlottefare.bsky.social · 29/06/2026
mRNA-Scaffolded Cytoplasmic Compartments www.annualreviews.org/content/jour...
annualreviews.org
mRNA-Scaffolded Cytoplasmic Compartments
The cytoplasm of vertebrate cells is compartmentalized into the cytosol and several messenger RNA (mRNA)-scaffolded condensates, present at steady-state conditions and in the absence of stress. They i...
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Gavin Woodruff @weirdworms.bsky.social · 26/06/2026
Caenorhabditis tropicalis followed a unique evolutionary path to self-fertility doi.org/10.1093/gene...
doi.org
Caenorhabditis tropicalis followed a unique evolutionary path to self-fertility
Abstract. Caenorhabditis nematodes provide three natural experiments in which a male/female species evolved to produce one with males and self-fertile herm
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Jeremy Yoder says no war @jbyoder.org · 21/06/2026
Shubin closes with a reminder of the vital importance of shared evolutionary history in basic biomedical research: we’re learning how to cure human disease thanks to work on fruit flies, worms, and even fish
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Dr. Jessica L Ware @jessicalwarelab.bsky.social · 21/06/2026
Excellent welcoming squad for the #Evolution meeting!! Five stars! ⭐️
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Luane Landau @lulandau.bsky.social · 21/06/2026
I think this was one of the best talks I’ve heard! Evolution 2026 starting amazingly! @neilshubin.bsky.social #Evolution2026
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Marco Fumasoni @marcofumasoni.bsky.social · 19/06/2026
Our paper on the evolution of cellular miniaturization is now out in PNAS! www.pnas.org/doi/10.1073/... A short recap 🧵
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Gavin Woodruff @weirdworms.bsky.social · 19/06/2026
! "Moreover, transphyletic transplantation experiments show that the blastopore lip of M. leidyi leads to the generation of a secondary body axis in embryos of the cnidarian Nematostella vectensis."
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Laurie Belcher @lauriebelch.bsky.social · 09/06/2026
The new OrthoFinder paper is out now! In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets www.nature.com/articles/s41... github.com/OrthoFinder/...
nature.com
OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature Methods
The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.
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Genome Biology and Evolution @genomebiolevol.bsky.social · 08/06/2026
Brault et al. propose guidelines for standardized π estimation, systematic reporting of summary statistics, and the adoption of richer metadata to ensure that population genomic data remain comparable and reusable across a wide range of systems. 🔗 doi.org/10.1093/gbe/... #genome #evolution
GBE | A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them
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John Stinchcombe @johnstinchcombe.bsky.social · 07/06/2026
Why are leaves the shape that they are? What controls intraspecific, genetic variation in leaf shape? New from my lab, in collaboration with many others, led by PhD student Amanda Peake: mapping the leaf shape polymorphism in Ipomoea hederacea.
Homozygous recessive entire leaf of Ivyleaf morning gloryHomozygous dominant, lobed leaf of Ivyleaf morning glory
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José Cerca @naturalselection.bsky.social · 02/06/2026
🧨 New publication out (I think this one is 🌶️ ): Cerca & @stelkens.bsky.social - "The identity crisis of speciation genomics". academic.oup.com/evolinnean/a...
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Luca Soldini @lucasoldini.bsky.social · 26/05/2026
How do alternative reproductive modes arise? In this @pnas.org paper, we show that hybridogenesis -where a haploid set of chromosomes is transmitted clonally across generations- acted as an intermediate step between sexual and asexual reproduction in stick insects. doi.org/10.1073/pnas...
doi.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Evolution Letters @evolletters.bsky.social · 25/05/2026
How predictable is evolution? Replicated C. elegans experiments show environmental differences and population bottlenecks jointly shape the repeatability of adaptation doi.org/10.1093/evle... Image credit: Wikimedia
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Gavin Woodruff @weirdworms.bsky.social · 17/05/2026
Comparative transcriptomics reveals an extracellular worm Argonaute as an ancestral regulator of LTR retrotransposons academic.oup.com/gbe/advance-...
academic.oup.com
Comparative transcriptomics reveals an extracellular worm Argonaute as an ancestral regulator of LTR retrotransposons
Abstract. Safeguarding the genome from non-self elements is essential for development, reproduction, and ageing. One of the major threats to genomic integr
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Joanna Masel @joannamasel.bsky.social · 16/05/2026
Our paper unpacking "fitness" is out doi.org/10.1093/gene.... How to define fitness depends on what question you ask. Selection acts on organismal vital rates, longer-term outcomes make sense for genetic lineages, models link them. "Invasion fitness" = speed, but sometimes probability matters more.
doi.org
Why there are so many definitions of fitness in models
Abstract. Evolutionary “fitness” is operationalized in many different ways in models. Its role is to quantify that which is favored by natural selection. G
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Gavin Woodruff @weirdworms.bsky.social · 15/05/2026
😀 Actually, what is a gain-of-function mutation? doi.org/10.1093/gene...
doi.org
Actually, what is a gain-of-function mutation?
Abstract. For more than a century, scientists have worked to characterize, understand, and predict the consequences of mutations. For almost as long, scien
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Jordan Theriault-Brown @jtheriault.bsky.social · 14/05/2026
Put simply: It coordinates action in more varied and context-dependent ways across more complex environments, AND it regulates a more complex internal environment. Highly recommend this chapter from Sterling and Laughlin! link.springer.com/article/10.1...
link.springer.com
Why an animal needs a brain - Animal Cognition
In Principles of Neural Design (2015, MIT Press), inspired by Charles Darwin, Sterling and Laughlin undertook the unfashionable task of distilling principles from facts in the technique-driven, data-s...
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Richard Lenski @relenski.bsky.social · 11/05/2026
New book "A Primer for Experimental Evolution" with coauthors Michael Rose, Margarida Matos, and Joe Graves. www.worldscientific.com/worldscibook... A compact primer for students and colleagues interested in planning and designing experiments to address questions in evolutionary biology.
worldscientific.com
A Primer for Experimental Evolution
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Gavin Woodruff @weirdworms.bsky.social · 11/05/2026
Microbial genetic screen identifies bacterial genes that compromise Caenorhabditis elegans reproductive fitness journals.asm.org/doi/full/10....
journals.asm.org
Microbial genetic screen identifies bacterial genes that compromise Caenorhabditis elegans reproductive fitness | mSystems
This study identifies a direct causal link between a specific bacterial gene and host reproductive fitness. Systematic screening of Escherichia coli mutants showed that deleting one gene severely impa...
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