Incorporating genetic load contributes to predicting Arabidopsis thaliana’s response to climate change @naturecomms.bsky.social www.nature.com/articles/s41...

I'm finding this little pipeline to get trees out of BUSCO runs quite convenient #phylogenomics github.com/jamiemcg/BUS...

The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.

"TAIR 12 is here!" Read more here: https://arabidopsis.org/news/breaking-news#307 #News

Plasmids use immune systems like #CRISPR-Cas to compete with other #plasmids, but do these systems confer an advantage? @davvi36.bsky.social &co show that CRISPR-Cas benefits resident plasmids but is constrained by toxin-antitoxin systems after horizontal transfer @plosbiology.org 🧪 plos.io/4qNbdDt

🐟💃

So I did something a bit different :). Thrilled to see this fun project out! 🐟 #genomics "Female-biased sex ratios despite stable genetic sex determination across a climatic gradient in a marine fish" www.biorxiv.org/content/10.6...

I submitted this ms to a journal about a 1.5 months ago, and the status remains "Awaiting Referee Assignment". The editor says they are struggling to find a second reviewer... Are these waiting times normal? Should I offer a fresh list of potential reviewers or is that inappropriate? 💔 #postdoclife

Are you excited about pangenomics? If so, join us in Edinburgh on 8-9th June to discuss the latest methods & insights from using these approaches across biodiversity! More details here: royalsociety.org/science-even... Organised together with @henrylnorth.bsky.social & @joanameier.bsky.social!

Would you say that Neurospora crassa is declining as a model organism for fungal biology? 💛 No way, that orange fun-guy is alive and well! 🔴 Yeah, not so many people work with it nowadays ... 🔵 Neuro-who? 📅 Ends: December 31, 2025, 10:03 PM UTC 📊 Show results

Whoop! New preprint has dropped - led by the amazing @trevormugoya.bsky.social. We developed a SV-calling and benchmarking platform called SaVor and test it on 1,165 Arabidopsis thaliana short read whole genomes. Do check out the paper, and try SaVor on your own data: github.com/ChabbyTMD/Sa...

A recent shift in centromere size and DNA content in Podospora pseudocomata co-occurs with the loss of a fungal genome defense system https://www.biorxiv.org/content/10.64898/2025.12.02.690432v1

Our paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social link.springer.com/article/10.1...

What if we could autocomplete DNA based on function? Today in @Nature, we share semantic design—a strategy for function-guided design with genomic language models that leverages genomic context to create de novo genes and systems with desired functions. 🧵 www.nature.com/articles/s41...

"When the female bugs lay their eggs, they rub the cultivated hyphae across the egg mass. The hyphae grow to envelope the eggs and physically exclude attentive parasitoid wasps until the bugs hatch." #fungi #symbiosis

Wow O_o

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.

Our paper was included in the Collection "Microbial Genomics of Eukaryotes" from the @microbiologysociety.org 🧬 😁 #genomics #longreadsequencing www.microbiologyresearch.org/content/micr...

O.o "From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes" | Nature share.google/IAaPSj5t9OvQ... #pangenome #fungi #yeast

A timetree of Fungi dated with fossils and horizontal gene transfers www.nature.com/articles/s41...

Wooo!

How do species diverge? Could the relative immobility of plants increase their likelihood of speciating in the same place?🧵

Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (www.science.org/doi/10.1126/... ), we find the opposite: animals exchange genes more, and for longer, than plants

"Rapid establishment of species barriers in plants compared with that in animals" by Monnet et al #Speciation www.science.org/doi/10.1126/...

mRNA A-to-I editing in vegetative cells of Fusarium #fungionsky #fungi #epigenetics link.springer.com/article/10.1...

Uhm 🤔, another "mutation is not random" paper: #mutation #genomics www.pnas.org/doi/10.1073/...

What causes viral transmission bottlenecks? This study uses barcoded virions to show that in the case of #influenza A #virus, early within-host replication dynamics (rather than a reduced inoculum population) drive loss of diversity during transmission @plosbiology.org 🧪 plos.io/4ngicDK

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

Check out our new paper on adopting a trait-based framework for protist diversity! We make the case for a unified protist trait database, how to build it, and how it could transform research on protist ecology and evolution. #protistsonsky

Sclerotina and its weird-ass arrangement of different chromosomes in two separate nuclei still follow normal meiosis, it turns out. #fungi #meiosis www.nature.com/articles/s41...

I'm super bummed to be missing #ESEB2025 @eseb2025.bsky.social due to a cancelled flight! Here's a quick overview of my talk "Gene- and genome-focused perspectives on microbial pangenomes" slated to be part of The Evolution of Microbial Pangenomes -- which I recommend you attend tomorrow (Fri) ! 1/n

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...

How predictably does complex trait adaptation proceed over space and time in wild populations? doi.org/10.1093/evle... Now in @evolletters.bsky.social by @skylerberardi.bsky.social, @paulrschmidt.bsky.social et al. 📷: Dr. Rush Dhillon

@charleston.bsky.social and colleagues introduce the ancestry-specific expected genetic relationship matrix (as-eGRM), an analysis framework that estimates the relatedness within ancestry components between admixed individuals, in the @ajhgnews.bsky.social latest article: bit.ly/3U5p0aI #ASHG

A pangenomics-enabled platform for the high-throughput discovery of antifungal resistance factors in crop pathogens https://www.biorxiv.org/content/10.1101/2025.07.18.665620v1

The auditorium is slowly filling up for the opening session and our inaugural keynote speech... #SMBE2025

Our description of the transcriptomic changes during sexual development in #Podospora anserina is out in @genomics.peercommunityin.org ! peercommunityjournal.org/articles/10.... @i2bcparissaclay.bsky.social @univparissaclay.bsky.social

New preprint: we advertise DAFNEE, a database of academia-friendly eco-evo-archaeo journals. 1/6 #AcademicPublishing #ecoevo #archaeology #EthicalPublishing #SocietyJournals #DiamondOpenAccess doi.org/10.32942/X24...

Happy to see this out! "Reconstructing NOD-like receptor alleles with high internal conservation in #Podospora anserina using long-read sequencing", now in ‪@microbiologysociety.org‬! 🧬 Keep reading for a simple explanation 🧵 1/n #Fungi #Allorecognition www.microbiologyresearch.org/content/jour...

Can genetic drift generate enough variation between subpopulations to allow for the evolution of defence against predators or parasites via multi-level selection? In www.sciencedirect.com/science/arti... we have explored this for a structured population model.

URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯 Any lab using @flybase.bsky.social please donate using the link in post below. This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.

Do you like potatoes? Don't miss our most recent work on tetraploid potato genome! @nature.com #potato #genomics #history #evolution

Sketch, capture and layout phylogenies www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/husonlab/phy...

We did it! We caught Starship #transposons moving between #fungal species in the lab, including between species separated by ~100my. We think Starships are a mediator of HGT in fungi, akin to conjugative elements in bacteria. Check out the preprint. www.biorxiv.org/content/10.1...

Getting massive FOMO from all the #ECFG17 posts. It looks fun!

On #InternationalDayofWomenandGirlsinScience let me remind you that we are NOWHERE NEAR parity. A few examples. 1. Women are credited less in science than men. www.nature.com/articles/s41...

New preprint! We find a novel signal of positive selection in georeferenced genotype data, then use this signal to identify in-progress selective sweeps in the malaria vector Anopheles gambiae: www.biorxiv.org/content/10.1...

The chance of the broccoli-headed fascists reaching NIH and destroying online NCBI tools and datasets we rely on isn't 0%, so it's worth making a list of the mirrors/alts offered by EMBL-EBI, etc that many of us (including me) are unaware of. #bioinformatics #genomics #biology #evosky #molevol

Widespread use of azole fungicides in agriculture may reduce the effectiveness of antifungal treatments for patients with aspergillosis. EMA highlights that nearly all 120,000 tonnes of azoles sold in the EU were used as pesticides, potentially contributing to #AMR www.ema.europa.eu/en/news/one-...

Our study on #lichen #symbiosis is out in @currentbiology.bsky.social! How can multiple microbes create a large, 3D, and structurally complex organism? To answer this question, we used #metagenomics, #metatranscriptomics, and a bit of protein structure modeling 🧵1/7 🧬 🖥️ 🧪 🦠 🧫 #SymbioSky