Pauline Raimondeau

a little boy is driving a red toy car on the street . Alt: a little kid is driving a red toy car on the street.

Updated tutorials for nQuack today. Want to predict ploidy level of sequence data? See this new tutorial on how to process and model data faster: mlgaynor.com/nQuack/artic...

@oso-tee.bsky.social Congrats 🔥

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

Adaptation is less accessible through mutations in promoters than in coding sequences when large effect sizes are needed Mutations within promoters and coding sequences are both involved in adaptation, but their relative contributions remain to be compared directly. Using the fungal enzyme cytosine deaminase, we examine...

Really excited to share our latest paper led by @simonaube.bsky.social. Fascinating results examining whether regulatory mutations can lead to adaptation as fast as coding mutations do. #mevosky #evobio #evoSky

www.biorxiv.org/content/10.1...

Symposia - SMBE 2026 - Copenhagen Denmark SMBE 2026 Symposia Check deadlines and important dates below.  Days Hours Minutes Seconds Conference Symposia We are now accepting proposals for symposium for the 2026 Annual meeting taking place in C...

📣 The Call for Symposia for the Society for Molecular Biology and Evolution (SMBE) 2026 Annual Meeting is now open.

🌍 The meeting will be in Copenhagen June 28th to July 2nd

🖊️ We invite you to submit a symposium proposal and help shape the scientific content of SMBE 2026

Best the organisers

VpmaxA and Amax plotted by C4 biochemical subtypes (a and b, respectively), growth forms (c and d, respectively) and growth locations (e and f, respectively).

Environmental conditions drive variation in C4 photosynthetic capacity more than species traits

Fan, et al.

📖 nph.onlinelibrary.wiley.com/doi/10.1111/...

#PlantScience @yuzhenfan.bsky.social

Map of my no-fly itinerary from Italy to Bougainville, PNG

I've set off to Bougainville,PNG, for another #NoFly journey. I want to complete my research there. Travelling the ~25,000km distance from Italy by🚢,🚅,&🚌,I'll emit ~10 times less than✈️ (computations to come).Here the long read on my motivations: gianlu777.substack.c... 1/🧵

Mechanisms, Detection, and Impact of Horizontal Gene Transfer in Plant Functional Evolution Abstract. Horizontal gene transfers (HGT) have been observed across the tree of life. While their adaptive importance in bacteria is conspicuous, the occur

So excited to see our review on how to detect horizontal gene transfers and their impact on plant functional evolution finally published in @theplantcell.bsky.social!
Great teamwork between @lrsv-toulouse.bsky.social and LGDP-Perpignan 😎🥳🌱
academic.oup.com/plcell/advan...

De-novo promoters emerge more readily from random DNA than from genomic DNA Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab!

"De-novo promoters emerge more readily from random DNA than from genomic DNA"

This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

Repressive cytosine methylation is a marker of viral gene transfer across divergent eukaryotes Abstract. Cytosine DNA methylation patterns vary widely across eukaryotes, with its ancestral roles being understood to have included both transposable ele

Happy to see our latest work out in @molbioevol.bsky.social. We revisit the evolution of 5-methylcytosine across neglected eukaryotic supergroups, establishing an ancestral repressive role silencing genome invaders, both transposons and viral elements👾: academic.oup.com/mbe/advance-... 🧵 1/7

Drought recovery in plants triggers a cell-state-specific immune activation - Nature Communications Post-drought rehydration triggers a preventive immune response in plants, revealing targets to enhance crop resilience by linking drought stress recovery with improved pathogen resistance.

Our #research on #drought #recovery, now published with @springernature.com in @natcomms.nature.com:
Drought recovery in plants triggers a cell-state-specific immune activation.
doi.org/10.1038/s414...

Read thread below 👇

Domestication Reduces Plant Immune Receptor Gene Repertoires Across Lineages Abstract. Plant domestication is sometimes associated with a reduction in the diversity of immune receptor genes, critical for pathogen recognition and def

Bourne et al. analyzed immune receptor gene repertoires of 15 domesticated crop species, showing that grapes, mandarins, rice, barley, and yellow sarson exhibit reduced immune receptor gene repertoires compared to wild counterparts.

🔗 doi.org/10.1093/gbe/evaf147

#genome #evolution #PlantSky

The European Reference Genome Atlas (ERGA) is a pan-European community initiative to coordinate the generation of reference genomes representing European eukaryotic biodiversity @ergabiodiv.bsky.social #eseb2025

Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis!
www.nature.com/articles/s41...

Today also, @thorstenreusch.bsky.social presented the fascinating work conducted on somatic mutations in the clonal seagrass Zostera! ✨ #ESEB2025

Also appreciated the citation format used: Author, year, unique keyword. No journal name 🙌

Inspiring talk from @marcrr.bsky.social presenting student Christabel Bucao’s work. Expression variability predicts retention and functional divergence of genes after WGD! « variability creates » #ESEB2025

YouTube video by Rosana Z-F Zenil-Ferguson. The importance of quantifying rate uncertainty

Unfortunately, I couldn't join in person #eseb2025, but the organizers kindly accommodated a video. Posted here in case you missed it!
youtu.be/n9Ls9-8p8x0?...

pangenome 'expansion' curves for cotton and soybean

Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts.

We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...

Picture of the Sagrada familia, symbol of Barcelona

Excited to be in Barcelona for #ESEB2025 So many great talks, familiar faces and cool posters already!

This collaboration was so much fun!! I’m excited to see it online! www.cell.com/trends/genet...

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals - Genome Biology Background Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypometh...

Paper led by @movillome.bsky.social on unbiased detection of (somatic) #TE insertions in #Arabidopsis with @pacbio.bsky.social long reads out after peer review. Thanks to academic editor Leandro Quadrana for shepherding it through the review process.
#plantscience
link.springer.com/article/10.1...?

Please RT!

I'm hiring a postdoc to work in my new lab at UCSB (!) on an NSF-funded project investigating the phenotypic consequences of WGD for photosynthesis and respiration.

Check out the full posting here:
recruit.ap.ucsb.edu/JPF02986

And more info about the lab here:
sharbroughlab.com

Il faut un sursaut collectif pour relancer l’action climatique et permettre l'accès à une transition pour tous : consolidation du cadre d’action publique, gouvernance solide, cap clair pour 2030 & 2040.

Dans notre rapport, nous formulons 74 recommandations : www.hautconseilclimat.fr/publications...

Could manage to add a bluesky widget on my website 🙌 ✨

👉 nicolasmouquet.free.fr

🤖 how to here : github.com/Vincenius/bs...

💡use you DID identifiers rather than your handle in the code (here is where to find it : ilo.so/bluesky-did/)

👏 thanks to @vincentwill.com for sharing 🧪

Qques mots forts que j'ai prononcés avec émotion @franceinfo.fr
C'est un mensonge de laisser croire que l'on s'adaptera sans casse irréversible dans une France à 4°C. On ne s'adapte pas a un effondrement de la biodiversité; on meurt avec!
Les régressions actuelles sont irresponsables & suicidaires.

Fig. 3 | DEEPSPACE synteny map highlighting positions of centromeric repeats. Collinear blocks between the same chromosomes are shown as transparent ‘braids’ and chromosome segments are visualized as color-gradient rectangles along an x-axis that scales each genome by its physical size. Regions that do not map between chromosomes are visualized as black ‘wedges’ in the map. These can be due to ineffective unique mapping in highly repetitive centromeres (e.g. Chr 9 IM62-IM767), expansion of centromeric arrays (e.g. Chr 11 IM62-IM767) or sequence presence/absence. The orange-blue color gradient indicates regions that are gene-rich (blue) or centromeres (orange); fully saturated colors indicate that all sequence in those intervals is masked by that annotation type. White regions have neither genes nor Cent728 repeats, and are likely repeat-rich pericentromeres.

Fig. 4 | Exploration of the pan-genome graph. A 2.34-2.37Mb on chromosome 1 is a complex region in the genome that illustrates how the pan-genome graph handles large scale presence594 absence variation. Here, any variants smaller than 52bp are excluded so that the large insertion deletions in this region are apparent. Haplotypes containing similar sequences are binned in the transparent rounded rectangles (“nodes”), divergent but syntenic/orthologous sequences have stacked nodes, and deleted sequences show the path outside of a node. B The first exon and the first 28bp of the first intron of a gene with family members across all four genomes is shown as an example of how SNPs and INDELs appear at the base pair level in a sequence graph. C The positions of aligned sequence retained in the graph (colored following the tubes in panels A-B) and that which is un-alignable and clipped (black) are presented in a pan-genome anchored by IM62.

Ok, fine I'm willing to admit it now: Mimulus is interesting www.authorea.com/doi/full/10....

k-mer-based diversity scales with population size proxies more than nucleotide diversity in a meta-analysis of 98 plant species Abstract. A key prediction of neutral theory is that the level of genetic diversity in a population should scale with population size. However, as was note

Hey, Miles' @milesroberts.bsky.social beautiful paper showing that sequence diversity missed by standard methods contributes to Lewontin's paradox is officially published in @evolletters.bsky.social. academic.oup.com/evlett/advan...

Simons Graduate Fellowships in Ecology and Evolution The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...

Check out this brand new fellowship from the Simon’s Foundation in Ecology and Evolution. Incoming grad students this year are eligible to apply. No citizenship restrictions. www.simonsfoundation.org/grant/simons...

Super excited to release a huge evolution project on the works for many years:

Evolution experiments synchronized across climates to understand rapid adaptation

Preprint: doi.org/10.1101/2025...
All data available: www.grene-net.org/data

#MOILAB
@ucberkeleyofficial.bsky.social
@hhmi.org

🧵👇