Pauline Raimondeau
@paulineraim.bsky.social
Postdoc Yale EEB | Plant comparative genomics & adaptation 🌿
Reposted by Pauline Raimondeau
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...
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.
media.tenor.com
October 14, 2025 at 1:32 AM
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...
Reposted by Pauline Raimondeau
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
), we find the opposite: animals exchange genes more, and for longer, than plants
September 12, 2025 at 7:55 AM
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
), we find the opposite: animals exchange genes more, and for longer, than plants
Reposted by Pauline Raimondeau
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
September 10, 2025 at 11:09 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Pauline Raimondeau
📣 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
🌍 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
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...
smbe2026.org
September 2, 2025 at 2:38 PM
📣 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
🌍 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
Reposted by Pauline Raimondeau
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
Fan, et al.
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience @yuzhenfan.bsky.social
September 8, 2025 at 4:19 AM
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
Fan, et al.
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience @yuzhenfan.bsky.social
Reposted by Pauline Raimondeau
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/🧵
September 3, 2025 at 8:01 AM
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/🧵
Reposted by Pauline Raimondeau
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...
Great teamwork between @lrsv-toulouse.bsky.social and LGDP-Perpignan 😎🥳🌱
academic.oup.com/plcell/advan...
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
academic.oup.com
August 28, 2025 at 8:08 AM
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...
Great teamwork between @lrsv-toulouse.bsky.social and LGDP-Perpignan 😎🥳🌱
academic.oup.com/plcell/advan...
Reposted by Pauline Raimondeau
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)
"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)
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...
www.biorxiv.org
August 28, 2025 at 6:37 AM
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)
"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)
Reposted by Pauline Raimondeau
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
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
academic.oup.com
July 28, 2025 at 10:03 AM
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
Reposted by Pauline Raimondeau
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 👇
Drought recovery in plants triggers a cell-state-specific immune activation.
doi.org/10.1038/s414...
Read thread below 👇
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.
doi.org
August 31, 2025 at 2:17 AM
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 👇
Drought recovery in plants triggers a cell-state-specific immune activation.
doi.org/10.1038/s414...
Read thread below 👇
Reposted by Pauline Raimondeau
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
🔗 doi.org/10.1093/gbe/evaf147
#genome #evolution #PlantSky
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
doi.org
August 11, 2025 at 7:48 AM
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
🔗 doi.org/10.1093/gbe/evaf147
#genome #evolution #PlantSky
Reposted by Pauline Raimondeau
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
August 20, 2025 at 9:06 AM
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
Reposted by Pauline Raimondeau
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...
www.nature.com/articles/s41...
August 20, 2025 at 6:23 AM
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...
www.nature.com/articles/s41...
Today also, @thorstenreusch.bsky.social presented the fascinating work conducted on somatic mutations in the clonal seagrass Zostera! ✨ #ESEB2025
August 19, 2025 at 2:24 PM
Today also, @thorstenreusch.bsky.social presented the fascinating work conducted on somatic mutations in the clonal seagrass Zostera! ✨ #ESEB2025
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
August 19, 2025 at 2:17 PM
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
Reposted by Pauline Raimondeau
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?...
youtu.be/n9Ls9-8p8x0?...
Zenil-Ferguson. The importance of quantifying rate uncertainty
YouTube video by Rosana Z-F
youtu.be
August 19, 2025 at 11:00 AM
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?...
youtu.be/n9Ls9-8p8x0?...
Reposted by Pauline Raimondeau
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...
We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...
August 18, 2025 at 4:51 PM
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...
We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...
Reposted by Pauline Raimondeau
This collaboration was so much fun!! I’m excited to see it online! www.cell.com/trends/genet...
August 9, 2025 at 1:24 PM
This collaboration was so much fun!! I’m excited to see it online! www.cell.com/trends/genet...
Reposted by Pauline Raimondeau
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...?
#plantscience
link.springer.com/article/10.1...?
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...
link.springer.com
July 31, 2025 at 7:43 AM
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...?
#plantscience
link.springer.com/article/10.1...?
Reposted by Pauline Raimondeau
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
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
July 8, 2025 at 4:44 PM
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
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
Reposted by Pauline Raimondeau
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...
Dans notre rapport, nous formulons 74 recommandations : www.hautconseilclimat.fr/publications...
July 3, 2025 at 5:37 AM
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...
Dans notre rapport, nous formulons 74 recommandations : www.hautconseilclimat.fr/publications...
Reposted by Pauline Raimondeau
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 🧪
👉 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 🧪
June 26, 2025 at 9:00 AM
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 🧪
👉 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 🧪
Reposted by Pauline Raimondeau
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.
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.
"Ce qu’on est en train de vivre aujourd’hui, c’est les trajectoires qu’on avait imaginées il y a 20 ans. La communauté des climatologues n’est pas du tout surprise par la vague de chaleur qui arrive. Elle est effrayée." @cassouman40.bsky.social ce matin sur @franceinfo.fr #VagueDeChaleur #DontLookUp
June 20, 2025 at 7:29 PM
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.
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.
Reposted by Pauline Raimondeau
Ok, fine I'm willing to admit it now: Mimulus is interesting www.authorea.com/doi/full/10....
June 10, 2025 at 10:15 PM
Ok, fine I'm willing to admit it now: Mimulus is interesting www.authorea.com/doi/full/10....