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Pauline Raimondeau

@paulineraim.bsky.social
1.5K followers 990 following 41 posts

Postdoc USheffield | Plant comparative genomics & adaptation 🌿

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Reposted by Pauline Raimondeau
Casey Dunn @caseywdunn.bsky.social · 05/10/2026
Interested in joining our lab (dunnlab.org) and YIBS as a postdoc? I'm looking for someone to work on siphonophores, diversity in the open ocean, or natural history. If that's you, please reach out this week to discuss a nomination for the Donnelley Postdoc Fellowship - yibs.yale.edu/donnelley-fe...
dunnlab.org
The Dunn Lab
Casey Dunn's laboratory in the Department of Ecology and Evolutionary Biology at Yale University.
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Haley A Branch @stressedbranch.bsky.social · 02/10/2026
New preprint out from my time as a postdoc in @jenncoughlan.bsky.social lab! In a range-wide survey of M. guttatus, we found a lack of stomatal regulation in response to drought, which led to our inability to draw predictions from other known trait-associations www.biorxiv.org/content/10.6...
biorxiv.org
Divergence in wilt tolerance across the range of Mimulus guttatus in the absence of stomatal regulation
Whether phenotypes and environments predict performance under stress is central to ecology and evolution and can reveal species' vulnerability to global change. We sampled Mimulus guttatus range-wide ...
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Pauline Raimondeau @paulineraim.bsky.social · 05/10/2026
Happy to share this preprint! I learnt so much throughout this project — from getting hands-on with plant physiology and measurements in the greenhouse to data analysis and the many discussions that followed. Grateful to have been part of the team 🌱
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Casey Dunn @caseywdunn.bsky.social · 25/08/2026
My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore.
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John Lovell @jotlovell.bsky.social · 19/05/2026
We are often asked whether pangenomes are worth the hassle. The files can be large and methods to explore them are much more challenging than linear references. Earlier this week, we preprinted a clear example of how and why pan-genome graphs are so important for trait discovery.
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Shelly Gaynor @shellygaynor.bsky.social · 15/04/2026
Revision of the Angiosperm Phylogeny Group (APG) classification has been underway! The group is requesting community feedback until April 22nd. Here is a link to a survey to gather feedback, which includes links to the manuscript and the new classification: docs.google.com/forms/d/e/1F...
docs.google.com
APG V Survey - Extended Deadline
Dear Colleagues: We are soliciting community input on a draft of APG V, which is available at https://docs.google.com/document/d/1M8ZWZoJTj1mFYUe_bRKrP-NCwwEzoGuC/edit?usp=sharing&ouid=11366933678134...
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Nicolas Mouquet @nmouquet.bsky.social · 09/03/2026
‪ 🌳 Do you want to contribute to research on how humans perceive forests? Take this quick, anonymous 10-min survey 🌲 👉 www.biodiful.org#/forest This will help us explore how people experience forest biodiversity! Please share on 🦋 & tag @biodiful.bsky.social to reach more participants 🙏💚 🌐🌍🦤🦑🪴🍁🧪
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Pauline Raimondeau @paulineraim.bsky.social · 10/03/2026
Introgression fuelling reproductive isolation? 👀 Impressive work & fascinating story ✨
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Pauline Raimondeau @paulineraim.bsky.social · 10/03/2026
Woooohoooo!!!! 🤩
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Jenn Coughlan @jenncoughlan.bsky.social · 10/03/2026
I am SO THRILLED to share our first fully-lab lab paper!!!!!! Led by @hybridzones.bsky.social & @hagarsoliman.bsky.social, w/ a major assist from @pfschwarz.bsky.social!!!!!!!!!!!!! Read more below, if you're curious (you should be- it's AWESOME!!!!!!!) link: www.sciencedirect.com/science/arti...
sciencedirect.com
Introgression and parental conflict shape repeated occurrences of postzygotic isolation in Mimulus
Postzygotic reproductive isolation is often thought to accumulate as a byproduct of neutral divergence. Yet it frequently evolves rapidly, in line wit…
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Luke Dunning @luketdunning.bsky.social · 28/02/2026
Awesome to see @cfcollins.bsky.social first paper out from her PhD - a huge amount of work!! Regulatory features determine the evolutionary fate of laterally acquired genes in plants url: academic.oup.com/mbe/article/...
academic.oup.com
Regulatory features determine the evolutionary fate of laterally acquired genes in plants
Abstract. Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. How
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Molecular Biology and Evolution @molbioevol.bsky.social · 02/03/2026
Collins et al. combined expression, methylation, and genomic data to investigate long-term persistence of laterally acquired genes in the grass Alloteropsis, showing that those capable of regulating their own expression are more likely to persist. 🔗 doi.org/10.1093/molbev/msag042 #evobio #molbio
doi.org
Regulatory features determine the evolutionary fate of laterally acquired genes in plants
Abstract. Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. How
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 09/02/2026
So cool. Multiple cell lineages contribute to the germline in maize -- and differences between apical and lateral branches! www.biorxiv.org/content/10.6...
biorxiv.org
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Botanical Society of America @botsocamerica.bsky.social · 09/02/2026
🏵 Check out the latest #AJB Synthesis article, by Haley Branch! 🏵 The sleeping giant needs coffee: Overlooked areas for integrating plant #ecophysiology & evolutionary biology doi.org/10.1002/ajb2... #botany #plantscience #ecology #evolution
Graphic announcing new AJB Synthesis article by Haley Branch.Methodological illustration for asking whether X affects plants. “Question” provides an example of a question that both ecologists and evolutionary biologists ask, with categories of traits often of interest. “Experiment” shows trait examples and comparisons (populations, environmental, across time). Types of traits are where evolutionary biologists could expand their breadth. “Outcome” describes lasting effects of whether X affects traits to the point that it is passed on and contributes to future generations or it leads to extinction. “Outcomes” is where ecophysiologists could expand their work. Images courtesy of Dr. Stefanie Sultmanis (vein density), Dr. Beatrice Harrison Day (root section), and Dr. Vanessa Tonet (leaf cavitation).
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Shelly Gaynor @shellygaynor.bsky.social · 14/10/2025
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...
media.tenor.com
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.
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Pauline Raimondeau @paulineraim.bsky.social · 16/09/2025
@oso-tee.bsky.social Congrats 🔥
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Camille Roux @crouxevo.bsky.social · 12/09/2025
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
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Christian Landry @christianlandry.bsky.social · 10/09/2025
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...
biorxiv.org
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...
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Center for Evolutionary Hologenomics @hologenomics.bsky.social · 02/09/2025
📣 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
smbe2026.org
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...
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New Phytologist @newphyt.bsky.social · 08/09/2025
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
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).
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dr. gianluca grimalda @ggrimalda.bsky.social · 03/09/2025
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/🧵
Map of my no-fly itinerary from Italy to Bougainville, PNG
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Camille Puginier @puginiercamille.bsky.social · 28/08/2025
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...
academic.oup.com
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
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Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 28/08/2025
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)
biorxiv.org
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...
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Alex de Mendoza @alexdemendoza.bsky.social · 28/07/2025
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
academic.oup.com
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
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Natanella Illouz-Eliaz @natanellae.bsky.social · 31/08/2025
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 👇
doi.org
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.
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Genome Biology and Evolution @genomebiolevol.bsky.social · 11/08/2025
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
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
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Rob Waterhouse @rmwaterhouse.bsky.social · 20/08/2025
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
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 20/08/2025
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...
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Pauline Raimondeau @paulineraim.bsky.social · 19/08/2025
Today also, @thorstenreusch.bsky.social presented the fascinating work conducted on somatic mutations in the clonal seagrass Zostera! ✨ #ESEB2025
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Pauline Raimondeau @paulineraim.bsky.social · 19/08/2025
Also appreciated the citation format used: Author, year, unique keyword. No journal name 🙌
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Pauline Raimondeau @paulineraim.bsky.social · 19/08/2025
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
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Rosana Zenil-Ferguson @roszenil.bsky.social · 19/08/2025
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
Zenil-Ferguson. The importance of quantifying rate uncertainty
YouTube video by Rosana Z-F
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John Lovell @jotlovell.bsky.social · 18/08/2025
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...
pangenome 'expansion' curves for cotton and soybean
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Pauline Raimondeau @paulineraim.bsky.social · 18/08/2025
Excited to be in Barcelona for #ESEB2025 So many great talks, familiar faces and cool posters already!
Picture of the Sagrada familia, symbol of Barcelona
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Megan Frayer @hybridzones.bsky.social · 09/08/2025
This collaboration was so much fun!! I’m excited to see it online! www.cell.com/trends/genet...
cell.com
The molecular evolutionary basis of species formation revisited
How do new species arise? This is among the most fundamental questions in evolutionary biology. The first genetic model for how reproductive barriers lead to the origin of new species was proposed nea...
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 31/07/2025
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...?
link.springer.com
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...
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Joel Sharbrough @jsharbro.bsky.social · 08/07/2025
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
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Haut conseil pour le climat @hc-climat.bsky.social · 03/07/2025
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...
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Nicolas Mouquet @nmouquet.bsky.social · 26/06/2025
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 🧪
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Christophe Cassou @cassouman40.bsky.social · 20/06/2025
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.
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Kevin Bird @stairwaytokevin.bsky.social · 10/06/2025
Ok, fine I'm willing to admit it now: Mimulus is interesting www.authorea.com/doi/full/10....
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.
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Emily Josephs @emjo.bsky.social · 12/06/2025
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...
academic.oup.com
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
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Dmitri Petrov @petrovadmitri.bsky.social · 02/06/2025
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...
simonsfoundation.org
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...
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Moi Expósito-Alonso (MOILAB) @mexpositoalonso.bsky.social · 30/05/2025
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 🧵👇
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Mike Wiser @drmikewiser.bsky.social · 27/05/2025
Ooh, I've run a session on basically "How to Conference" for the undergrad diversity program at the Evolution conference for the past few years. Some of what I cover:
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David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 27/05/2025
This week in my graduate-level Science Communication class, we're discussing scientific conferences, including how to find a conference that's helpful for you, how to make the most of attending a conference, networking, and effective presentation skills. Anyone have any advice to share? 🧪🦑🌎
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Dr. David Miller 🏳️‍🌈 @davidimiller.bsky.social · 22/05/2025
🧪 Detailed data viz NYT article, out today, on the extent of funding cuts at the National Science Foundation. This "broken pie chart" is neat & new to me: Powerfully shows the slowdown in new NSF awards across areas. www.nytimes.com/interactive/...
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Arthur Leung @aleungplants.bsky.social · 15/05/2025
New #CAM paper dropped! nph.onlinelibrary.wiley.com/doi/abs/10.1... #plantscience
nph.onlinelibrary.wiley.com
A high‐quality genome of the Atacama Desert plant Cistanthe cachinalensis and its photosynthetic behavior related to drought and life history
Crassulacean acid metabolism (CAM) photosynthesis has independently evolved many times in arid-adapted plant lineages. Cistanthe cachinalensis (Montiaceae), a desert annual, can upregulate CAM facul...
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Sam Yeaman @samyeaman.bsky.social · 08/05/2025
Are you interested in the genomic basis of repeated adaptation? The RepAdapt group now has >70 members working to re-run their whole genome shotgun datasets through a common SNP calling pipeline, sharing VCFs, and working together to analyse data. Please contact me if you'd like to contribute!
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Stéphane Foucart @sfoucart.bsky.social · 30/04/2025
Chute de 63% de l’abondance des insectes volants entre 2021 et 2024 (UK). Je pensais avoir donné l’information la plus importante de la journée, mais en fait non. La contraction de 0,3% du PIB américain est ce qui compte vraiment. www.lemonde.fr/planete/arti...
lemonde.fr
La rapidité de l’effondrement des populations d’insectes confirmée par une expérience de science participative
Des milliers de Britanniques ont enregistré avec régularité les impacts d’insectes sur les plaques minéralogiques de leurs voitures. Résultat : une disparition vertigineuse de 63 % de ces bestioles vo...
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