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Rémi Allio

@remiallio.bsky.social
61 followers 79 following 5 posts

PhD - Phylogenomics - Molecular Biology - Evolution - My research aims to understand the links between ecological traits and molecular evolution. Current target: Weevils! remiallio.github.io

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Reposted by Rémi Allio
Prof. Jeff Ollerton @jeffollerton.bsky.social · 18h
Want to conserve #birds, #mammals and other vertebrates? Then don’t forget their #insects. Our new Nature Reviews Biodiversity paper explores the many ways vertebrates depend on insects — for food, shelter, protection and much more. I’ve written about it here: jeffollerton.co.uk/2026/09/30/w...
jeffollerton.co.uk
Want to conserve birds and mammals? Then conserve their insects – our new paper in Nature Reviews Biodiversity sets out the details
It’s sometimes easy to forget quite how much of the living world depends upon insects. That might seem an odd thing for someone who has spent much of his career studying insects and their relations…
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Emmanuel F.A. Toussaint @toussaintlab.bsky.social · 03/09/2026
JOB ALERT // 🔥New Permanent Research & Collection Officer position at the Geneva NHM @mhngeneve.bsky.social 🔥We are looking for an entomologist to join our team at the Museum !🦋🐜🐞🦗🦟🔬🧬🧪🇨🇭. Please RT massively ! Ad here (in French but don’t hesitate to DM for details : www.geneve.ch/administrati...
geneve.ch
Chargé ou Chargée de recherche en entomologie à 80-100%
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Centre de Biologie pour la Gestion des Populations @cbgpmontpellier.bsky.social · 10/09/2026
Soutenance de thèse au CBGP! Mardi 15 sept., 13h "Histoire évolutive et écologique des charançons Ochyromerini : vers une compréhension de l’émergence des systèmes de pollinisation de couvain en zone tropicale" par Benjamin ZELVELDER @umontpellier.bsky.social www.youtube.com/live/zIOAzSG...
poster de la soutenance de thèse de Benjamin Zelvelder
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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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Jakob Jilg @weevil-see.bsky.social · 01/08/2026
Spread the word! The Weevil Workers meetings consist of a series of presentations on any aspect of the study of weevils (Curculionoidea). Topics include systematics, faunistics, biogeography, evolution, biology, ecology, pests/biological control agents, etc. www.curculionoidea.org/weevil-worke...
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Joanna Masel @joannamasel.bsky.social · 27/07/2026
Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social
academic.oup.com
Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models
Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig
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Flo Débarre @flodebarre.eurosky.social · 26/11/2024
#HelloESR Voici un kit de démarrage de chercheuses et chercheurs en écologie-évolution en poste en France go.bsky.app/HM6CfJ5 Aidez-moi à le compléter ! Une contrainte : une auto-nomination de chercheur doit s'accompagner d'une nomination de chercheuse
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Laura Alencar 🇧🇷🐍🦎 @alencarlrv.bsky.social · 11/06/2026
Interested in #macroevolution, #macroecology, and mountain biodiversity? I'm recruiting a #postdoc for an NSF-funded project at Yale, in collaboration with Martha Muñoz (Yale) and Maya Stokes (Florida State University). I'll be at #Evol2026 and happy to chat! Link below
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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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The Royal Society @royalsociety.org · 05/06/2026
Professor Joe Felsenstein FRS is elected a Fellow of the Royal Society. After initially working on population genetics theory of recombination, of migration, and of speciation, his main focus has been on phylogenetic inference. #RSFellows royalsociety.org/people/joseph-fels…
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Matthew Hahn @3rdreviewer.bsky.social · 02/06/2026
Very happy to announce a big new paper from the lab, led by grad students @smishra677.bsky.social and Laia Pomar-Pallarès (in collaboration with @roblanfear.bsky.social). We introduce a new way to study introgression, with accompanying software (DAFT) 1/n 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
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Molecular Biology and Evolution @molbioevol.bsky.social · 25/05/2026
Wong et al. present IQ-TREE version 3, with new features including mixture models, gene and site concordance factors, integration with phylogenomic divergence time estimation, and a fully featured sequence simulator. 🔗 doi.org/10.1093/molbev/msag117 #evobio #molbio #compbio
MBE | IQ-TREE 3: phylogenomic inference software using complex evolutionary models
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Niklas Wahlberg @lepphylo.bsky.social · 03/06/2026
Finally we know where the enigmatic Caribbean genus Calisto goes in the tree of life, thanks to the amazing work by Rayner Nunez! Mixture models seem to be the way to go! doi.org/10.1111/syen...
doi.org
Mixture models unveil the origin of the enigmatic Satyrinae butterfly genera Calisto and Llorenteana (Lepidoptera, Nymphalidae, Satyrinae)
We provide the first reliable hypothesis on the phylogenetic position of Calisto and Llorenteana within the tribe Satyrini, based on genomic data representing all subtribes. We apply for the first t.....
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MU-Peter Shimon 🀄 @mu-peter.bsky.social · 01/06/2026
Ok, this is cool... Treemble: A graphical tool to generate Newick strings from phylogenetic tree images🧪 academic.oup.com/bioinformati... Treemble is a native desktop application for macOS and Windows and is freely available, with documentation, at treemble.org.
Treemble views and performance.
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Rémi Allio @remiallio.bsky.social · 27/05/2026
1/2 New tool for #Phylogenomics 🚀 GABBI is an open-source pipeline that designs target-capture kits using whole-genome alignments across multiple taxa instead of a single reference genome. 👉more informative loci, better phylogenetic resolution, less reference bias - even with #museum specimens! 🪲
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Enric Frago @enricfrago.bsky.social · 27/05/2026
Interested in #plant #herbivore #predator #symbiont interactions and #thrips #biocontrol? I am recruiting a permanent lab technician at #CBGP #Montpellier. All backgrounds and identities welcome. Please repost! @cbgpmontpellier.bsky.social More info here: recrutement.cirad.fr/offre-de-emp...
recrutement.cirad.fr
Cirad - Technicien·ne en écologie des interactions et gestion des populations d'insectes nuisibles
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Laurie Belcher @lauriebelch.bsky.social · 26/05/2026
We’re hiring for OrthoFinder! Great role for someone who enjoys scientific software development: Python, data analysis, workflows, Git, scalability, and making tools nicer to use. Comparative genomics or open-source bioinformatics experience would be a lovely bonus. my.corehr.com/pls/uoxrecru...
my.corehr.com
Job Details
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Rémi Allio @remiallio.bsky.social · 26/05/2026
We are very glad to introduce a new method for designing phylogenetically informative target-enrichment datasets that leverages recent whole-genome alignment methods to identify thousands of shared and homologous regions across a broad range of reference taxa! Please, check out Benjamin's preprint!
GABBI: an automated, open-source pipeline, integrating genome alignments into phylogenetic markers selection
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Gael Kergoat @gkergoat.bsky.social · 01/04/2026
Paper alert! 📣 Really cool study stemming from the Master thesis of #Benjamin_Zelvelder @cbgpmontpellier.bsky.social @inrae-dpt-spe.bsky.social with @remiallio.bsky.social #insect host-shifts between #parasitic and non-parasitic plants! #Proc.B @royalsocietypublishing.org doi.org/10.1098/rspb...
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Rob Denton @rddenton.bsky.social · 27/10/2025
Genome assembly fresh of the supercomputer, total size = 29,892,519,935 base pairs 🦎🧬
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Gael Kergoat @gkergoat.bsky.social · 17/09/2025
Our monograph (128 pages!) of the brood-pollinator #weevil genus #Derelomus is now out in @ejtaxonomy.bsky.social ! 😃 #OA Huge revision work led by #Julien_Haran @cirad.bsky.social / @cbgpmontpellier.bsky.social with some #integrative_taxonomy approaches to help clarifying some species complexes!
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Mick Westbury @mick2474.bsky.social · 09/09/2025
🦣🍖🧬 Fully funded 3-yr PhD in palaeogenomics & bioinformatics! Help me push non-model palaeogenomes beyond their limits @DTU in Denmark. Start: Feb 2026 (flexible) Application deadline: 24 Oct 2025 For details click here: tinyurl.com/BioExtPhD Reposts appreciated 😁
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Jonathan Romiguier @selfishmeme.bsky.social · 04/09/2025
You may have missed this #ant poster at #ESEB2025, but be sure not to miss the article just published in #openacess in @nature.com: www.nature.com/articles/s41...
nature.com
One mother for two species via obligate cross-species cloning in ants - Nature
In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...
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Gael Kergoat @gkergoat.bsky.social · 04/09/2025
Will be at #Ento25 next week in #Glasgow! I will give a talk on some overlooked #pollinators (based on results we got @cbgpmontpellier.bsky.social) Will also be there as EIC of #Systematic_Entomology @royentsoc.bsky.social; do not hesitate to contact me if you have any questions about the journal!
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Nature @nature.com · 03/09/2025
A common type of ant in Europe breaks a fundamental rule in biology: its queens can produce male offspring that are a whole different species go.nature.com/4mOb5T9
go.nature.com
‘Almost unimaginable’: these ants are different species but share a mother
Ant queens of one species clone ants of another to create hybrid workers that do their bidding.
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Nature @nature.com · 03/09/2025
How is this possible? This ant can lay eggs of two different species, birthed by the same mother
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Anton Suvorov @antonsuvorov.bsky.social · 24/08/2025
My very first post on here. I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
biorxiv.org
GhostParser: A highly scalable phylogenomic approach for the identification of ghost introgression
A growing body of empirical research shows that interspecific gene flow is a widespread biological force that shapes evolutionary histories across the Tree of Life. Computational approaches designed t...
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Rosa Fernández @rosafernandez.bsky.social · 15/08/2025
FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲 @gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social @csic.es www.nature.com/articles/s42...
nature.com
FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life
Communications Biology - FANTASIA, a protein language model-based tool, enables large-scale functional annotation across ~1000 animal proteomes, revealing novel gene functions in both model and...
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alexgilardet.bsky.social @alexgilardet.bsky.social · 06/02/2025
A high-throughput aDNA extraction method for large-scale sample screening 🦣🦬🧬 onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
A High‐Throughput Ancient DNA Extraction Method for Large‐Scale Sample Screening
Large-scale DNA screening of palaeontological and archaeological collections remains a limiting and costly factor for ancient DNA studies. Several DNA extraction protocols are routinely used in ancie...
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Laurie Belcher @lauriebelch.bsky.social · 18/08/2025
Super interesting session on post-phylogenomics this morning at #eseb2025 I have a poster on the new version of Orthofinder - there will be a suggestion box 🎁 P03.076 on Thursday
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Rémi Allio @remiallio.bsky.social · 18/08/2025
If, as it is commonly thought, you only see weevils as pest species, it is time to change your mind! Have a look at Benjamin’s poster at #eseb2025 tonight! He will introduce you to the unexpected diversity of very cute weevils involved in the pollination of tropical trees! 🌴🌙 #ANR POLLIDIV
Benjamin Zelvelder’s poster about transitions from antagonists to mutualists in weevils evolutionary history #eseb2025Derelomini sp on Attalea in Costa RicaBenjamin inspecting flowers in Costa Rica’s canopy
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Martin Johnsson @mrtnj.bsky.social · 18/08/2025
Aurélien Tellier with the nice idea of using DNA methylation markers for demographic inference for recent time. #eseb2025 elifesciences.org/articles/89470
elifesciences.org
Improved inference of population histories by integrating genomic and epigenomic data
The developed statistical method paves the way for next generation demographic and selection inference by combining information from several heritable genomic and epigenomic markers.
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Molecular Biology and Evolution @molbioevol.bsky.social · 13/08/2025
Gregarious behaviour in butterfly larvae has evolved multiple times - Cicconardi, @ebablab.bsky.social et al. use genome data of 60 Heliconiini species, identifying signatures of convergent molecular evolution, on both coding and noncoding loci. 🔗 doi.org/10.1093/molbev/msaf179 #evobio #molbio
doi.org
Convergent Molecular Evolution Associated With Repeated Transitions to Gregarious Larval Behavior in Heliconiini
Abstract. Collective behavior forms the basis for many antipredator strategies. Within Lepidoptera, larval gregariousness has evolved convergently across m
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Toni Gabaldón @tonigabaldon.bsky.social · 17/08/2025
#eseb2025 has started. So many friends and colleagues around. This is amazing. Welcome everyone to Barcelona!
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C. Brandon Ogbunu @cbo.bsky.social · 27/07/2025
Biologist folk (especially in evolutionary biology and/or ecology, but it don’t matter): Can you give me your favorite examples of trade offs in biology? Organism or system don’t matter. Primary literature or reviews preferred.
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Gael Kergoat @gkergoat.bsky.social · 26/07/2025
Happy about our grad. student #Zhe-Yuan_Yu (@cbgpmontpellier.bsky.social & @isyeb.mnhn.fr) 1st paper, where she & @tonyrobillard.bsky.social described a new 🦗 species from Madagascar 😀 A follow-up study, focusing on the historical biogeography of the genus Xenogryllus should come very soon !!
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Anne Charmantier @annecharmantier.bsky.social · 26/07/2025
Huge thank you @aeastephens.bsky.social‬ for initiating the TrendsTalk series 'Disability in ecology and evolution' in T.R.E.E. providing visibility for disabled researchers in #Ecology & #Evolution to make our field more #inclusive www.cell.com/trends/ecolo...
cell.com
Disability in ecology and evolution
In this TrendsTalk series 'Disability in ecology and evolution' in Trends in Ecology and Evolution, we will be hearing from people about their experiences being disabled in ecology and evolution. We a...
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Jonathan Romiguier @selfishmeme.bsky.social · 22/07/2025
New article about Messor harvester ant phylogeny and evolution funded by @erc.europa.eu in @isemevol.bsky.social resjournals.onlinelibrary.wiley.com/doi/10.1111/...
resjournals.onlinelibrary.wiley.com
Phylogenomics of Messor harvester ants (Hymenoptera: Formicidae: Stenammini) unravels their biogeographical origin and diversification patterns
Phylogenomic analysis of 2524 ultraconserved-element loci from 58 Messor harvester ant species helps in redefining taxonomic groups of the genus. Messor ants emerged in the Irano-Indian area around ...
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