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

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

academic.oup.com

Joanna Masel@joannamasel.bsky.social · 8mo ago

Sequence alignments are notoriously prone to error. Our latest preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. www.biorxiv.org/content/10.6... @phylowheeler.bsky.social 1/10

#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

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

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/...

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.

nature.com

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 https://royalsociety.org/people/joseph-felsenstein-38106/

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...

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

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...

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.....

doi.org

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.

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! 🪲

Rémi Allio@remiallio.bsky.social · 2mo ago

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!

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...

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...

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!

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 3mo ago

A new method based on genome alignments provides a highly resolutive target enrichment set for weevils (Coleoptera, Curculionoidea) https://www.biorxiv.org/content/10.64898/2026.05.09.724036v1

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...

Genome assembly fresh of the supercomputer, total size = 29,892,519,935 base pairs 🦎🧬

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!

🦣🍖🧬 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 😁

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...

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...

nature.com

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!

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

‘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.

go.nature.com

How is this possible? This ant can lay eggs of two different species, birthed by the same mother

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...

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...

biorxiv.org

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...

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...

nature.com

A high-throughput aDNA extraction method for large-scale sample screening 🦣🦬🧬 onlinelibrary.wiley.com/doi/10.1111/...

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...

onlinelibrary.wiley.com

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

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

Aurélien Tellier with the nice idea of using DNA methylation markers for demographic inference for recent time. #eseb2025 elifesciences.org/articles/89470

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.

elifesciences.org

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

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

doi.org

#eseb2025 has started. So many friends and colleagues around. This is amazing. Welcome everyone to Barcelona!