Nicolas Nesi

La pomme de terre a pour ancêtre… la tomate, selon une étude récente Une équipe internationale a publié, le 31 juillet, dans la revue de biologie « Cell », une surprenante découverte : l’apparition de tubercules chez l’ancêtre de la pomme de terre, il y a 9 millions d’...

www.lemonde.fr/sciences/art...

Cette loi affaiblit la protection de l’environnement sous la pression de l’agro-industrie.

✍️ La pétition envoie un message fort : les citoyens ne veulent pas sacrifier le vivant. Pour espérer un referendum il faut qu’on soit 4,8 millions.

✒️ Alors on signe.
👥 On partage.
🗣️ Et on interpelle !

Here is a very cool piebald Ethiopian epauletted fruit bat (Epomophorus labiatus) that we caught last month in Lilongwe, Malawi! 🦇

Piebaldism is a rare genetic condition caused by the absence of melonocytes in certain patches of skin and fur.

#bats #research #fieldwork #malawi #wildlife

**JOBS ALERT**

The Virology Unit at @PasteurCambodia
hiring 1 Scientist and 2 Postdocs to join our fast-moving, field-connected, research-driven team on emerging viruses and zoonoses.

🧪🧬🥼🦠🔬🐓💉🦇😷

Limited time to apply — and we need people to start ASAP.**👇

Ever wanted to infer a morphological or total-evidence phylogeny in BEAST2?
It’s long overdue, but we now have a tutorial on Taming the BEAST to talk you through the process 💻🌳⚙️
Thanks to Joëlle Barido-Sottani for helping me pull this together!
taming-the-beast.org/tutorials/To...

Fun fact: The greater sage grouse attracts females of its species by inflating two yellow air sacs on its chest and bouncing them around to produce a unique sound.💄🐦🍸 #naturalhabitatshorts #naturalhabitok #naturalhabitat

Ethical scientific journals and where to find them....here is DAFNEE, a #database of non-profit journals in #Ecology and #Evolution #EvoBio, to choose an ethical place where to publish your next articles! (1/2)

dafnee.isem-evolution.fr

🧪 #science

Physalia megalista, a cnidiran with a gas filled float, raised sail, and long blue tentacles hanging below. Image credit: Dalila Destanović

Excited to share our study on sailing siphonophores, AKA bluebottles or man-o'-war! 🌊 we received hundreds of samples from scientists around the world, part of a huge effort to sequence genomes and test for multiple species 🧬 out today in @currentbiology.bsky.social doi.org/10.1016/j.cu... 🦑🧪📌

can we have in the future SmartCite for onlyoffice please?

Fun fact: The Spix's disc-winged bat has suction cups on its thumbs and ankles that let it stick to surfaces. It uses these to stick to the inside of banana leaves to roost 🦇🪠🤝 #naturalhabitatshorts #naturalhabitok #naturalhabitat

MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update) Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...

The new version of MetaPhlAn v4.2.2 released!

📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs

Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...

Two icons of the Mesquite program, with leaves of the mesquite tree against a black background (first icon) and against the blue sky and sun (second icon).

Mesquite 4.beta2 released! Much faster reading of files with thousands of matrices. New features since 4.beta include Trace All Changes (known from MacClade) and Import GenBank Numbers. www.mesquiteproject.org & discuss at groups.google.com/g/mesquite-p...
‪@bembidion.bsky.social ‬🧪 #evolbio

Revised phylogeography of the common brushtail possum (Trichosurus vulpecula) reveals new insights into genetic structure across Australia Abstract. Understanding genetic relationships within species is essential for identifying distinct genetic lineages and informing conservation strategies,

We're not playing (dead), you'll enjoy this! New research by Shelby Middleton reveals a revised taxonomy & new sub-species of Australia's brush-tailed possum! Could you possumbly get more cute? Impossumable! 🌍🧪👇

academic.oup.com/zoolinnean/a...

@linneansociety.bsky.social @pezoporus.bsky.social

SHARK: web server for alignment-free homology assessment for intrinsically disordered and unalignable protein regions Abstract. Whereas alignment has been fundamental to sequence-based assessments of protein homology, it is ineffective for intrinsically disordered regions

SHARK: web server for alignment-free homology assessment for intrinsically disordered and unalignable protein regions. #ProteinHomology #WebServer #Bioinformatics #Genomics 🧬 🖥️ @narjournal.bsky.social‬
academic.oup.com/nar/advance-...

Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain - Nature Microbiology ChronoStrain accurately profiles low-abundance strains in longitudinal samples by jointly modelling nucleotide sequencing errors, strain presence/absence and the temporal information associated with e...

🚨 Out now!

Chronostrain - a method to profile low abundance strains in longitudinal microbiome samples 🦠💻

@travis.gibsonlab.io @younhk.bsky.social @gibsonlab.io @harvardmed.bsky.social @broadinstitute.org

#MicroSky 🦠 #MicrobiomeSky

www.nature.com/articles/s41...

ACE2 from Pipistrellus abramus bats is a receptor for HKU5 coronaviruses - Nature Communications This work shows that receptor use in merbecovirus is clade-specific by clustering them into clades based on the receptor-binding domain (RBD) of their spike proteins. While MERS-CoV and its close rela...

Our study screening the majority of all published Merbecovirus RBD’s for cell entry phenotypes is now published in Nature Communications!
(1/5)
shorturl.at/gYz4E

Using museum specimens for microbiome analyses?

We tested it out - and it seems these samples could be an untapped resource for understanding host-microbe interactions! ⬇️

New blog post!
In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup.
Check it out for the full results:
rrwick.github.io/2025/05/27/d...

A new method for trimming alignments in #phylogenomics — PhyIN. It identifies and trims regions with high phylogenetic discord. Able to trim well even on single loci — an advantage for gene tree/species tree studies. #evolbiol #phylogeny 🧪http://doi.org/10.7717/peerj.18504 Some backstory... 🧵

🎉Bat Conservation Win 🎉
Livingstone’s fruit bat (𝘗𝘵𝘦𝘳𝘰𝘱𝘶𝘴 𝘭𝘪𝘷𝘪𝘯𝘨𝘴𝘵𝘰𝘯𝘪𝘪) has been officially downlisted from Critically Endangered to Endangered by the IUCN!

Autocycler: long-read consensus assembly for bacterial genomes Motivation: Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using ...

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

Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use)

github.com/rrwick/Autoc...

Le chacal doré, un nouveau venu en France qui pourrait s’établir durablement Des individus de cette espèce aperçue sporadiquement en France depuis 2017 ont été vus en Occitanie et en Normandie, ces dernières semaines. Depuis les années 1960, la population installée notamment d...

www.lemonde.fr/planete/arti...

Fun fact: Common murre chicks leap off cliffs before they can fly, bouncing off rocks on the way down to reach the ocean, where their dad takes over raising them at sea
🐧🪨🌊 #naruralhabitatshorts #naturalhabitok #naturalhabitat

The Genius Bat: The Secret Life of the Only Flying Mammal|Hardcover An awe-inspiring tour of bat world by the world’s leading expertWith nearly 1500 species, bats account for more than twenty percent of mammalian species. The most successful and most diverse gro...

Yossi Yovel's book is out! 🦇 Yossi, the Batman, is not only a super original neuroscientist, he's also a great writer and adventurer. Recenlty he's been releasing, one by one, his tales from the jungles. Get his book on promotion here: bit.ly/TheGeniusBatBN

My paper about type I error rates in Qst/Fst comparisons is now published in @genetics-gsa.bsky.social. Check it out here: academic.oup.com/genetics/adv...

Fun Fact: Some species of tarantulas keep frogs as “pets” in a mutualistic relationship. The frogs eat insects that would otherwise threaten the tarantulas’ eggs, and in exchange, the tarantulas offer them protection from predators.
🐸🕷️🦮 #naturalhabitatshorts #naturalhabitok #naturalhabitat

SPECIAL ISSUE Part 2! This month @genomeresearch.bsky.social publishes a diverse collection of articles offering novel biological and clinical insights gained using long-read DNA and RNA sequencing technologies and other long molecule approaches.
tinyurl.com/Genome-Res-3...

Massive inter-species introgression overwhelms phylogenomic relationships among jaguar, lion, and leopard Abstract. Phylogenomic analyses of closely related species allow important glimpses into their evolutionary history. Although recent studies have demonstra

academic.oup.com/sysbio/advan...

Healthy microbiome—moving towards functional interpretation AbstractBackground. Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to d

A new metagenomic health index developed as an answer to recent developments in microbiome definitions, helping distinguish between healthy and unhealthy microbiomes

Healthy microbiome—moving towards functional interpretation doi.org/10.1093/giga...