Nicolas Nesi

A new era in natural history publishing begins. 🐢✨

Introducing the Handbook of the Reptiles of the World!

My lab is hiring a 2-yr hummingbird evolution and genomics postdoc and a 1-yr salaried research and lab tech. Both with full U. Wyoming benefits. Please spread the word! Info below. Best consideration date Nov 1, start dates early Spring 2026.

And then there were none: Australia’s only shrew declared extinct The tally of Australian mammals extinct since 1788 is now 39 species – far more than for any other country

As I argue in #PlatypusMatters, Australia has the world's best mammals, but is sadly the worst place on Earth to be a mammal, with the planet's worst #extinction rate.
The Christmas Island shrew is now the latest species to be officially declared extinct.
www.theguardian.com/environment/...

A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).

A paper in Nature Ecology & Evolution presents a time-calibrated phylogeny of Fungi. This timescale suggests an older age of crown Fungi, as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems. #phylo 🧪

Super excited to finally share this! #CollectionsAreEssential

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

🖥️ Explore the latest from Bioinformatics Advances: "Termal: A fast and interactive terminal-based viewer for multiple sequence alignments"

Full article available: https://doi.org/10.1093/bioadv/vbaf208

Check out our new preprint! We compare sequence versus synteny approaches for resolving a challenging #phylogenetic problem. In this case, synteny is far more informative! Also includes the first chromosome-level #genome for the enigmatic #fish family Gyrinocheilidae. doi.org/10.1101/2025...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

On measures of influence and discordance in phylogenomic analyses Abstract. As models are approximate descriptions of real biological processes, and data are collected often with errors and contaminations, sensitivity or

Scientists often use models to study how species evolved, but these models are not always perfect. Here, Ziheng Yang (Darwin Wallace Medal winner) looks at how small changes in data or assumptions can affect the results of these studies. Check it out below 👇🌍🧪

ASTER: A Package for Large-Scale Phylogenomic Reconstructions Abstract. Many algorithms are available for inferring species trees from various input types while accounting for gene tree discordance. Several quartet-ba

C. Zhang, R. Nielsen and S. Mirarab integrate all ASTRAL-like methods into a single package called ASTER, comprising several tools that collectively enhance the scalability, accuracy, and versatility of species tree inference.

🔗 doi.org/10.1093/molbev/msaf172

#evobio #molbio #compbio

Ces « bibliothèques de l’ombre » où les scientifiques du monde entier partagent gratuitement des articles « Un monde de pirates » (2/5). Les sites sur lesquels les articles scientifiques sont mis à disposition, en toute illégalité, sont très populaires au sein de la communauté universitaire. Rapides, effi...

www.lemonde.fr/series-d-ete...

A workflow for statistical analysis and visualization of microbiome omics data using the R microeco package. #Microbiome #OmicsData #DataAnalysis #R @natprot.nature.com 🧬 🖥️
www.nature.com/articles/s41...

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

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

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... 🧵