Matthieu Leray, PhD

🤔Looking to make your #code more #reproducible? Check out our new and improved guide to Reproducible Code! 🧪🌍️

Find it here👇️
buff.ly/10TeNok

@nhcooper123.bsky.social
@britishecologicalsociety.org

Time to publish responsibly: DAFNEE, a database of academia-friendly journals in ecology and evolutionary biology Abstract. The current economics of scientific publishing reveal a profound imbalance: academia pays prices far exceeding the actual costs of publication. R

Responsible publication of your research!

To help you do this @nicolasgaltier.bsky.social and coauthors have put together a handy database of academia-friendly journals, DAFNEE. You can read about it in their article recently published in @jevbio.bsky.social:

doi.org/10.1093/jeb/...

A schematic image showing Recent changes in reef zonation of western Atlantic coral reefs, brought about by lack of recruitment of elkhorn, staghorn, and massive boulder corals. Without these key reef builders, the reefs have already measurably eroded. Image credit: Rashpal Dhilon. Adapted from ref. 6, which is licensed under CC BY 4.0. The panel on the left labeled Late Pleistocene to ~1978 shows a vibrant ecosystem, the middle panel (the 1980s) is depleted but still many corals remain (though some key species are lost). The panel on the right (2020s) is like a moonscape with a few hardy species left.

Very effective illustration of what has happened to Florida's coral reefs in response to anthropogenic climate and environment change. The loss of this important ecosystem is all but complete - attempts to rescue it discussed here: www.pnas.org/doi/10.1073/... 🪸🧪🌊

A hex sticker with a text that reads Hello Data Science with green, yellow and pink scatterplot points in the background. There is a web address www.hellodata.science

📖 Big news! We just released the first five chapters of our new book, Hello Data Science. It is a fully open-access resource written for beginners. Please help us spread the word! A few points about the book are below 👇

🔗 www.hellodata.science

#rstats #datascience #tidyverse

Ecological insights from three decades of forest biodiversity experiments - Nature Reviews Biodiversity Experiments manipulating tree species diversity and measuring effects on ecosystem function have been important tools for assessing how biodiverse forests can accumulate biomass, store carbon and help...

🧪

Now that shutdown is over, I'm looking forward to #SICB2026 in Portland, Oregon in January! Please check out Session 18: A Stinging Sense of Self: Cnidarian Cell Type Evolution on Sunday Jan. 4 at 10:00am! Also please reach out if you're interested in making lunch/dinner plans during the conference!

My first hairy #shrimp!!! Suuuuuper stoked to see this rare holy grail species!
The #hairyshrimp (Phycocaris simulans) aka the #AlgaeShrimp, is a nearly impossible to see tiny tiny tiny little varmint.

#phycocarissimulans #🦐 #calimari #muckdiving #tulamben #tulambenbali #bali

🚨 Research Highlight | New tools—Surprising findings: A new study shows human impacts cause relatively little changes in energy flow on coral reefs

📖 Read the research highlight ➡️ buff.ly/J52H2WN

📖 Read the full paper ➡️ buff.ly/W98t51d

Release Next time I'll try to be FASTA · tseemann/any2fasta New features Option -k is keep processing even when some inputs fail option -g to include GBK version suffix option s to strip desc from>id desc in ID lines Support for PDB protein structure forma...

💾 any2fasta 0.8.1 is released!

The FASTA format is now 40 years old (Pearson & Lipman) and any2fasta makes it easy for your scripts and pipelines that accept FASTA to also accept other formats, even if compressed! eg. .gbk.gz

#bioinformatiocs #microbiology #genomcs
github.com/tseemann/any...

Adult male (small) and female (large) of Armillifer sp. Looks like a big and small crinkle cut french fry, also with paired hooks at the front. Both photos from this paper: https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0000320

Adult female Linguatula serrata. Looks like a wrinkly tube, a bit wider at the front and tapering to a tail. There are some hooklike bits at the front.

🚨 Don't eat uncooked snake! Your eyes & lungs can be parasitized by pentastomids, which are a CRUSTACEAN. Adults lack so many features that they weren't believed to be arthropods at all until their DNA was sequenced (and sperm morphology, but that was not widely accepted). Yet, they are!
#Crustmas 🧪

Thanks @cfrederica.bsky.social for your hard work on that one! Also thanks to the reviewers and editor at @animalecology.bsky.social for the feedback that helped improve the paper. Will submit there again for sure.

So nice to see this one out! Congrats @cfrederica.bsky.social

Colombia bans all new oil and mining projects in its Amazon Colombia will no longer approve new oil or large-scale mining projects in its Amazon biome, which covers 42% of the nation’s territory, according to a Nov. 13 statement by its environment ministry. Ac...

Very proud to be Colombian right now! 🇨🇴 I hope all neighboring countries follow suit soon! news.mongabay.com/short-articl...

Coral Bleaching: The Equatorial‐Refugia Hypothesis

🔗 buff.ly/xtRwbvO

Excited to share that my lab is moving to HKU @swimshku.bsky.social early next year! Really looking forward to working with great colleagues in the Baker, Schunter, Mcilroy, Gaitan and Russell labs, @bonebraking.bsky.social, @jonscibulski.bsky.social and others in the School of Biological Sciences

Here, we show that deep below, corals and feather stars don’t just share space – they share microbes. Endozoicomonadaceae + Nitrosopumilaceae inhabit both hosts in a “promiscuous” symbiosis that may fuel nitrogen cycling in the deep sea.
doi.org/10.1186/s401... 🌊🪸🧪 #Bioinformatics 🧬💻 #SymbioSky

The Brown and Stachowicz labs are looking for a postdoc for an NSF-funded project on the thermal dependence of disease in eelgrass! As a bonus you get to be based at the Bodega Marine Lab! Interested? Find out more here: brown-ecology.com/join-us/

The sponge-ctenophore debate was one of the first that excited me as an undergrad. It’s so cool to still see new papers coming out on the topic!

"Our data are exquisite. Our world is empty."

An amazing piece on the coral reefs of the future by Rick MacPherson.

bluesky Global Ecology Feed Digest #38 Curated digest of the bluesky Global Ecology feed on biodiversity, ecosystems & conservation at large scales. Terrestrial, freswater & marine realms.

🌐 Global Ecology feed Digest #38, Nov 3-10, 29 posts!

✨For the lazy (yes we are!) & friends who don't like social media but might benefit from this feed, here’s a DIGEST crafted with 💚 for you to share

👉 globalecologybs.github.io/feeddigest.g...

DM if you want to receive the link weekly

🌍🦤🦑🪴🍁🧪

🦭 New study reveals overlooked intraspecific variation in prey quality and its influence on predator energy budgets. By identifying key ecological drivers, they emphasize the need to integrate such variability into bioenergetic models.

Read the full paper here! ➡️ buff.ly/vecdcwH

The hitchhiker’s guide to cross-species DNA delivery Microbial hitchhikers are rewriting the rules of horizontal gene transfer. He, Patkowski, et al. reveal how phage satellites assemble chimeric infective particles that deliver DNA across species bound...

The hitchhiker’s guide to cross-species DNA delivery

@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez

www.cell.com/trends/micro...

Oxygen supersaturation has been reported to protect aquatic animals from heat waves. We tested this in a large collaborative experiment on many species of fish and crustaceans. Our new paper in @plosbiology.org shows that the effect of hyperoxia on thermal tolerance is negligible. Unfortunately.

Advert for Art and Science session at upcoming ICRS in Auckland New Zealand. July 19-24 2026. Abstract deadline December 1, 2025.

Please join us in this uplifting and inspiring session bringing Art and Science together at the upcoming International Coral Reef Symposium in Auckland, New Zealand, July 19-24 2026. See you all there! Fighting to save reefs through Art!🧪🪸🧬🌎🌊🐙🦠🌿

Mesquite's two icons, one against a black background, and one against a sun on a sky blue background.

Mesquite 4.02 update released! It fixes a few bugs and adds Codon Alignment and various other improvements. Also, much faster with genomics files with 1000s of loci. www.mesquiteproject.org 🧪 #evolbio
@bembidion.bsky.social

The cover of the Cleaning Biodiversity Data in R book. It has an illustration of an Pacific Cleaner Shrimp in the middle of a navy background. The shrimp has a bright red-orange shell, pale-yellow body and white whiskers.

Still want to make cleaning biodiversity data shrimp-ler? 🦐

Good news: We just updated our Cleaning Biodiversity Data in R book, so you still can! We've updated data for 2025, added new content & fixed lots of silly typos 😀

Live the shrimp-le life:
cleaning-data-r.ala.org.au

#rstats #ecology 🧪🌏

Call for abstracts Reefs Reimagined: Art and Reefs. International Coral Reef Symposium July 19-24, 2026. Submission deadline Dec 1, 2025.

Join our session to discuss the role of art in coral reef conservation at the International Coral Reef Symposium in Auckland, New Zealand July 19-24, 2026. Abstract deadline Dec 1, 2025. 🧪🪸🌎🌊🧬🌐🌿🐡🐙

Okinawa had its hottest September at 1.6C above the average. I filmed this mass coral bleaching last year, but didn't have the heart to share. Total annihilation of the first few meters of depth. This stuff happens before our eyes, and yet people who think it isn't real keep gaining power.