Matthieu Leray, PhD

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.

Bridging the gap between individual specialization and species persistence in mutualistic communities Mutualistic interactions among organisms are fundamental to the origin and maintenance of biodiversity. Yet, the study of community dynamics often relies on values averaged at the species level, igno...

What sustains biodiversity? 🌿🌸🐝🐦‍⬛ It’s not just about species, it’s also about individuals.
 
Our new paper in @esajournals.bsky.social Ecol. Monogr. shows how the way individuals specialize on their mutualistic partners can scale up to shape species persistence.
 
🔗 doi.org/10.1002/ecm....

In massive #collaborative #effort, we assembled published & unpublished #fish 🐟 #eDNA 🧬 metabarcoding datasets, covering ~2000 sampling sites/>100 river systems globally. 🐟 🐠 🐡 🌐 🌍

Now results out in 2 #parallel #preprints @biorxiv-ecology.bsky.social

#aquatic #biodiversity #meta-analysis
1/6🧵

JOB OPPORTUNITY: Lecturer in Marine Biology and Scientific Diving (University of Plymouth)

www.jobs.ac.uk/job/DOS637/l...

#jobs #lecturer #scientificdiving #plymouth #coralreefs #university #marinescience #marinebiology #marineecology #jobopportunity

A roadmap for equitable reuse of public microbiome data - Nature Microbiology In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

I'm grateful to be part of Data Reuse Consortium contributing to the paper "A roadmap for equitable reuse of public microbiome data" published in Nature Microbiology @natmicrobiol.nature.com. It proposes solutions for the data recycling🧵⬇️
www.nature.com/articles/s41...
#microsky 🧪🦠💻🧬👩‍🔬
@i2sysbio.es

Please help me get a job in a different country

For the recent coral reef science arrivals, here are two starter packs so you can find your people! If you want to be added, please let me know. I have been adding people as they come through my feed. go.bsky.app/Qo5Gh2H go.bsky.app/QSafBeL 🌎🌊🧪🌐🐟🪸🐙🌿

Calling all isotope ecologists.
IsoEcol 2026 will be held between October 12-17th, 2026 at the University of Hong Kong
See www.isoecol.com/2026/ for more

Taxon‐specific BLAST percent identity thresholds for identification of unknown sequences using metabarcoding The identification of organisms in environmental samples using metabarcoding relies on factors such as taxonomic assignment methods, genetic markers, reference databases and confidence thresholds ...

📖Published📖

Pappalardo et al. developed taxon-specific confidence thresholds for eukaryotes at different taxonomic levels to optimize the accuracy of BLAST-based taxonomic assignments for metabarcoding 🧬 🌍 🧪 Read more here 👇

My group at NOAA/Miami is hiring a postdoc to lead a marine eDNA biodiversity effort (Bio-GO-SHIP). You'll develop and deploy high-throughput metabarcoding assays for ocean DNA. Help make foundational contributions to global marine biodiversity monitoring! t.co/p53s7E0YiL

Evolutionary consequences of extreme climate events Simon Baeckens and Colin Donihue review case studies of rapid evolutionary change in response to extreme climate events and sketch a framework for future studies in the rapidly changing climate of the...

Extreme climate events can catalyze rapid evolutionary change! in our new Current Biology (@currentbiology.bsky.social) piece, Colin and I argue it’s time to study their evolutionary consequences systematically — beyond opportunistic observations. www.cell.com/current-biol...

How thoughtful experimental design can empower biologists in the omics era - Nature Communications Here, the authors discuss principles of experimental design that are relevant for all biology research, along with special considerations for projects using -omics approaches, highlighting common expe...

I am really excited to see this article on basic experimental design principles published. Definitely will be mandatory reading for incoming graduate students in my lab. Maggie Wagner who led this article did an amazing job with the illustrations of basic principles www.nature.com/articles/s41...

Taxon‐specific BLAST percent identity thresholds for identification of unknown sequences using metabarcoding The identification of organisms in environmental samples using metabarcoding relies on factors such as taxonomic assignment methods, genetic markers, reference databases and confidence thresholds ...

This is great - we a huge need in the #eDNA community to have data-informed standards for eDNA identity cutoffs, not just the bog-standard 97%
besjournals.onlinelibrary.wiley.com/doi/full/10....
For Chordata there is no cutoff that leads to 0% error when assigning species!! (Table S4)

Taxon‐specific BLAST percent identity thresholds for identification of unknown sequences using metabarcoding The identification of organisms in environmental samples using metabarcoding relies on factors such as taxonomic assignment methods, genetic markers, reference databases and confidence thresholds ...

🗣NEW PAPER: Taxon‐specific BLAST percent identity thresholds for identification of unknown sequences using metabarcoding - Pappalardo et al. - Methods in Ecology and Evolution - Wiley Online Library besjournals.onlinelibrary.wiley.com/doi/full/10....

Nanopore metagenomics: from sample to analysis 2026 In this in-person workshop, learn how to extract DNA from metagenomic samples, prepare libraries, carry out nanopore sequencing and analyse data.

Registration now open for our #Nanopore #Metagenomics workshop 2026.

From sample to analysis this course provides an overview of lab and in-field, real-time nanopore #sequencing using @nanoporetech.com platform.

buff.ly/nxk6meF

🧬 🖥️

Editorial: Accountability, voice, and trust - responsible use of GenAI in scientific publishing Over the last few years, the development and rapid advancement of Generative Artificial Intelligence (GenAI) and Large Language Models (LLMs) such as ChatG

Many of us are using LLMs in coding and scientific writing. They are very helpful tools, but we need to be thoughtful as we integrate them into our work flows to preserve accountability, voice and trust. academic.oup.com/evlett/advan.... An editorial at @evolletters.bsky.social for discussion:

Jim Estes, biologist who revealed how sea otters shape entire ecosystems, died on May 20, aged 79 When Jim Estes first arrived in the Aleutian Islands in 1970, he expected a routine wildlife survey. What he found was the outline of a scientific revelation. In places where sea otters thrived, the…

Jim was an incredible ecologist. I own several of his books, and cite his research reguarly. www.butlernature.com/2025/08/20/j...

Diagram of a template design for a CTmax apparatus. Aeration, mixing mechanisms (pump), and heating elements are in an ‘equipment section’ that is physically separated with a screen from the part of the arena containing the animals (‘animal arena’; here with fish). A submerged temperature sensor (or data logger) is used to log temperatures, in addition to a temperature sensor with a display that is used to score CTmax in real time. The time and temperature should only be visible to the data recorder (and/or video camera), not to the person observing animals for end points.

📖Published📖

Raby et al. provide a comprehensive, practical guide for designing and conducting experiments to measure critical thermal limits, with an emphasis on CTmax 🌍 🧪 👇

buff.ly/iZN6Xdg

Help TaMIS Thrive in Memory of Dr. Eric Crandall, organized by Medina Lab Penn State Biology Dr. Eric Crandall was an Assistant Research Professor of Biol… Medina Lab Penn State Biology needs your support for Help TaMIS Thrive in Memory of Dr. Eric Crandall

Help TaMIS Thrive in Memory of Dr. Eric Crandall gofund.me/00c84a15

The American Lobster’s Baby Bust - bioGraphic A potentially dire change in spawn timing threatens the future of lobster in the Gulf of Maine.

The American Lobster’s Baby Bust

A potentially dire change in spawn timing threatens the future of lobster in the Gulf of Maine

www.biographic.com/the-american...

ecoevojobs.net 2025-26

The 2025-26 Eco-Evo job list is out. Good luck to those applying!

docs.google.com/spreadsheets...

Stronger El Niños reduce tropical forest arthropod diversity and function Nature - Time-series data from tropical forests tracking weather and declines in arthropod diversity and function show that fluctuations in species were largely dependent on their El Niño...

New article out today in Nature - intensified El Niño events under climate change appear to be chipping away at tropical forest arthropod diversity.

This is already leading to substantial losses in arthropod function in primary forests across the tropics.

rdcu.be/ezAxP

Study finds mysterious DNA split in great white sharks defies current explanations White sharks (Carcharodon carcharias) almost went bottom-up during the last ice age, when sea levels were much lower than they are today and sharks had to get by with less space.

Genetic analysis shows great white sharks have distinct mitochondrial DNA differences unexplained by current theories, leaving the cause of this divergence unresolved. doi.org/g9v72q

BioTIME 2.0: Expanding and Improving a Database of Biodiversity Time Series Motivation Here, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The up...

🚨New data paper/open data alert!🚨 BioTIME v2.0 is out now! We've expanded the database with improved spatial and taxonomic coverage, with a new R package! As always, free, public, and open acess :)

Paper:
onlinelibrary.wiley.com/doi/10.1111/...

Database:
biotime.st-andrews.ac.uk

Plasticity in climate change responses Recent research has shown that climate change can both induce and modulate the expression of plastic traits but our understanding of the role of phenotypic plasticity as an adaptive response to clima...

Plasticity in climate change responses - just published in Biological Reviews

What in the role of phenotypic plasticity as an adaptive response to climate change?

Looking at mechanisms from the subcellular to the community and ecosystem levels.

With Stollewerk, @davidboukal.bsky.social, et al.

Empirical evidence of widespread exaggeration bias and selective reporting in ecology - Nature Ecology & Evolution Analysing >18,000 effect sizes from recent ecology studies published in five leading journals, the authors identify widespread under-powered designs, exaggeration bias, selective reporting and few ...

Empirical evidence of widespread exaggeration bias and selective reporting in ecology 🌎🌐🧪 www.nature.com/articles/s41...

The Galapagos Islands, where a sea lion hunts salema fish

Marine protected areas can protect fish and maintain healthy ecosystems. As demonstrated by two related papers in this issue, however, such areas are only effective against illegal fishing when established limitations are enforced.

Learn more this week in Science: scim.ag/3H6oeXQ

bumping again: I am hiring a project coordinator /researcher for an interagency freshwater mussels project (USFS 🌲 lead). Position will be based out of USFS Northern Research Station in Wisconsin and starts Sep. 15, For more information/to apply, www.ugajobsearch.com/postings/438...

AdDeam: A Fast and Scalable Tool for Estimating and Clustering Reference-Level Damage Profiles AbstractMotivation. DNA damage patterns, such as increased frequencies of C→T and G→A substitutions at fragment ends, are widely used in ancient DNA studie

Thrilled to see this out in Bioinformatics! AdDeam is a powerful tool to rapidly estimate aDNA damage from BAM files and cluster them to flag outliers—great for large/small aDNA projects and ancient metagenomics to find contigs likely to be modern. Great work by Louis Kraft!
doi.org/10.1093/bioi...

A comment I wrote for you is now online at @natcomms.nature.com:

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

Oh, oh, it says "time travel will likely remain forever off the table in our universe" with a citation, so read it maybe? (am I doing the click-bait thing right? 🥲).