Matthieu Leray, PhD
@mattleray.bsky.social
Staff Scientist at 📍 Smithsonian Tropical Research Institute.
Symbiosis | Trophic ecology | eDNA | Coral reefs🪸🧬🫧
Symbiosis | Trophic ecology | eDNA | Coral reefs🪸🧬🫧
Reposted by Matthieu Leray, PhD
🌐 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
🌍🦤🦑🪴🍁🧪
✨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
🌍🦤🦑🪴🍁🧪
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.
globalecologybs.github.io
November 10, 2025 at 12:02 PM
🌐 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
🌍🦤🦑🪴🍁🧪
✨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
🌍🦤🦑🪴🍁🧪
Reposted by Matthieu Leray, PhD
🦭 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
Read the full paper here! ➡️ buff.ly/vecdcwH
November 10, 2025 at 11:02 AM
🦭 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
Read the full paper here! ➡️ buff.ly/vecdcwH
Reposted by Matthieu Leray, PhD
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...
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
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...
www.cell.com
November 9, 2025 at 9:39 AM
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...
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
Reposted by Matthieu Leray, PhD
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.
November 5, 2025 at 10:34 AM
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.
Reposted by Matthieu Leray, PhD
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!🧪🪸🧬🌎🌊🐙🦠🌿
October 27, 2025 at 12:13 PM
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!🧪🪸🧬🌎🌊🐙🦠🌿
Reposted by Matthieu Leray, PhD
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
@bembidion.bsky.social
October 25, 2025 at 12:37 AM
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
@bembidion.bsky.social
Reposted by Matthieu Leray, PhD
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 🧪🌏
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 🧪🌏
October 15, 2025 at 4:12 AM
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 🧪🌏
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 🧪🌏
Reposted by Matthieu Leray, PhD
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. 🧪🪸🌎🌊🧬🌐🌿🐡🐙
October 14, 2025 at 3:16 AM
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. 🧪🪸🌎🌊🧬🌐🌿🐡🐙
Reposted by 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.
October 2, 2025 at 10:24 AM
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.
Reposted by Matthieu Leray, PhD
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....
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....
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...
doi.org
October 2, 2025 at 1:12 PM
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....
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....
Reposted by Matthieu Leray, PhD
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🧵
Now results out in 2 #parallel #preprints @biorxiv-ecology.bsky.social
#aquatic #biodiversity #meta-analysis
1/6🧵
September 29, 2025 at 1:32 PM
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🧵
Now results out in 2 #parallel #preprints @biorxiv-ecology.bsky.social
#aquatic #biodiversity #meta-analysis
1/6🧵
Reposted by Matthieu Leray, PhD
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
www.jobs.ac.uk/job/DOS637/l...
#jobs #lecturer #scientificdiving #plymouth #coralreefs #university #marinescience #marinebiology #marineecology #jobopportunity
September 29, 2025 at 5:30 AM
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
www.jobs.ac.uk/job/DOS637/l...
#jobs #lecturer #scientificdiving #plymouth #coralreefs #university #marinescience #marinebiology #marineecology #jobopportunity
Reposted by Matthieu Leray, PhD
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
www.nature.com/articles/s41...
#microsky 🧪🦠💻🧬👩🔬
@i2sysbio.es
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.
www.nature.com
September 29, 2025 at 10:56 AM
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
www.nature.com/articles/s41...
#microsky 🧪🦠💻🧬👩🔬
@i2sysbio.es
Reposted by Matthieu Leray, PhD
Please help me get a job in a different country
If universities anywhere are hiring an Evolutionary Biologist/Paleontologist please let me know! I'm on the market for Tenure Track positions!!
You can find more about my research on fish evolution here: rtfigueroa.wixsite.com/my-site
You can find more about my research on fish evolution here: rtfigueroa.wixsite.com/my-site
September 25, 2025 at 7:19 PM
Please help me get a job in a different country
Reposted by Matthieu Leray, PhD
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 🌎🌊🧪🌐🐟🪸🐙🌿
February 4, 2025 at 3:11 AM
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 🌎🌊🧪🌐🐟🪸🐙🌿
Reposted by Matthieu Leray, PhD
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
IsoEcol 2026 will be held between October 12-17th, 2026 at the University of Hong Kong
See www.isoecol.com/2026/ for more
IsoEcol 2026 – 14th International Conference on the Application of Stable Isotope Techniques in Ecological Studies
www.isoecol.com
September 15, 2025 at 8:39 AM
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
IsoEcol 2026 will be held between October 12-17th, 2026 at the University of Hong Kong
See www.isoecol.com/2026/ for more
Reposted by Matthieu Leray, PhD
📖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 👇
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 👇
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 ...
buff.ly
September 12, 2025 at 11:00 AM
📖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 👇
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 👇
Reposted by Matthieu Leray, PhD
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
https://explore.msujobs.msstate.edu/cw/en-us/job/509519
t.co
September 8, 2025 at 3:54 PM
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
Reposted by Matthieu Leray, PhD
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...
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...
www.cell.com
September 8, 2025 at 7:17 PM
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...
Reposted by Matthieu Leray, PhD
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...
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...
www.nature.com
August 7, 2025 at 7:43 PM
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...
Reposted by Matthieu Leray, PhD
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)
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 ...
besjournals.onlinelibrary.wiley.com
August 29, 2025 at 6:50 AM
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)
besjournals.onlinelibrary.wiley.com/doi/full/10....
For Chordata there is no cutoff that leads to 0% error when assigning species!! (Table S4)
🗣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....
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 ...
besjournals.onlinelibrary.wiley.com
August 29, 2025 at 2:55 AM
🗣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....
Reposted by Matthieu Leray, PhD
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
🧬 🖥️
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
🧬 🖥️
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.
buff.ly
August 27, 2025 at 10:01 AM
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
🧬 🖥️
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
🧬 🖥️
Reposted by Matthieu Leray, PhD
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:
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
academic.oup.com
August 22, 2025 at 12:52 PM
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:
Reposted by Matthieu Leray, PhD
Jim was an incredible ecologist. I own several of his books, and cite his research reguarly. www.butlernature.com/2025/08/20/j...
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…
www.butlernature.com
August 24, 2025 at 4:57 PM
Jim was an incredible ecologist. I own several of his books, and cite his research reguarly. www.butlernature.com/2025/08/20/j...