Matthieu Leray, PhD

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? 🥲).

Theory of host-microbe symbioses: Challenges and opportunities Growing insight into microbial symbioses highlights the need to model these systems mathematically. We discuss three areas requiring theoretical advan…

Trainees and faculty that I had the privilege to be a part of did something quite special. The context here is that experimental and theoretical biologists were in a room together on Coconut Island, Hawaii for 3 weeks to hammer out a vision #holobiont theory. 🧵
www.sciencedirect.com/science/arti...

Change. . .

Come be my colleague (& @jacquelyngill.bsky.social's and other great folks)!

UMaine is hiring a Genetics Facilities Manager to lead the CORE eDNA and DNA Sequencing Labs. Hiring range is $75-85k (up $20k from previous round)

fa-ewca-saasfaprod1.fa.ocs.oraclecloud.com/hcmUI/Candid...

Join marine researchers @UBC (ubcoceans.ubc.ca). CERC in Ocean Ecological Modeling (research.ubc.ca/media/file/c...). $8M to work at the intersection of oceanography, fisheries, ecology, biodiversity, etc, in the context of environmental change, ecosystems, biogeochemistry & living marine resources.

The Nice Declaration “Our Ocean, Our Future: United for Urgent Action” adopted by acclamation at the UN Ocean Conference (#UNOC3) last month in Nice required a recorded vote by the UN General Assembly. Results:
- 162 in favour
- 1 against (US)
- no abstentions
press.un.org/en/2025/ga12...

Proteobacteria with chemosynthetic potential are highly enriched in the gills of Hypoplectrus reef fishes A variety of marine invertebrates are known to form associations with chemosynthetic bacteria, but to the best of our knowledge this has not been documented in fishes. Here, we apply genome-resolved m...

New peprint out: "Proteobacteria with chemosynthetic potential are highly enriched in the gills of Hypoplectrus reef fishes"
www.biorxiv.org/content/10.1...
Please let us know if you have any suggestions to make this paper better!

🐠🦈 Just out: In this paper we ask "How has reef trophic structure changed since humans started removing predatory fishes from Caribbean coral reefs?".

www.pnas.org/doi/10.1073/...
Illustrations @cookedillustrations.com

What is common knowledge in your field, but shocks outsiders?

By age 60, you'll have >100 billion cells containing mutations in genes related to cancer ('driver genes'). That's 2-3% of all your nucleated cells.

You're accumulating ~20 mutations PER CELL PER YEAR ... but still no super-powers.

What animals do at scale: a new lens on behaviour and conservation - Lancaster University As environmental changes speed up, it's becoming more important to understand how animals behave on a large scale. A new approach called macrobehaviour combines the study of animal behaviour with big-...

Nice little overview of my research direction these days www.lancaster.ac.uk/sci-tech/abo... @lec-reefs.bsky.social @lancasteruninews.bsky.social

A Metadata Checklist and Data Formatting Guidelines to Make eDNA FAIR (Findable, Accessible, Interoperable, and Reusable) Environmental DNA (eDNA) has emerged as a transformative tool for biodiversity monitoring and species detection, yet inconsistent metadata practices hinder data interoperability and reuse. To address...

🚨 Out now in #EnvironmentalDNA led by #MiwaTakahashi: Results of a huge, global effort to facilitate the publication of raw and processed #eDNA data & ensure that dataset we are currently generating, adhere to the #FAIR principles & won't be lost. @gbif.org, #ENA,
doi.org/10.1002/edn3...

Our new paper on the historical and scientific basis of Darwin’s ‘coral reef paradox’ is out @currentbiology.bsky.social! Summary below by @gobyone.bsky.social.

Also with @paulinenarvaez.bsky.social
@oclaripv.bsky.social
and Vale Parravicini!

Free-access link:
authors.elsevier.com/a/1lDFm3QW8S...

Very useful, thank you!

There are recordings, but unfortunately due to privacy reasons @physaliacourses.bsky.social is unable to make them available for downloading (even to participants).

My material is all available on github though: github.com/BertvanderVe....

AutoMLST2: a web server for phylogeny and microbial taxonomy. #MicrobialTaxonomy #Phylogeny @narjournal.bsky.social‬ 🧬 🖥️
academic.oup.com/nar/advance-...

A small cunner (Tautogolabrus adspersus) peers through strands of sugar kelp (Saccharina latissima) in a lush kelp forest ecosystem on Cashes Ledge in the Gulf of Maine.

Kelp forests on the coast of Maine are in decline owing to rapid ocean warming and are being replaced by turf algae, which alter the ecosystem’s chemistry, hindering the recovery of kelp forests.

Learn more in this week's issue of Science: scim.ag/4dwzl8j

A sphere with a mossy texture resembling a marimo ball, surrounded by cherry shrimp of various sizes.

It's a shrimp world we're all just living in it

The planktonic microbiome of the Great Barrier Reef Large genome databases have markedly improved our understanding of marine microorganisms. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pela...

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂

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

New paper out showcasing the metabolic flexibility of a marine symbiosis in response to environmental changes driven by seasonal upwelling — beautifully led by @isimorel.bsky.social at @mpimarinemicrobio.bsky.social

Considering the massive benefit using Nanopore provided for building the GBR-MGD—HQ/complete Pelagibacter, SAR86, Prochlorococcus, etc pMAGs+ chromosome-level picoeukaryote eMAGs + HQ Crassvirales vMAGs—seems fitting to share this preprint during London Calling.

@nanoporetech.com #nanoporeconf

Just out in PNAS! www.pnas.org/doi/10.1073/... "The evolution of thermal performance curves in response to rising temperatures across the model genus yeast". Beautiful work using experimental evolution forecasting climate impacts on biodiversity by Jennifer Molinet @jennifermolinet.bsky.social

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...

Really happy to announce that the updated version of BioTIME is out!!🚨 This is the largest #database of #biodiversity #timeseries - now with 708 studies and >56 thousand species from across the planet!🦊🐀🐦🐊🐟🐙🦋🐞🌲🍀
& over 400 co-authors sharing their data🤩🤩
onlinelibrary.wiley.com/doi/10.1111/...

Le dessous des images - Quand la Chine convoite Taïwan - Regarder l'émission complète - Arte Diffusée sur les réseaux sociaux chinois en mars 2025, cette vidéo dévoile un navire destiné à des débarquements armés de grande envergure. Une mise en scène spectaculaire qui alimente la propagande chinoise et rend plus concrète que jamais la menace d'une invasion de Taïwan.

Le dessous des images - Quand la Chine convoite Taïwan - Regarder l'émission complète - Arte

Joint species distribution modelling of multiple taxonomic groups shows that water quality explains most of the variation in aquatic community composition along a lake trophic gradient - Aquatic Ecolo... A key component of conservation biology is understanding how community composition responds to environmental conditions, including stressors (e.g., eutrophication). However, this is complicated by the...

NEW PAPER: Joint species distribution modelling of multiple taxonomic groups shows that water quality explains most of the variation in aquatic community composition along a lake trophic gradient doi.org/10.1007/s104....

#AcademicSci 🧪