Tom Hughes presents LIMPET - a new pipeline for detecting erroneous sequences in reference databases for #metabarcoding. Some databases contain more errors than others, but even highly curated databases can contain errors that will impact taxonomic assignment and ecological inference #UKDNAWG26
📖Published!
Comparing passive and active kelp restoration techniques along an urbanised coast🌿
Passive restoration through water quality improvements facilitates substantial kelp gains, offers increased scalability and provides broader ecosystem benefits across seascape scales🌊
🔎 buff.ly/3KHXyVt
Our new paper is out in Oikos. We link the evolutionary history of seagrasses with the latitudinal distributions of extant species, showing that ancestral niche legacy still shapes present-day ranges and diversification patterns. doi.org/10.1002/oik.11820
graphic describing the recovery of different ecosystem components, by Elliott, M., Á. Borja, R. Cormier, 2025. Managing marine resources sustainably – But how do we know when marine management has been successful? Ocean & Coastal Management, 265: 107623.
Now, it has achieved a good ecological status, sensu #WFD, for most of the ecosystem components, such as #phytoplankton, #benthos or #fish….
This has happened in many other European countries, thanks to the #WFD
#GES4SEAS #MOOC #oceanoptimism
We've got ISSUES. Literally.
We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?
arxiv.org/abs/2601.07563
A 🧵 1/n
Book cover for Reproducible Code guide. The cover has a red background with a large yellow-bodied black-headed stag beetle.
Excited to launch the new improved Reproducible Code guide from @britishecologicalsociety.org @methodsinecoevol.bsky.social FREE online here! www.britishecologicalsociety.org//wp-content/... Amazing work by some very talented ECRs. We hope it’s useful!
DNA barcoding reference dataset revealed overlooked diversity and clarified biogeography of fishes in the largest European river system – Volga River.
🔗 doi.org/10.3897/arph...
@mbmg.pensoft.net
🌊 A few weeks ago I shared my PhD roadmap on metabarcoding for river biomonitoring — with a focus on peninsular Spain. What’s working, what isn’t, and what’s next for our freshwater ecosystems. 🔬
Looking for openly available:
- before-after data in space
- with a restoration measure inbetween (e.g. dam/invasive spec. removal, urban green space creation...)
- min. 10 sites (quadrats / random places along a stream / ponds...)
- species data, env. data of some sort, GPS coordinates
New Publication in The Journal of Fish Biology!
"Hidden in the gut: Metabarcoding reveals overlooked predation by the invasive European catfish (Silurus glanis)"
onlinelibrary.wiley.com/doi/10.1111/...
Had a great time at the SEM Malacology Forum presenting two research projects — one poster on the restoration of the Piles River and an oral communication on the sequencing of Iberian freshwater molluscs. 🐚🌊 #Malacology #Biodiversity #Metabarcoding
DNA metabarcoding identifies more invertebrate species under the Water Framework Directive than conventional methods, showing promise for faster and finer river health monitoring in Slovakia’s Carpathian streams.
🔗 doi.org/10.3897/mbmg...
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🧵
To move from research to routine use, we propose a roadmap 🛣️ — focused on implementation in Spain, but adaptable to other regions.
Why do results differ between bulk, eDNA & morphology? 🤔
We show in our article concrete examples from our data of false positives, false negatives & other sources of variability — and propose solutions.
📊 See the summary in the table 👇
💧 eDNA from rivers gave the most divergent results vs. bulk metabarcoding & morphology ID.
👉 Same pattern seen in other studies, even with a different methodology.
⏳ The spatiotemporal scale of the eDNA signal is still unclear — we must understand it better before using it in routine biomonitoring.
In our NW Spain case study, we compared three complementary approaches:
🧪 Bulk (homogenized) tissue metabarcoding
💧 eDNA (water sample) metabarcoding
🔎 Traditional morphological ID
We examined false positives/negatives and other sources of variability driving discrepancies.
📢 We’ve just published the discussion & roadmap from my PhD thesis: a critical look at how metabarcoding of macroinvertebrates can (and cannot yet) be used for routine river biomonitoring.
Let me walk you through the key take-homes, and where the method still needs work. 🧵
doi.org/10.1002/2688...
In just months, macroinvertebrates recolonised step by step.
📊 DNA metabarcoding + classical ID revealed a rapid shift from pioneer taxa to sensitive EPT groups (Ephemeroptera, Plecoptera, Trichoptera).
Good ecological status achieved in under 2 years!
Opening the bottom valves of the Matalavilla dam released the first ecological flows in half a century, breathing life back into the Valseco stream.
💧 A simple change, a huge ecological impact.
Our new paper shows how a small Iberian stream, dry for 50 years, bounced back to good ecological status in <2 years after environmental flows were restored. 🌊🪱
👉 doi.org/10.1111/rec.70198
#RiverRestoration #EnvironmentalFlows #FreshwaterEcology
It's actually amazing how long I've been waiting for this. No more guessing which column has the querycovperc!
Plus, gzipped fastas for makeblastdb! Finally!
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
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)
Researchers have filmed thousands of climbing catfish scaling waterfalls, providing a rare insight into the daring migration of an enigmatic fish.
Learn more: https://scim.ag/4lDlFux
![4-panel comic. (1) [Person 1 with ponytail flanked by person with short hair and another person speaking into microphone at podium] PERSON 1: In the early 2010s, researchers found that many major scientific results couldn’t be reproduced. (2) PERSON 1: Over a decade into the replication crisis, we wanted to see if today’s studies have become more robust. (3) PERSON 1: Unfortunately, our replication analysis has found exactly the same problems that those 2010s researchers did. (4) [newspaper with image of speakers from previous panels] Headline: Replication Crisis Solved](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreibwuu57ullc7vacjyno6c5z3gtyakkg2qub6cn3dbbjdpn2kaowmi)
4-panel comic. (1) [Person 1 with ponytail flanked by person with short hair and another person speaking into microphone at podium] PERSON 1: In the early 2010s, researchers found that many major scientific results couldn’t be reproduced. (2) PERSON 1: Over a decade into the replication crisis, we wanted to see if today’s studies have become more robust. (3) PERSON 1: Unfortunately, our replication analysis has found exactly the same problems that those 2010s researchers did. (4) [newspaper with image of speakers from previous panels] Headline: Replication Crisis Solved
Replication Crisis
xkcd.com/3117/
📖Published📖
Sources of uncertainty in DNA metabarcoding of whole communities: Implications for its use in biomonitoring 🧬 🌍 🧪 Find the article here 👇
buff.ly/6zJRh9R
We want to thank reviewer #2 for the very constructive comments. We were able to incorporate all of them. The manuscript is now much more clear.
