Alvaro Fueyo

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!

Conservation paradoxes: 36 species which are invasive in some areas but still need protecting elsewhere. Issue 623: Some species are invasive and economically costly in some areas, but conservation priorities in others. A study identifies 36 such species, finding them to be conservation priorities due to...

environment.ec.europa.eu/news/conserv...

DNA barcoding reference dataset revealed overlooked diversity and clarified biogeography of fishes in the largest European river system – Volga River This study represents the first thorough genetic assessment of freshwater fishes from the Volga River basin – the longest (3,690 km) river in Europe. DNA barcode sequences (COI) were studied in ...

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

Evaluating the potential of DNA metabarcoding for ecological status assessment under the Water Framework Directive: A case study on benthic invertebrates from Western Carpathian streams Routine biomonitoring under the Water Framework Directive (WFD) follows a conventional methodology primarily based on the morphological identification of taxa within the five biological quality elemen...

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.

Technical challenges in the implementation of macroinvertebrate DNA metabarcoding in river biomonitoring: A case study from peninsular Spain—Advantages, limitations and roadmap This study evaluates the opportunities and challenges of using DNA metabarcoding of river macroinvertebrates for routine ecological status assessment under the EU Water Framework Directive. By reanal....

📢 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.

Back to life after 50 years: effects of environmental flow restoration on macroinvertebrate biodiversity and river ecological status. A case study of the Valseco stream, Spain The construction of dams and reservoirs to meet increasing water and electricity demands has significantly altered many natural river flows, posing threats to the ecological integrity of freshwater e...

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...

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)

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

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.

Birds of the World - AviList: A Unified Global Checklist of the World’s Birds is Now Available AviList, a unified global checklist of birds, that provides the most current and authoritative taxonomy of birds around the world was released today by experts in taxonomy, nomenclature, and bioinform...

A monumental taxonomy unification effort has just been published - thanks to all those who've collaborated for years to make this happen!
birdsoftheworld.org/bow/news/avi...

Creo que croacia es del espacio schengen desde 2023 🤔

(PDF) Assessing DNA metabarcoding and environmental DNA for biomonitoring fluvial ecosystems using macroinvertebrates in peninsular Spain PDF | Fluvial ecosystems play a vital role in supporting biodiversity, providing freshwater, and sustaining human societies. Despite their importance,... | Find, read and cite all the research you nee...

😇 Para los curiosos que se la quieran leer o al menos echar un vistazo, está disponible a través de este enlace:
www.researchgate.net/publication/...

Esta tesis ha desarrollado como un Doctorado Industrial en colaboración con Taxus Medio Ambiente y @universidadoviedo.bsky.social. Y ha sido financiada por el Ministerio de Ciencia e Innovación y la agencia Sekuens del Principado de Asturias.
@crueuniversidades.bsky.social
@filarramendi.bsky.social