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

Connecting the distribution and diversification of marine plants

Integration of the evolutionary history with distribution of extant species is necessary to explain present-day diversity, particularly for ‘foundation' species, such as seagrasses, which create habi...

doi.org

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

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!

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

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

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

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 ...

doi.org

🌊 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. 🔬

Alvaro Fueyo@afueyo.bsky.social · 12mo ago

📢 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...

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...

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...

doi.org

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🧵

📢 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...

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....

doi.org

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

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...

doi.org

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!

Antonio Camargo@apcamargo.bsky.social · last yr.

A BLAST update adding support for compressed files and csv output with headers is a Good Friday night surprise! blast.ncbi.nlm.nih.gov/doc/blast-ne...

🌎👩‍🔬 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)

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

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

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.

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...

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...

birdsoftheworld.org

🧵 #HiloTesis | ¿Cómo se mide el estado de un río? ¿Puede el ADN decirnos si un río está sano? ¡Te cuento cómo he aplicado tecnologías basadas en ADN para evaluar la salud ecológica de los ríos en la Península Ibérica!

Any excuse to post this blast from the past from the last AEET conference that I went to in Almería. Still probably the best poster I've seen in the last few years courtesy of @ibartomeus.bsky.social. #SIBECOLAEET2025

The taxonomic biases in biodiversity data are growing over time. The amount of data we are collecting is growing, but the biases get bigger. We need to make a conscious effort to study the understudied! #SciComms #Science #Taxonomy 🧪 image from Troudet et al 2018 @natureportfolio.bsky.social

I will forever be haunted by this footage. Trawling has only been filmed underwater a few times in documentary history, and never with such clarity. What’s so heart-rending about these shots is watching how the animals don’t just get swept up — they swim for their lives. 🌎🦑🧪

Ok people. I’m drawing silhouettes this afternoon. If you have a paper coming up and you are in need of a #silhouette please let me know and I will have it ready today. As always I upload all my silhouettes to phylopic.org I also have tutorials on how to put a silhouette in a plot in R.

PhyloPic

PhyloPic is an open database of free silhouette images of animals, plants, and other life forms, available for reuse under Creative Commons licenses. Download silhouettes for use in educational materi...

phylopic.org

Can insect bulk samples be used in #metabarcoding without homogenising them? Our research shows: it’s technically possible but yields poorer data and is more expensive and time-consuming. Paper out now: @mbmg.pensoft.net mbmg.pensoft.net/article/1298... @leeselab.bsky.social #nondestructivelysis

Homogenization of insect bulk samples yields more comprehensive yet comparable biodiversity data than non-destructive lysis

The rapid advancement of molecular biodiversity monitoring tools, particularly DNA metabarcoding, has improved specimen identification in bulk samples, such as those from Malaise traps, where traditio...

mbmg.pensoft.net