Luke E Holman

Integrating eDNA and acoustic-trawl data to provide small pelagic biomass estimates for fish stock assessment Abstract. Accurate abundance estimates of fisheries resources are essential for sustainable fisheries management. In response to the growing need for devel

New paper by Cristina Claver (@azti.bsky.social), published in @icesmarine.bsky.social JMS.

We combine #eDNA and acoustic-trawl data in a Bayesian joint model to estimate biomass of the European anchovy in the Bay of Biscay.

From the potential of eDNA to operational use

🔗 doi.org/10.1093/ices...

🧬📘 New publication! "Invasion Genomics" explores how genomic techniques and data are revolutionising the study of biological invasions. ✍️ by @dan_g_bock and @riuslab.bsky.social 👇https://www.cabidigitallibrary.org/doi/10.1079/9781800626263.0000

I do not want your AI slop
I do not want it in my mop
I do not want it in my house
I do not want it in my mouse
I do not like brain-rotting AI spam
I do not want it, Sam Alt-man

🦣🍖🧬 Fully funded 3-yr PhD in palaeogenomics & bioinformatics! Help me push non-model palaeogenomes beyond their limits @DTU in Denmark.

Start: Feb 2026 (flexible)
Application deadline: 24 Oct 2025

For details click here: tinyurl.com/BioExtPhD

Reposts appreciated 😁

In this blog post, Guest Editor Dr Luke Holman discusses their recent #PhilTransB issue, 'Shifting seas: understanding deep-time human impacts on #marine ecosystems': royalsociety.org/blog/2025/08...

Some thoughts on how our recent theme issue came together

A marine illustration featuring two contrasting marine ecosystems in one perspective.

Here's an illustration I did for the Royal Society Publishing journal and their special release "The shifting seas". It was great fun to work on this hugely educational piece and I wanted to thank @lukeeholman.bsky.social in particular for giving me this opportunity 😊

Thank you so much for your beautiful art. You really captured how humanity has challenged the oceans, while also providing hope for future flourishing seas through recovery and restoration.

🌊

New theme issue of #PhilTransB out today ‘Shifting seas: understanding deep-time human impacts on #marine #ecosystems’. Read here: royalsocietypublishing.org/toc/rstb/202...

Shifting seas: understanding deep-time human impacts on marine ecosystems | Philosophical Transactions of the Royal Society B: Biological Sciences Humans have interacted with, and impacted, marine ecosystems for millennia. During this time, the oceans have experienced ecosystem degradation through harvesting, habitat change, pollution, the introduction of invasive species and climate change. Despite ...

🔗 doi.org/10.1098/rstb.2024.0026

Thank you to all the amazing authors who trusted us with their research. Not to mention our wonderful artists Jacek Matysiak (www.instagram.com/big.hippo.art/) and Maddy Dall (www.instagram.com/maddydall/) who brought the issue to life with their beautiful illustrations.

Contributions use bones 🦴, shells 🐚, old catch records 📜, logbooks 📖, marine sediments 🧪 & more to reach before monitoring began. Using stable isotopes 🧬, ancient DNA 🧫, ecosystem models 🌍 & other tools, they reveal fresh insights into our impact on the seas 🌊.

My amazing co-guest editors @ruththurstan.bsky.social @kbohmann.bsky.social @mikkelwp.bsky.social @tangeolsen.bsky.social & non-Bskyers Ol Craig, David Orton, James Scourse and I found only enthusiasm and interest from our networks - the amazing research rolled in!

There wasn’t an obvious place to bring together data from archaeology 🏺, ecology 🌿, and marine geology 🌊…

Then I saw a call from @royalsocietypublishing.org 📣 for theme issues — and suddenly, everything clicked! 💡🧩

A couple of years ago we were beginning to see exciting interdisciplinary datasets coming out of @erc.europa.eu 🌍 @seachange-erc.bsky.social 🌊. It was amazing to begin to understand the complex dance of climate 🌡️, humans 🧍‍♂️🧍‍♀️, and marine biodiversity 🐟🪸 across centuries! ⏳✨

Shifting seas: understanding deep-time human impacts on marine ecosystems | Philosophical Transactions of the Royal Society B: Biological Sciences Humans have interacted with, and impacted, marine ecosystems for millennia. During this time, the oceans have experienced ecosystem degradation through harvesting, habitat change, pollution, the introduction of invasive species and climate change. Despite ...

🐚 Out today “Shifting Seas – Understanding Deep-Time Human Impacts on Marine Ecosystems.” 🌊

A theme issue asking how, when, and where humans have impacted oceans over millennia.

🔗 doi.org/10.1098/rstb.2024.0026

🧶 below on how it came to life!...

New paper out now in @natcomms.nature.com!

Multiproxy analysis reveals the earliest evidence of whale bone working and broadens the range of taxa known to have been used in the Bay of Biscay during the Late Paleolithic 🐋

Paper 🔗 www.nature.com/articles/s41...

Did you know that most 18/19thC coastal plantations were located at places where the largest Indigenous towns once stood centuries earlier? A great example of how deep-time land use practices create legacies that drive future, cumulative human-ecosystem engagements. 🔗 www.nature.com/articles/s43...

Did llamas make it to southeast South America before Europeans? 🦙

Our manuscript used #archaeology, isotopes, and palaeogenomics #aDNA to find out 🦙🦴🧬

In summary, nope. Just guanacos hanging on into early historical times.

Read it here: authors.elsevier.com/c/1kvQy,rVDB...

Reposts appreciated 😁

Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for gene...

🙌 Thanks to amazing co-authors @kbohmann.bsky.social sky.social, @mikkelwp.bsky.social @seachange-erc.bsky.social, many others not on 💙☁️, & our funders @erc.europa.eu.

Dive into the full study here: doi.org/10.1111/1755...

Lots more detail in the supplements!

💡 Some takeaways:

Different eDNA methods give us different snapshots of ancient biodiversity. Interpret ancient records with care —methodological biases can shape ecological conclusions.

When your material crosses 2-4k years BP be careful interpreting alpha diversity changes.📝

📊 Consistent beta diversity

Despite the richness differences, both methods produced similar beta diversity patterns, highlighting consistent shifts in community composition over time.

Phew!

📉 Very different richness across methods!📉

Our results showed opposing alpha diversity trends:

• Metabarcoding = lower ASV richness in older sediments

• Metagenomics = lower genus richness in younger sediments

A clear reminder that the method truly matters! 🎯

🔍 What taxa overlapped? 🔍

We found that only 3 metazoan genera overlapped between methods:

• Oikopleura (larvacean)
• Gadus (cod)
• Clupea (herring)
(+ 🌿seagrass🌿)

Interestingly we found that only metagenomics provided reliable detections beyond 4k years for all taxa.

🔬 What did we do?🔬

We sampled a long (30m+), old (20y+) marine sediment core from the Skagerrak, North Sea, performing 18S(v9) metabarcoding and shotgun-metagenomic sequencing to see what these very different techniques tell us about ancient oceans.

Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for gene...

🚀 Excited to share our new paper:
“Navigating Past Oceans: Comparing #Metabarcoding and #Metagenomics of Marine Ancient Sediment eDNA”

DOI: doi.org/10.1111/1755...

We dive into 8,000 years of marine life from Skagerrak sediments to show what different tools tell us about past #oceans! 🌊🧬

We have so much more to do to support women in STEM! 👩‍🔬 Here at GLOBE, across Danish academia🇩🇰, and around the 🌍

🚀 Follow these great women, read & cite their work, and stay aware of the biases that can make us miss out on talented researchers & amazing collaborators! 💙 #WomenInSTEM #EquityInScience

Finally, the super talented Lene Bruhn Pedersen! 🧪✨ Her lab skills are crucial to keeping our projects running. 🔬💡

Lene is looking for new opportunities in Copenhagen as our project wraps up. If you need the best lab tech in town, reach out! 👀📢

🔗 More about Lene: seachange-erc.eu/people/lene_...

Working with us on @seachange-erc.bsky.social, we’re lucky to have Giulia Zampirolo! 🧬✨ She brings deep expertise in ancient metagenomics to help us decode past oceans. 🌊

📢 Her latest paper: 🔗 doi.org/10.1016/j.cu...

👀 More about Giulia (not on bluesky) 🔗 seachange-erc.eu/people/giuli...

Next up, the fantastic Kristine Bohmann! 🧬✨ A metabarcoding & eDNA wizard who is simultaneously:

🌊🔍 PI of @seachange-erc.bsky.social (@erc.europa.eu)
🌬️🦠 Leading the airDNA project (DFF)
🧪🌍 Heading the eDNA group at GLOBE

Follow her for top-notch eDNA research! 🚀💡

🔗 @kbohmann.bsky.social