A hell of a nuisance

Posted on January 24, 2026 by lembrechtsjonas

Non-native species can be, pardon my words, a hell of a nuisance sometimes.

Case in point: invasive pine species in the Southern Hemisphere. Did you know that there are no (none!) native pine species south of the equator? Given how common pines are here in Western Europe, I always found that hard to fathom. But given how common they are in the Southern Hemisphere, it becomes downright mind-boggling.

For over a century, pines have been among the most widely used genera in plantation forestry across many Southern Hemisphere countries, including Chile and Argentina, but also South Africa and New Zealand. The problem is: once they’re there, they start spreading. And many types of native vegetation – such as the iconic Araucaria forests of Chilean Patagonia, or the grasslands of the Patagonian steppe – are highly vulnerable to pine invasion. You can almost see the invasion front creep forward.

The forefront of the Pine invasion, with the Lonquimay-volcano in the background

Even worse, once they’re established, these pines are devastating for native biodiversity. They grow into complex, tangled forests that are extremely hard to get through (“unleashed” pines don’t need straight lines anymore – let alone straight stems). They acidify the soils and smother out the light, resulting in near-deserts underneath their needly branches.

A dense stand of expanding lodgepole pines, with stems growing in all directions, creating an understory that is almost impossible to pass

For nature conservation in places like Patagonia, this is a nightmare. And to make matters worse, it’s pretty tough to get rid of them once they’re established. When I had the opportunity to visit Malalcahuello National Reserve in central Chile (home to the famous ‘monkey puzzle tree’ (Araucaria araucana) forests), I got to see the trouble in action. Pine removal is simply a lot of manual labour, and the end result is far from pretty.

But when they’re gone, they’re gone, right?
…Right?

Experimental sites in the Patagonian steppe before (left) and after (right) pine removal. The left picture shows the density and complexity of the pine canopy, the right picture the ‘desert’-like emptiness that remains here after pine removal.

That’s exactly what we set out to test in a paper just published in the Journal of Vegetation Science, led by our colleagues from the University of Concepción in Chile. From previous work, we already knew how bad pines are for native ecosystems: they significantly reduce the richness and abundance of native species, and cause major changes in microclimatic conditions (air and soil temperature) and soil properties (reductions in nitrogen, potassium, and pH). The big question was: do those systems recover after pine removal?

First, a little good news. Yes, we did see a recovery of microclimatic conditions to levels close to uninvaded control sites, driven by the reduction in pine canopy cover and litter. But… that’s where the good news ended.

Strong effects of pine removal (green) on microclimate conditions, as compared with pre-removal conditions (orange). Where pine canopy reduced maximum temperatures significantly, its removal resulted in consistently high maxima.

We also looked at how native understory diversity responded to pine removal, two years after the intervention. The result? It didn’t do shit. The desert remained just as deserted after pine removal as it was before – especially in the sites that had been most heavily invaded.

Understory plant species diversity parameters as a function of the ton per hectare of pine biomass that was removed, before (orange) versus after (green) pine removal for the Araucania forest site. The graph shows the complete lack of change in understory vegetation, despite the substantial change in pine canopy.

This tells us that the legacy effects of pine invasion are strong, at least up to two years after removal. If anything bounced back at all, it was pine seedlings. Native species barely benefited from the improved microclimate conditions.

Pine seedling

So is this a gloomy story?
Yeah – maybe this time it is.

But that doesn’t make it any less important. It’s crucial to know that some conservation problems are simply a pain in the ass. At least now we know, and we can keep searching for better solutions. Our paper suggests that effective management of invasive conifers must move beyond tree removal alone, and include complementary restoration actions that address persistent abiotic and biotic legacies.

Scattered pine trees in between a few old and persistent Araucaria trees

And perhaps this is, once again, a warning: if you can prevent those pines from establishing in the first place, it’s a whole lot cheaper (and far less annoying) than trying to get rid of them later.
But that’s a different story altogether. Because first we need to know which species to act on before they become annoying… and that’s simply not how we humans tend to work.

An impressive Araucaria-tree, looking out at the volcano

Reference

Fuentes-Lillo et al. (2026) Beyond Control: Short-Term Legacy Effects of Invasive Nonnative Trees May Halt Biodiversity Recovery. Journal of Vegetation Science. https://onlinelibrary.wiley.com/doi/10.1111/jvs.70110

Posted in General | Tagged , , , , , , | Leave a comment

Don’t mess with physics

Posted on December 22, 2025 by lembrechtsjonas

Gather ‘round, my friends, because this one is important! A few years ago, we released our Global maps of soil temperature – a project that brought climate data much closer to the conditions that actually matter for the organisms living in and on the soil. However, and this is the important bit: some of our maps are physically impossible.

While defying physics sounds like a big no, I’d say it’s not truly a surprise (I already wrote about similar issues in a warning here). The first version of these maps was always meant as a stepping stone, a workable product that could get our data into the hands of ecologists worldwide, and would be a step up – but not yet a leap – from what we were using up till then. But now, thanks to some careful detective work by Tomas Uxa, we can actually quantify just how our maps break one of the basic rules of heat transfer in soils. His opinion paper on the matter in Global Change Biology is thus a must-read.

Here’s the deal: heat in soils behaves predictably. One key rule is that temperature fluctuations get smaller as you go deeper. Simple, right? Not (always) so in our maps. When comparing two soil depths, an average of 26% of the grid cells – and up to 46% for certain bioclimatic variables – showed reversed patterns. In other words, deeper soils sometimes had bigger temperature swings than shallower ones. Physically impossible (and also only present in less than 5% of the raw data).

Breakdown of the physically impossible differences between the two soil layers of our global mpas, for the relevant bioclimatic variables

Why did this happen? To create our maps, we trained independent machine learning models for each soil depth. Separate models. Separate datasets. And while ML is amazing, it doesn’t inherently respect the laws of physics. The result: maps that are mostly useful, but occasionally rebellious.

Global breakdown of the number of bioclimatic variables per grid cell that is physically impossible. Note that the areas of ‘worst offence’ don’t match with the areas that are suggested to be excluded based on the extrapolation outside of the environmental space of the training data (b-c)

Uxa’s recommendation is practical: the maps are still incredibly useful, but when working with multiple depths, use each depth separately and keep this caution in mind. Any analysis that relies on comparing the two depths directly may produce physically impossible results and should be avoided.

Regional distribution of the proportion of suspicious grid cells among the seven considered soil bioclimatic variables (a) in the European Alps and (b) on the southern margin of the Congolian rainforest. Note that the mismatch closely relates to environmental complexity and steep environmental gradients, such as distinct topography changes or sharp biome transitions. The white areas represent glaciers and water bodies.

And the timing couldn’t be better. We’ve just in earnest started the work on the follow-up: Global maps of soil temperature 2.0, a new version that will hopefully solve many of the problems of its predecessor. The new version will incorporate over three times the data we had before, cover environmental variation better, and – crucially – move toward a one-model approach across depths and months. This should align our predictions more closely with physical reality. We’re also planning higher spatial resolution thanks to the explosion of computing power – so ecologists can finally get the detail that matters at scales that matter.

Up till then, a note of caution: handle our first-generation global soil maps (and really, any global maps) with care, and read Uxa’s piece to understand the quirks. And stay tuned… 2.0 promises to be a big leap forward.

Posted in General | Tagged , , , | Leave a comment

Twelve years of blogging (and counting)

Posted on December 18, 2025 by lembrechtsjonas

With the end of the year in sight, I always reflect a bit on this website and what it has achieved. Quite a shock to realize now that I’ve been blogging consistently for more than twelve years! Even better, the visitor statistics are still showing a steady increase. And yes, that genuinely makes me happy. It feels like quiet confirmation that all those hours spent writing and reflecting were not entirely in vain.

Visitor stats of The 3D Lab since its foundation in 2013 at the start of my PhD.

That feels like a good excuse for some reflection: what does it actually mean to blog as a scientist, and would I recommend it to others?

When I started the blog, I did so more or less on day one of my PhD. Unsurprisingly, there wasn’t much research output to talk about yet – because, well, the research still had to happen. In those early years, the blog had much more of a travel-magazine vibe. It was full of fieldwork stories and photos from the mountains, documenting places and adventures rather than results.

Slowly but surely, those travels turned into datasets, and those datasets turned into papers. At that point, the blog evolved with them. I made it a habit – also from day one – to write a blogpost about every paper on which I was a co-author. I often get the question where I find the time to do that, and honestly: it is often hard to squeeze into an already full schedule. But my thoughts have always been simple: if I can’t find two hours or so to summarize the key findings of a paper, why did I even bother contributing to it in the first place?

For me, blogging about published papers thus always – foolishly perhaps – trumps writing new ones. It’s a way of celebrating past wins before chasing the next deadline. Otherwise, it’s very easy to get stuck in a rat race where papers pile up but joy may disappear.

As my network grew, the audience of the blog grew with it. And I think providing this extra layer on top of a scientific paper – where I highlight what I find important – helps get the message across more clearly and, I hope, more convincingly. It reduces the risk of papers being forgotten and buried under the ever-growing avalanche of scientific output. Just as importantly, it helps reinforce the idea that each individual paper has value – to me, and to others – rather than being just another brick in a publication wall.

The blog has also given me space to tell stories that don’t fit neatly into the standard scientific paper format (like this one). Several of those posts have been among the most read. Early on in the ChatGPT hype, for instance, I wrote a post about how I perceived its pros and cons for research. Another well-visited piece dives into the surprisingly non-trivial question of which microclimate sensor to choose, a post I still occassionally share with people that ask me that question.

It’s also been an excellent platform to publicize new global research networks and invite people to join. That worked particularly well for initiatives like SoilTemp (now MEB) and EcoFracNet. One post I still hear about is the one where we offered free microclimate sensors to be installed in as remote places as possible, to help fill gaps in our global database. That kind of outreach simply doesn’t fit anywhere else as naturally.

And yes, the blog still occasionally features fieldwork photos and travel reports – although I’m definitely less of a nature photographer now than I was during my PhD.

So, would I recommend blogging to other scientists?

In general: yes, if you’re comfortable with it being a slightly slower medium. Blogging works best when combined with other forms of outreach; otherwise it’s hard to get the word out. Twitter used to be ideal for that, and while I never really managed to recreate that dynamic elsewhere, LinkedIn has become the most workable alternative for now. It’s not the same, though.

One big advantage is that writing blogposts is surprisingly therapeutic. It forces you to slow down and really think about your published work. Even without a large audience, that process alone helps sharpen your understanding of the bigger picture you’re contributing to. You could post the same insights directly on social media, but to me that always feels fleeting.

So yes, I’ll keep on blogging. If only to keep forcing myself to think about what I want to tell people, and why I’m doing what I’m doing in the first place. And I hope you’ll stick around, keep reading, and occasionally stumble upon a useful nugget or two along the way.

Posted in General | Tagged , , , , | Leave a comment

Sarane rocks!

Posted on December 18, 2025 by lembrechtsjonas

You wouldn’t guess it from the amount of work she has already put into getting the global MIREN Rocks network off the ground and moving forward, but Sarane is only at the very beginning of her scientific trajectory. That trajectory just received a major boost: Sarane has been awarded an FNRS FRIA doctoral grant, allowing her to start a PhD on her beloved rock cliffs and their ecology.

This is a fantastic achievement for her, and wonderful news for us as a team. It gives us the certainty that MIREN Rocks can now deliver much more in-depth science than would have been possible without her central role.

In her PhD, co-supervised by Alain Vanderpoorten (University of Liège) and myself (Utrecht University), and in close collaboration with Koenraad Van Meerbeek (KU Leuven), Sarane will work with the global vegetation database collected by MIREN Rocks partners worldwide. In parallel, she will zoom in on the mechanisms shaping rock vegetation in the Meuse valley (Wallonia). There, we will develop high-resolution microclimate models using in-situ sensors and drone-derived digital surface models, and set up a split-plot experiment to assess the role of physical (vegetation removal) and chemical (climbing chalk) disturbance on cliff vegetation.

And this is only the beginning – there is much more in the pipeline for this PhD and for the global MIREN Rocks network. So if you love cliffs even one tenth as much as Sarane does, I strongly recommend following her work.

The best place to do so? Instagram, via @mirenrocks.

Congrats again, Sarane, and looking forward to work together further the coming years!

Posted in Belgium | Tagged , , | Leave a comment

A new chapter: looking back, looking forward

Posted on December 5, 2025 by lembrechtsjonas

Last year I wrote about a major milestone: moving The 3D Lab to Utrecht University and stepping into my role as assistant professor in ecological scaling. Today, I’m happy to share the next chapter in that story: as of November, I am officially tenured!

Tenure is often described as “academic job security,” and for anyone still navigating the postdoc world, I can confirm that the feeling is every bit as relieving as you imagine. It feels like finally having the space to breathe. The space to build. The space to think in decades instead of seasons, the way so many of us dream to be able to do science during the postdoc years.

And when I look back on the past few years, that shift in timescale is exactly what has brought me the greatest joy.

Building for the long term

What I’ve enjoyed most since coming to Utrecht is the ability to invest in long-term work. After years of living from grant to grant, I can finally dare to trust the foundations I was building for research that will grow, evolve, and mature far beyond the typical academic time horizon. I was doing that before, but always with the gnawing feeling that things might end prematurely.

Now also, many of the ideas that once existed only as half-finished notes in my drawer – ideas that were too slow to fit within a postdoc cycle – are finally taking shape. And more importantly: they’re taking shape with a team.

The 3D Lab is growing into a vibrant, cohesive group of people who support each other, learn from each other and build together. Watching that happen has been one of the most rewarding parts of this job. It’s a privilege to see ideas come alive not just through my own effort, but through shared enthusiasm.

And it’s of course still a struggle. Supporting that team requires more money, of course, so many projects are still slow and waiting for some stroke of luck to whip them up into action, but now the time and flexibility is there for patience.

Teaching as joy

Another (un)expected source of joy has been teaching. Having the room in my workday to help raise the next generation of scientists—from the more than 300 bachelor students to the many master thesis projects, and from the PhD students to the young scientists in the team—each bringing their curiosity and their questions—is something I value immensely.

There is something uniquely grounding about teaching. It reminds me why we do science in the first place. It keeps me accountable. And it pushes me to think carefully about what and how we teach, and what message we want them to receive.

There is, of course, a downside: it’s impossible to maintain the same amount of research output now that my teaching load has grown substantially. These are trade-offs we all face, and choices we all have to make. But I did decide I’m willing to pay the price – a few fewer scientific manuscripts – in exchange for creating opportunities for others to become the change we need.

From “My Science” to “Our Future”

One of the most profound shifts this assistant professor position brought me is the freedom to look beyond my own research papers and ask bigger questions. If I have thirty years of science ahead of me – give or take – what are the problems I want to contribute to solving? What will the world look like in 2055? And what role can ecology, microclimate science, and biodiversity research realistically play in guiding that future?

Ever since I first started doing science, my core question has been simple: why is that plant growing where it is?
Now, I want to go further. Not just understanding why plants are where they are, but asking: what do we need to do to help the right plants grow where we need them? And once they are there, what can those plants do for us – and for the rest of nature?

It’s a daunting line of thought, but also an energizing one. My ambition has grown – not in the sense of personal achievement, but in terms of impact. I want my science to matter not only within my field, but in the world beyond it. This also brought me back much closer again to the ecology where it all began for me. Especially my postdoc was a lot more methodological, but now I want to be talking a lot more about the nature we’re trying to save, and how to do that. That work will involve a lot of ‘a solution for nature’ and ‘nature as a solution’, two things that go nicely together.

Utrecht is the perfect environment for this. It is a university that not only allows but actively encourages its people to work across disciplines, to connect with societal partners, and to tackle the complex challenges facing our planet. I feel supported – and yes, sometimes gently pushed – to think bigger and collaborate wider. And for that, I’m truly grateful.

I don’t know about other places, but I like that in Utrecht the time to think, discuss and learn is build in to our job – officially 10% of my time, if I’m not mistaken – and that has thought me already a lot.

The honest part

Of course, there’s a darker side to ambition. When you start looking 30 years ahead, the horizon can feel impossibly far away. The problems we’re trying to address are complex, urgent, and often overwhelming. I know I won’t “save the world” – none of us will, individually, and when I think of that long-term vision, sometimes I worry about how much ‘world-saving’ will eventually fit into my day-to-day schedule.

But I do believe in the ripple effect.

I do believe that one of the most meaningful things I can do in the decades ahead is create opportunities for as many others as possible to contribute to those ripples. If I can help equip a generation of scientists, collaborators, and students to do world-saving work – together – that is impact.

That is enough.

Onward

So I’m really looking forward to this next chapter as a tenured scientist: to long-term vision, to interdisciplinary collaboration, to teaching with purpose, to scaling up ecology in every sense of the word, and to the remarkable people I get to work with every day.

And above all: to create the conditions for others to shine.

If any of this resonates – if you’re interested in joining the lab, collaborating, or thinking together about microclimate, species redistributions, or ecological scaling – my door (physical or virtual) is always open.

The journey continues.
And it’s only getting more exciting.

Posted in General | Tagged , , , , | 3 Comments

The night

Posted on December 2, 2025 by lembrechtsjonas

[ENGLISH] A cold, dark autumn night. My alarm goes off at 1:15 a.m., and for a moment I wonder what on Earth I was thinking. Then it hits me: I had been invited for a night-time interview on NPO Radio 1, in the weekly programme The Night of NTR Science.
Ninety minutes of uninterrupted conversations about science—yes, that is exactly the sort of thing you can wake me up for.

And there is so much to talk about.
So much we have learned over the years that we urgently need to start applying.
So much work left if we want to protect this beautiful planet we call home.

During the interview, we explored the state of nature today—still far more fragile than many realise—and the enormous value it brings us in return. We talked about what smart, science-based nature management can do, and how nature-based solutions must become a central part of creating a healthier, more resilient world.

The full conversation is now available as a podcast (in Dutch).
Highly recommended for anyone who wants to dream along with me about how we can steer our world in a better direction.

You can listen to the programme via the Radio 1 website:
https://www.nporadio1.nl/fragmenten/de-nacht-van/019a9eb4-d2f8-72e9-8159-453f690c6735/2025-11-20-het-grootste-burgeronderzoek-naar-geluid-ooit-natuurgeluid-maakt-gezonder
(Don’t forget part 2, featuring sharp and surprisingly awake questions from the audience!)

Or listen to it as a podcast on any platform:
https://plinkhq.com/i/1603391400
Or directly on Spotify:
https://open.spotify.com/show/5Cp2lQfmbSOKrZ5b6VZZoJ

[NEDERLANDS] Een koude, donkere herfstavond. Mijn wekker gaat om 1u15, en heel even vraag ik me af waarom ik dit mezelf aandoe. Maar dan herinner ik het me: ik ben uitgenodigd voor een nachtelijk interview op NPO Radio 1, in het programma De Nacht van NTR Wetenschap.
Negentig minuten onafgebroken praten over wetenschap – daar mag je me nu eens altijd voor wakker maken.

Want er is zoveel om over te praten.
Zoveel inzichten die we intussen hebben maar dringend moeten beginnen toepassen.
Zoveel werk dat nog voor ons ligt als we onze prachtige planeet willen beschermen.

In het gesprek doken we in de staat van onze natuur – die helaas alsmaar meer zorgwekkend is – en in alles wat die natuur voor ons terugdoet. We spraken over de rol die slim, wetenschappelijk onderbouwd natuurbeheer kan en moet spelen. Over hoe nature-based solutions een sleutel zijn om onze wereld gezonder en veerkrachtiger te maken.

Het volledige interview is nu te beluisteren als podcast.
Warm aanbevolen voor iedereen die graag even wil meedromen over hoe het anders en beter kan.

Beluister het gesprek via de website van Radio 1:
https://www.nporadio1.nl/fragmenten/de-nacht-van/019a9eb4-d2f8-72e9-8159-453f690c6735/2025-11-20-het-grootste-burgeronderzoek-naar-geluid-ooit-natuurgeluid-maakt-gezonder
(En vergeet deel 2 niet, met een reeks scherpe vragen van een verrassend wakkere luisteraarsgroep! – scroll naar helemaal onderaan)

Je kunt het interview ook beluisteren als podcast, op alle platformen:
https://plinkhq.com/i/1603391400
Of gewoon via Spotify:
https://open.spotify.com/show/5Cp2lQfmbSOKrZ5b6VZZoJ

Posted in General | Tagged , , | Leave a comment