Virtual SoilTemp symposium

Posted on March 6, 2023 by lembrechtsjonas

I am very happy to invite you to a virtual SoilTemp symposium, on May 8th, 2023, from 15h-17h30 Brussels time.

Please, let me know your interest in this symposium through this form!

Final program looks as follows:

Monday May 8th (main event)

15h00-15h05 Trickle in – welcome screen
15h05-15h20 SoilTemp overview (Jonas Lembrechts, 12’+3’)
15h20-15h30 SoilTemp database (Rémy Beugnon, 10’+0’)
15h30-15h45 DirtClim (Dave Klinges, 12’+3’)
15h45-16h00 MIRRA: real-time microclimate sensor (Pieter De Frenne, 12’+3’)
16h00-16h15 ForestClim (Stef Haesen, 12’+3’)

16h15-16h25 Break

16h25-16h40 Global soil frreeze/thaw project (Jeremy Johnston, 12’+3’)
16h40-16h45 Soil moisture fluctuations affect forest temperature buffering (Caroline Greiser, 5’+0’)
16h45-17h10 4 community presentations (Robert Weigel, Matej Man, Diana Stralberg, Martin Dovciak, 5’+0’)
16h10-17h20 How to submit your data? (Jonas Lembrechts, 10’+0’)

17h20-17h45 General questions (0’+25’)

Friday May 12th (add-on session)

9h00-9h05 Trickle in – welcome screen
9h05-9h35 SoilTemp overview, database and main projects (Jonas Lembrechts, 25’+5’)
9h35-9h45 How to submit your data (Jonas Lembrechts, 10’+0’)
9h45-10h30 General questions (0’+45’)

Picture by Stijn Van de Vondel

Please spread the word and invite your colleagues! This symposium is open to all and THE opportunity to get in touch with the network towards publication of the database itself. We will soon start one final push for data submissions towards that publication, which we plan to finish in autumn 2023 (so this will be the final chance for anyone to contribute data and get an invite to co-author our big database). More information on this will follow!  

Looking forward to seeing many of you at our symposium!

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The impact of the pines

Posted on March 2, 2023 by lembrechtsjonas

Picture this: it’s the 20th century and people are planting pine trees all over Chile. Pines of the genus Pinus, that is, which is very different from the native Araucaria araucana (the monkey puzzle tree). The latter might very well be called the ‘Chilean pine’ by some, but lacked the versatility for those wanting efficient wood production and erosion protection. So: in come the Pinus-pines, to help the economy!

A line of lodgepole pines (Pinus contorta) planted above the treeline at the foot of the Lonquimay-volcano

These might have looked like good ideas – and perhaps still do too many – but now the tables have drastically turned: these pines have spread like wildfire and are causing havoc on the ecosystem. Indeed, those pine trees have the tricky habitat not to remain where they are, and especially in the native Chilean landscape of Araucaria forests and Patagonian steppe, pine trees come across very little resistance. As a result, the once so characteristic landscape is now a tangled mess of pine branches and trunks.

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

But what’s happening beneath these dense canopies? How much are the microclimate and soil suffering from these stubborn pine trees? And, even more importantly, what is the impact of these changes on the native vegetation? In a recent study led by our Chilean partners from the University of Concepcíon, we set out to investigate this effect for invasions of lodgepole pine (Pinus contorta). We measured everything from temperature to soil pH to nutrient availability across a gradient of pine biomass, from scattered individuals to dense entanglements.

Pinus contorta biomass significantly correlates strongly with a wide range of environmental conditions: more pines result in buffered temperatures, loss of light, loss of Potassium, decreased pH and increased litter depth.

Our results – published in ‘Diversity – were alarming – the impact was as huge as we suspected based on visual assessment alone. The more pine trees, the worse it got. The local micro-environment was drastically altered, resulting in a loss of light and nutrients, decreased pH, and increased litter depth, amongst others. But our biggest worry? The native plant diversity was virtually wiped out in the most densely invaded plots.

Native plant species richness (top) and abundance (bottom) decreased significantly with increasing pine biomass, both in the Araucaria-forest (left) and on the Patagonian steppe (right).

Our study revealed that it is probably the interplay of all these environmental factors – all so dramatically changed from background conditions – that explains the progressive drop in native plant species in the understory. Indeed, few native species likely have the necessary flexibility to deal with changes in all these defining environmental characteristics at once. The mechanisms behind the loss of biodiversity of native species associated with plant invasion would thus not only depend on the competition exerted by P. contorta, but also on the modifications that this species exerts on the abiotic environment. Moreover, these microenvironmental changes can have significant effects on other functional groups (e.g., pollinators, decomposers) with important consequences for the whole trophic network of the invaded ecosystems.

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

So, what’s the plan of action? Can we get rid of these pine trees, and if so, what happens to the microenvironmental conditions? How long will it take for the ecosystem to bounce back? Once that question is answered, it is of course still a matter of finding affordable solutions to get those stubborn pine trees out of there…

A lodgepole pine seedling just popped up after experimental pine removal, suggesting that recovery of the native vegetation will not be that easy.

Reference

García, R. A., Fuentes-Lillo, E., Cavieres, L., Cóbar-Carranza, A. J., Davis, K. T., Naour, M., Lembrechts, J.J. & Pauchard, A. (2023). Pinus contorta Alters Microenvironmental Conditions and Reduces Plant Diversity in Patagonian Ecosystems. Diversity, 15(3), 320.

The forefront of the Pine invasion, with the Lonquimay-volcano in the background
An impressive Araucaria-tree, looking out at the volcano

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Failure

Posted on February 8, 2023 by lembrechtsjonas

I started tracking my time at work in detail at the start of my postdoc in 2018, using the amazing app ‘Timeular’. This series of stories provides some insights into postdoc life using that data.

In a postdoc, not everything goes according to plan. In fact, it’s more likely that they won’t! It’s important to realize that that is totally ok. But it’s important to understand that this is perfectly normal and an inherent part of the scientific process. We can try new things, experiment, make changes, backtrack, change direction. We can fail!

I know he academic climate of recent decades has not been forgiving of failure, but it’s a crucial and valuable aspect of scientific discovery. After all, if success was guaranteed, would it still be considered true science?

Through my time tracking practices, I now have a clear understanding of the amount of time I have spent on ‘failed’ projects – those that I invested hours into but never got published. Note that this is of course just one type of failure and does not include rejected proposals, failed experiments with published negative results, or the countless micro-failures encountered along the way. To give a visual representation, I created a plot of the 35 most time-consuming papers of my PhD.

Ranking of my 35 most time-consuming papers, coloured by my authorship position, with a border colour for their status. Green borders indicate ongoing papers for which I’m confident we will get them published eventually. Red borders are for cancelled papers – papers that I’m confident will never get published.

Good news first: the largest chunk of my time went towards a paper that actually got published! This is our Global maps of soil temperature-paper, a massive effort with a looooong co-author list. However, it’s evident that a significant portion of my time was also dedicated to projects that didn’t see the same success. The list of 35 time-consumers includes seven (7!) cancelled papers and several others that are yet to be published.

One particular project that deserves mention is the cancelled paper ranked second in terms of time invested. It was an ambitious attempt to apply the theoretical concept of higher-order interactions (HOIs) to real-world data. At the time, HOIs were and still are a hot topic, but modeling them correctly proved to be challenging. Most prior attempts were limited to experimental communities, petri dishes, or simple models.

I started modelling on my messy real-world community data (in parallel to a theoretical ecologists who was making data-free models of the same), and solved roadblock after roadblock. Our goal was to confirm the theory through real-world findings, and we worked tirelessly to overcome each obstacle. Despite these efforts, the limitations of the data became increasingly apparent and the impact of methodological decisions was more noticeable. Nevertheless, we completed a manuscript with a story we were confident about and submitted it to our first high-impact journal.

However, the manuscript faced rejection after rejection, luckily with constructive feedback from reviewers. We took their comments into account and worked to make the manuscript better and clearer, highlighting more and more of the unearthed methodological limitations up front. Despite these efforts, the limitations became increasingly difficult to ignore and started to overshadow the findings that I first had been so proud of. After several rejections, we ultimately made the difficult decision to cancel the project, recognizing that we couldn’t get a good grip on higher-order interactions (HOIs) with this messy data. It was a failure.

The list contains other failures.

The list of failures also includes valuable learning experiences. For instance, there were some engaging master’s theses that I invested a lot of time in, but the students had to leave before the manuscript was finished and I no longer had the capacity or expertise to complete them. Another paper that I was enthusiastic about got overtaken by a new one with a more sophisticated methodology, while a dataset that didn’t fit the original research question eventually found use for a different purpose. I also invested a lot of effort into some analyses, only to discover that they would require even more work and were not aligned with what I had promised to the funders.

Although these projects may not have ended in publication, they are not true failures. I learned a lot from each of them and some of that knowledge has, and will continue to, inform my future work in different ways. While the “publish or perish” mentality is prevalent in the scientific community, I firmly believe that the real value of science lies in the learning. Publishing is a great way to share your learning with others, but not all learning has to be public. Personal growth as a scientist and a person is equally important and even if it’s not reflected on your CV, it will benefit you in the long run. I hope this story will encourage you to embrace failures in your own scientific journey.

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Exotic plant species thrive at high(er) elevations

Posted on January 26, 2023 by lembrechtsjonas

Sometimes one needs patience to answer a research question. Lots of it. The Mountain Invasion Research Network (MIREN) already asked itself this important question back in 2006: how fast are non-native species travelling uphill along mountain roads? Now it’s 2023, and for the first time we have an answer to this, thanks to long-term vegetation monitoring by a team of researchers across the globe, and the work of MIREN master-turned-PhD candidate Evelin Iseli, whose work now got published in Nature Ecology & Evolution (!). What follows is the English translation of the press release by our university. The paper itself can be found here!

Suppose you put your hiking boots in your backpack, fly to another continent and go hiking in the mountains. Chances are that you may find that seeds of local vegetation travelled the whole way with you in the mud on the soles of your shoes. If these fall off your shoe abroad, an alien plant may sprout where that seed has fallen. Thus, without realising it, you contribute to the spread of non-native plant species.

Moving uphill

Ecologists from the global MIREN-network found that the number of non-native plant species in mountain areas around the world has significantly increased in the past decade. Until now, alien plant species were advancing less in mountains compared to their increase at lower elevations. But due to climate warming on the one hand and increasing human influence at high elevations on the other, it now appears that non-native plants in mountains are also advancing steadily uphill.

The number of non-native species increased by 16% in mountain areas.

“Although the presence of native species in mountains is relatively well documented, long-term studies of alien species in mountain areas are very rare,” says Jonas Lembrechts, biologist at UAntwerpen. Lembrechts and his colleagues have therefore been monitoring non-native species along mountain roads since 2007, in 11 mountain areas around the world: in Norway, Switzerland, the Canary Islands, New South Wales, Victoria (Australia), central and southern Chile, India, Hawaii, Montana and Oregon.

“There are big differences in the speed of the invasion, but the general increase is unmistakable,” says Lembrechts. The study of the 11 mountain regions worldwide shows an increase in the number of alien species by as much as 16% over the past decade.

Mainly European plant species

Moreover, in 10 of the 11 regions studied, the scientists found the alien species at significantly higher altitudes than ten or even just five years ago. Moving to higher altitudes to follow their preferred climate is a well-known strategy for plants to defend themselves against climate change. Only, the rate at which alien species are climbing upwards is higher than if climate alone were the culprit.

“Europe is the largest exporter of exotic plants to mountainous regions worldwide, says Jonas Lembrechts. Left: Trifolium pratense from Western Europe in the Norwegian Scandes. Right: the European Taraxacum officinale in the Chilean mountains.

“Exotic species often enter new regions through the lowlands, where most of the people are,” says Lembrechts. “From there, they find their way to the mountains. But with a little help from humans, their spread can sometimes be lightning-fast, especially along mountain roads and trails.”

Off balance

Often these are then also European plant species, research shows. “Europe is currently by far the biggest exporter of exotic plants to mountain areas worldwide,” Lembrechts explains. “Not so strange, when you consider that in recent centuries it was also mainly Europeans who started visiting mountain areas on other continents, for tourist and commercial purposes.”

However, this is not good news. “Mountain nature is often very fragile,” says Lembrechts. “Alien plant species can threaten or drive out native species, which are important in the local ecosystem, throwing the system out of balance.”

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The mystery of the Dark and Light Beetles on Possession Island

Posted on January 26, 2023 by lembrechtsjonas

New paper out! Espel, D.; Coux, C.; Pertierra, L.R.; Eymar-Dauphin, P.; Lembrechts, J.J.; Renault, D. Functional Niche Partitioning Occurs over Body Size but Not Nutrient Reserves nor Melanism in a Polar Carabid Beetle along an Altitudinal Gradient. Insects 2023, 14, 123.

The southern Indian Ocean is home to the little known archipelago of Crozet. Despite its harsh weather and lack of substantial human presence, the island is a haven for penguins and elephant seals. Among the island’s inhabitants is a seemingly ordinary beetle, the Amblystogenium pacificum. It crawls over and under the rocks, hunting for smaller things to eat, and just lives his normal beetly life. There is just one thing with this beetle that sparked the interest of the (unusually persistent colony of) French scientists on the island: there are two colour versions of it. A light and a dark one.

Star of the show: the endemic Carabid beetle Amblystogenium pacificum

Now, we wouldn’t be scientists if we didn’t want to dig deeper into this.

Scientists have proposed several hypotheses to explain this phenomenon, including Gloger’s rule, which states that darker coloration is a common response among insects exposed to cold conditions. If Gloger’s rule were at play, we would expect to see a fitness advantage in the darker insects when it’s colder. However, it’s rarely that simple in ecology. It’s worth noting that previous studies have observed that the proportion of dark beetles increases by about 8% for every 100 meters in altitude on the island. This results in a clear distinction in the spatial distribution of the two morphotypes. More recent observations made in fellfield habitats have reported that the proportion of brown to black beetles ranges from a 2:1 ratio of brown insects at low altitudes to a 2:1 ratio of black adults at higher altitudes. This further supports the idea that Gloger’s rule may be at play. But as scientists, we can never jump to conclusions too quickly, and we must always keep an open mind to other possibilities.

Find the beetle, happily running across a soft ‘moss forest’. Picture by Diane Espel

Nevertheless, there were both dark and light individuals across the entire elevation gradient on the island. This raises the question of whether the dark beetles fare better at higher elevations (in terms of being bigger, having more nutrient or lipid reserves, etc.) and vice versa.

However, there are other rules that come into play, such as Bergmann’s rule, which states that insects tend to get larger as the temperature gets colder. This is because larger body sizes in endothermic species often correspond to a smaller surface area to volume ratio and reduced heat dispersion in colder climates. Additionally, there is the rule of sexual size dimorphism, which states that female insects are typically larger than males.

So, how does all of this play out on our windy island? The good news is that the elevation (and thus climate) gradient is responsible for many trait differences among the beetles. However, it turns out that coloration does not seem to be a major factor in determining the performance of the beetles. Bergmann’s rule does appear to be at play, as elevation does seem to boost beetle body size (although at the very top of the mountain, the extremely harsh conditions have made them smaller again). Sexual dimorphism is also present, with females having more lipid and sugar reserves (which is pretty clever of them, if you ask me).

Body size as a function of altitude for dark (blue) versus light (green) male (dashed) versus female (full line) beetles. Elevation clearly affects body size, but with virtually no difference between the two colorations or even genders.

However, a so-called ‘functional hypervolume analysis’ did not show clear niche partitioning of the insects along the studied altitudinal gradient, and we had to conclude that niche partitioning was happening for body sizes rather than coloration types.

In conclusion, the mystery of the dark and light beetles on Crozet Island remains unsolved. The absence of clear patterns in the relationship between temperature and size highlights the complexity of the interactions between insects and their environment. Factors such as low temperatures and limited resources at higher altitudes likely play a role in shaping the beetles’ functional traits. But hey, isn’t that what science is all about? Asking questions and trying to find answers, even if they’re not always easy to come by. So let’s just say, the adventure continues!

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A robot as co-author

Posted on January 19, 2023 by lembrechtsjonas

Ok, I’ll bite. The internet is literally full of fancy people jumping on the bandwagon called ‘ChatGPT’. The amount of lists I’ve seen floating by with ‘you are only using 1% of ChatGPTs full potential’ or ‘this is how I convinced the queen to marry me by using ChatGPT and so can you’ cannot be counted. But the thing is: we HAVE to talk about it. As this thing is a game changer (whether a big or a small game changer I leave open to discussion).

The potential applications for ChatGPT are numerous, but – let’s be honets – it’s important to acknowledge that it’s not as good as it looks for many questions you could ask it. Despite the opportunities it presents, there are also risks to consider. I have gained *some* insight on the tool and its appropriate usage now, and I wanted to share my perspective as an ecologist and lab leader.

First of all, it is important to note – as many have done before – that ChatGPT should not be used to write academic papers. Despite its ability to generate coherent introductions, deeper analysis of the text reveals a lack of credibility and depth. The tool lacks the capability to cite credible sources and often creates made-up papers as a result. It is thus unlikely that a thesis written by the robot would pass scrutiny: the introduction might sound good enough, but for the methods and results, and any depth in the discussion, they are still entirely on their own.

I know some of these people, but never ever have I published in Enviornmental Modelling & Software. So Veraverbeke, Bauwens & Muys, time to get writing!

Despite its limitations, ChatGPT can be a powerful tool when used correctly. Here are a few ways I have found it useful in my work:

  • Improve first drafts. Using ChatGPT to improve first drafts can be an effective way to save time and improve the overall quality of writing. By quickly jotting down ideas and creating a rough storyline, I can then feed this rough text through ChatGPT to improve sentence structure and coherence. This added step allows me to focus on refining and polishing the content, rather than spending time on correcting grammar and sentence flow. The ability to quickly identify and incorporate the good suggestions while discarding the bad ones, has significantly reduced the time and effort required to finalize my writing. Additionally, this approach ensures that the grammar and flow of sentences are already on point when I start polishing things myself, which ultimately leads to a polished and well-written final draft.
  • Ask it to change the tone of text. Why settle for plain and boring text when you can jazz it up with a little help from ChatGPT? By using it to change the tone of your text, you can add some pizzazz to your blog posts and tweets. ChatGPT can even serve as your personal brainstorming buddy, suggesting intriguing snippets of text and clever wordplay to make your writing more attractive. And while I can’t say I use the final version it proposes, I do like to sneakily steal a few improvements here and there. So next time you’re struggling to add a touch of personality to your writing, don’t be afraid to turn to ChatGPT for a little inspiration. (Ok, I admit, all the witty wordplay is entirely ChatGPTs-doing, this paragraph was significantly more boring!)
  • Shortening texts: I asked ChatGPT to suggest how to shorten a project proposal from 8 to 4 pages. It came up with great suggestions to regroup or rewrite sentences in a more compact way, which also helps with email writing and other types of writing that need to be concise.
  • Annotate R-code. This is a relatively new discovery for me, but I think it will be a GREAT tool for my students! I just feed in a piece of R-code and ask it to annotate it, and it writes down in text what all the steps mean. For students, who are often unfamiliar with many of the tips and tricks of R that I learned over the years, this can make R-code I sent them a lot easier to understand.
  • Suggesting formatting for things I am not familiar with writing: For example, I haven’t written too many recommendation letters yet, so I ask ChatGPT for an example by feeding it some keywords for the candidate in question. This gets rid of the ’empty page’-issue where you don’t know how to start writing and lets you build on a good foundation.

My final words are perhaps the most important part of this blogpost: we HAVE to discuss this tool with our students. They are more tech-savvy then we are, so they will find out about it. Yet they might not get all the pro’s and cons, and they might especially brush over the ethics. Can they use it? Sure, I’m all in favour of getting all the help one can, the main goal of their work (in their master or PhD thesis, mind you, not in other courses) in my opinion is anyway to advance science and grow as a human in the process. They can use whatever tool they want, be it a fancy and expensive measurement tool or a chatty robot. As long as they know the strengths and weaknesses. That’s the same for that fancy measurement tool for that matter.

It’s a common question – is the text I’ve written still mine when I’ve utilized a language model like ChatGPT? I firmly believe it is. While the model may offer suggestions, I ultimately have the final say on what to include or not. Think of it as having a co-author, one who carefully reads and offers suggestions, but it’s ultimately up to me to decide what makes the final cut.

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