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Thijs Janzen

@thijsjanzen.bsky.social
147 followers 278 following 29 posts

Scientific Programmer @ TRES, University of Groningen, Netherlands

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Reposted by Thijs Janzen
Fons van der Plas @fonsvanderplas.bsky.social · 01/10/2026
We have an open PhD position on how nitrogen deposition affects plant and arthropod biodiversity. The research includes large-scale fieldwork across Northwestern Europe with hands-on experiments. Interested? See www.wur.nl/en/vacancy/p...
wur.nl
PhD: Effects of atmospheric nitrogen deposition on plant and insect diversity
Are you a highly motivated and enthusiastic ecologist who wants to uncover how nitrogen deposition affects plant and arthropod biodiversity? Are you excited by the idea of combining large-scale fieldw...
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Jonathan Eisen @phylogenomics.bsky.social · 30/09/2026
Wow. Just wow. Did I say wow?
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bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 13/09/2026
DNA methylation correlates with lifespan and predicts remaining lifespan in the zebra finch www.biorxiv.org/content/10.64898/20…
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Hanna Kokko @kokkonut.bsky.social · 23/09/2026
There is still time to apply! I'll start reading the applications this Friday.
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EvoBio Crash Course @evobiocc.bsky.social · 23/09/2026
The Evobio Crash Course is coming back for its fifth edition! Join us from December 7 to December 18 for an incredible line up of classes and tutorials from amazing researchers in the field! The course is open to all, completely free and held online. Registration is OPEN, please share widely!
Poster for the Evobio Crash Course. Online from December 7-18, 2026.
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Thijs Janzen @thijsjanzen.bsky.social · 24/08/2026
Update to 1.71.13: cran.r-project.org/web/packages... New additions are better support for polytomous trees, and the information table has been updated accordingly. Enjoy!
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 20/06/2026
Caste-specific ageing emerges from the evolution of resource allocation in eusocial insects www.biorxiv.org/content/10.64898/20…
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Thijs Janzen @thijsjanzen.bsky.social · 16/06/2026
The treestats package has been updated to version 1.71.12, in case you haven't kept track of the latest improvements, I got you covered! cran.r-project.org/web/packages... 1/7
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Chris Simms @chrisnsimms.bsky.social · 11/06/2026
This discovery amazed me: A whale "graveyard" extending over 1,200 km. The remains or fossils of about 480 whales found in a total survey area of about 0.64 square kilometres, with one of the fossils dating back more than 5 million years. 🧪 🐋 🦑 🦊 #cetaceans www.livescience.com/animals/whal...
livescience.com
Scientists discover 5 million-year-old whale graveyard stretching for hundreds of miles in the Indian Ocean
Researchers have discovered a "megasite" of dead whales along with new species of marine life feasting on the corpses.
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Stephen Turner @stephenturner.us · 02/02/2024
Phylogenetic tree statistics: a systematic overview using the new R package 'treestats' www.biorxiv.org/content/10.1... 🧬🖥️ github.com/thijsjanzen/... cran.r-project.org/web/packages...
cran.r-project.org
treestats: Phylogenetic Tree Statistics
Collection of phylogenetic tree statistics, collected throughout the literature. All functions have been written to maximize computation speed. The package includes umbrella functions to calculate all...
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Menno Schilthuizen @schilthuizen.bsky.social · 09/06/2026
Explore this gift article from The New York Times. You can read it for free without a subscription. www.nytimes.com/2026/06/08/o...
nytimes.com
Opinion | 3,000 Different Species Are Killed for Supper. Why Do We Allow It?
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Stephen Heard @stephenbheard.bsky.social · 26/05/2026
Good teaching has a substantial amount of stand-up comedy, costuming, or whatever else can grab student attention. At first this felt cheap - but I learned to work with it.
scientistseessquirrel.wordpress.com
Good teaching is 15% straight-up entertainment – and that’s OK
I spent a good fraction of my career’s work effort on teaching, and – like most academics – I had very nearly no idea what I was doing. I’d never had a moment’s formal training in teaching, and, at…
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Riley Cran @rileycran.bsky.social · 25/03/2026
New work for GitHub: Monaspace. 🔤 A superfamily of 5 open-source typefaces for code. Full case study here: lettermatic.com/custom/monas...
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Loukas Theodosiou @bioinformatician.bsky.social · 12/03/2026
#ggtree has a relatively steep learning curve. But after looking at a few Python alternatives eg., toytree, ETE, Bio.Phylo it's hard to match its layout versatility. 21 tree variants with just a few lines of code. #rstats #phylogenetics #bioinformatics
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Eduardo Amorim @cegamorim.bsky.social · 13/03/2026
Dogs evolved to eat your leftovers! Comparing dog & wolf genomes revealed dogs have up to 30 EXTRA copies of the amylase gene (AMY2B) that helps digest starch. This is a key genomic signature of living alongside humans & table scraps for thousands of years 🐕 www.nature.com/articles/nat... #2026MMM
Adapted from Axelsson et al. 2013 Fig 2c: Histogram showing the distribution of diploid amylase copy number in wolf (n=35, blue) and dog (n=136, red). Dogs carry more copies of the starch-digesting gene AMY2B than wolves. Additional copies make dogs better than wolves at digesting starchy foods like grains & vegetables.
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Thijs Janzen @thijsjanzen.bsky.social · 03/03/2026
Love the video explainer! Such a smart and smooth way to bring abroad your topic and avoid people having to wade through the bureaucratic representation of it. (and the pub setting is lovely as well)
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Groningen Institute for Evolutionary Life Sciences @gelifes.bsky.social · 11/12/2025
💃DaNCES with #carnivores – interested in studying predator-prey interactions? Read more about the DaNCES framework by @marinapapa.bsky.social and others, simulating #collectivebehavior of #predators and #prey below ⬇️ doi.org/10.1177/1059... #Biology #Science #Research #AdaptiveBehavior
doi.org
A Data-Inspired Framework to Simulate Collective Behaviour of Predator-Prey Systems - Marina Papadopoulou, Hanno Hildenbrandt, Charlotte K. Hemelrijk, 2025
The collective escape of prey from predators is a classic example of adaptive behavior in animal groups. Across species, individual prey have evolved a large re...
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Groningen Institute for Evolutionary Life Sciences @gelifes.bsky.social · 16/12/2025
#Coralreefs are dying off rapidly: we have reached the first #climate tipping point. 🧪 “Humans are changing the world so quickly that #corals can’t keep up anymore.” Sancia van der Meij, a marine biologist from #GELIFES, expresses her concern: rug.nl/research/gelifes/_news/2025/20251017-coral-reefs
rug.nl
Koraalriffen sterven af – en dat heeft grote gevolgen voor mens en dier
Wereldwijd sterven koraalriffen dermate snel af, dat we inmiddels het eerste klimaat-kantelpunt hebben bereikt, rapporteerden wetenschappers afgelopen...
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Groningen Institute for Evolutionary Life Sciences @gelifes.bsky.social · 21/01/2026
🔔 Update: A new #PhDPosition at the University of Groningen (@rug.nl)! If you: 🧪 have a Master's in #Biology 🌱 are interested in #PlantBiology, #Physiology, and/or #MolecularBiology Then this is a perfect opportunity! We at #GELIFES are looking forward to working with you 😉 #PhD #PhDLife
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Shaun Killen @shaunkillen.bsky.social · 25/11/2025
🧵1/9 There are 35,000+ fish species, but we have formal social-behaviour classifications for a tiny fraction. Most knowledge lives in the experience of researchers, fishers, divers, aquarists, naturalists, and Indigenous communities, but almost none of it is centralised. So we built ShoalBase.org.
shoalbase.org
ShoalBase | Join, Explore, Contribute Now
ShoalBase offers a global database on fish social behaviour, supporting research, conservation, and ecology through community contributions and visual data mapping.
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Matthew Asker @masker.science · 10/12/2025
Up to 10 doctoral positions at the Max Planck Institute for Evolutionary Biology now open for application! Start date September 2026. More info here: www.evolbio.mpg.de/imprs
Poster advertising doctoral positions in 2026 at the International Max Planck Research School for Evolutionary Biology.
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Thijs Janzen @thijsjanzen.bsky.social · 11/12/2025
Woah, that R logo is absolute fire! Immediately set it as my application icon! (and also, the workshop looks really cool as well!)
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Thijs Janzen @thijsjanzen.bsky.social · 06/12/2025
This is wonderful. High-end Technology together with straightforward ecology.
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 04/12/2025
Statistical and structural bias in birth-death models www.biorxiv.org/content/10.64898/20…
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Mike Morrison @mikemorrison.bsky.social · 12/11/2025
Play a little game and choose the right icon for each role in science. Play our CRediT Roles icon game/survey, and help make scientific authorship clearer and more accessible! creditsurvey.sciux.org #OpenScience #ScienceUX
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George Turner @dlimnothrissa.bsky.social · 26/11/2025
Part 1 version 1 of my Malawi cichlid ID guide is out now. 2 more parts for follow, with my intention being to revise, expand and improve each over time. This one is essentially a companion to our whole genome sequence paper in Science (Blumer et al. 2025). ecoevorxiv.org/repository/v...
ecoevorxiv.org
Identification of the Cichlid Fishes of Lake Malawi/Nyasa Part 1: Cyrtocarina (the ‘benthic’ or ‘hap’ sub-radiation).
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Dugdale Research Group @hannahdugdale.bsky.social · 18/11/2025
Congratulations to Dr @euantheyoung.bsky.social who defended his PhD yesterday on 'Family matters: The role of trade-offs in shaping human life-histories and health' research.rug.nl/en/publicati... @rug.nl supervised with @erikpostma.bsky.social @lummaalab.bsky.social 🎉
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Mark A. Hanson @hansonmark.bsky.social · 11/11/2025
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing: a 🧵 1/n Drain: arxiv.org/abs/2511.04820 Strain: direct.mit.edu/qss/article/... Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below.

1. The four-fold drain
1.1 Money
Currently, academic publishing is dominated by profit-oriented, multinational companies for
whom scientific knowledge is a commodity to be sold back to the academic community who
created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis,
which collectively generated over US$7.1 billion in revenue from journal publishing in 2024
alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit
margins have always been over 30% in the last five years, and for the largest publisher
(Elsevier) always over 37%.
Against many comparators, across many sectors, scientific publishing is one of the most
consistently profitable industries (Table S1). These financial arrangements make a substantial
difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor &
Francis revenues were generated in North America, meaning that North American
researchers were charged over US$2.27 billion by just two for-profit publishers. The
Canadian research councils and the US National Science Foundation were allocated US$9.3
billion in that year.A figure detailing the drain on researcher time.

1. The four-fold drain

1.2 Time
The number of papers published each year is growing faster than the scientific workforce,
with the number of papers per researcher almost doubling between 1996 and 2022 (Figure
1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material
has aligned well with the competitive prestige culture in which publications help secure jobs,
grants, promotions, and awards. To the extent that this growth is driven by a pressure for
profit, rather than scholarly imperatives, it distorts the way researchers spend their time.
The publishing system depends on unpaid reviewer labour, estimated to be over 130 million
unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of
peer-review for decades, but the scale of the problem is now worse, with editors reporting
widespread difficulties recruiting reviewers. The growth in publications involves not only the
authors’ time, but that of academic editors and reviewers who are dealing with so many
review demands.
Even more seriously, the imperative to produce ever more articles reshapes the nature of
scientific inquiry. Evidence across multiple fields shows that more papers result in
‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow
progress until one considers how it affects researchers’ time. While rewards remain tied to
volume, prestige, and impact of publications, researchers will be nudged away from riskier,
local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with
limited progress whereas core scholarly practices – such as reading, reflecting and engaging
with others’ contributions – is de-prioritized. What looks like productivity often masks
intellectual exhaustion built on a demoralizing, narrowing scientific vision.A table of profit margins across industries. The section of text related to this table is below:

1. The four-fold drain
1.1 Money
Currently, academic publishing is dominated by profit-oriented, multinational companies for
whom scientific knowledge is a commodity to be sold back to the academic community who
created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis,
which collectively generated over US$7.1 billion in revenue from journal publishing in 2024
alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit
margins have always been over 30% in the last five years, and for the largest publisher
(Elsevier) always over 37%.
Against many comparators, across many sectors, scientific publishing is one of the most
consistently profitable industries (Table S1). These financial arrangements make a substantial
difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor &
Francis revenues were generated in North America, meaning that North American
researchers were charged over US$2.27 billion by just two for-profit publishers. The
Canadian research councils and the US National Science Foundation were allocated US$9.3
billion in that year.The costs of inaction are plain: wasted public funds, lost researcher time, compromised
scientific integrity and eroded public trust. Today, the system rewards commercial publishers
first, and science second. Without bold action from the funders we risk continuing to pour
resources into a system that prioritizes profit over the advancement of scientific knowledge.
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Sebastian Höhna @hoehna.bsky.social · 11/11/2025
PhD position available in evolutionary genomics/bioinformatics (hoehnalab.github.io/job_adverts/...). Topic: analyzing gene expression evolution across several firefly species and linking expression changes to genomic architecture. The position is jointly supervised with @anaevolcatalan.bsky.social
hoehnalab.github.io
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Marianthi Tangili, PhD @mtangili.bsky.social · 10/11/2025
Extremely proud of my good friend and colleague @euantheyoung.bsky.social whose work is featured in @nrc.nl. Read bellow for some excellent science and fascinating results. 👪🤰👶🧬
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Euan Angus Young @euantheyoung.bsky.social · 10/11/2025
1/13 New paper out! www.science.org/doi/10.1126/... Historical records across thousands of women showed that mothers with more children had shorter lifespans during a famine, fitting an evolutionary explanation for why we age @hannahdugdale.bsky.social @lummaalab.bsky.social @erikpostma.bsky.social
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Hadley Wickham @hadley.nz · 06/11/2025
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.
github.com
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
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Henrik Bengtsson @henrikbengtsson.bsky.social · 05/11/2025
The detectCores() apocalypse is creeping up on us 👻🐛 As more people are getting access to 128+ CPU cores, code spinning up parallel cluster with detectCores() workers fails - not enough #RStats connections available Friends, do *not* default to detectCores(), bc www.jottr.org/2022/12/05/a...
jottr.org
Please Avoid detectCores() in your R Packages
The detectCores() function of the parallel package is probably one of the most used functions when it comes to setting the number of parallel workers to use in R. In this blog post, I’ll try to explai...
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Thijs Janzen @thijsjanzen.bsky.social · 31/10/2025
Potato-tomato
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Dugdale Research Group @hannahdugdale.bsky.social · 15/10/2025
Congratulations to Dr @friggspeelman.bsky.social who was awarded a PhD yesterday 🎉 @rug.nl on 'Socially monogamous partnerships in birds: Causes, consequences, and pair-bond strength' research.rug.nl/en/publicati... A fantastic achievement!
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Jamie Winternitz @jcwinternitz.bsky.social · 13/10/2025
Join Our Citizen Science Project! We are mapping the house mouse hybrid zone in Schleswig-Holstein, DE, and you can help. Visit our House Mouse Hybrid Zone Project website to learn more jwinternitz.github.io/mouse-hybrid.... Funded by @dfg.de at @uni-hamburg.de #DFG #musmusculus #wildmice
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Edward T Eng @edwardteng.bsky.social · 04/10/2025
Muyuan Chen has turned structural biology into an immersive experience with his new video game Meowtabolism, now available on Steam. Try the demo here: store.steampowered.com/app/4045010/... Give Muyuan feedback: steamcommunity.com/app/4045010 #ScienceGaming #StructuralBiology #CryoEM #STEMOutreach
store.steampowered.com
Meowtabolism - Examining Feline Behavior within Unicellular Algae on Steam
Explore the interior of an algal cell on your four paws. Built with experimental data and populated with actual protein structures, Meowtabolism offers a glimpse of the vast world inside the basic fun...
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Darshak Bhatt @darshakbhatt.com · 12/09/2025
Very glad to share my first last-author paper, now published in iScience! 🎉In this study, we addressed a key challenge in virus-based cancer therapy: macrophage-mediated suppression, which limits viral infection and restricts T cell activation in tumors. Link: www.sciencedirect.com/science/arti...
sciencedirect.com
Alphavirus replicons encoding IFN-γ enhance cancer virotherapy by overcoming macrophage-mediated suppression
Interference by tumor-associated macrophages may significantly reduce the efficacy of therapeutic viruses designed to infect cancer cells and activate…
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Thomas Lin Pedersen @thomasp85.com · 11/09/2025
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN. It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package. Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
tidyverse.org
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
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Charlotte Huyghe @charlottehuyghe.bsky.social · 08/09/2025
Even the cichlid fish eggs of Lake Tanganyika are highly diverse! Picture by Grégoire Vernaz and Anja Haefeli www.horizons-mag.ch/2025/09/04/f...
horizons-mag.ch
Fishing for biodiversity
Horizons - In brief
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Roberto Rozzi @robertorozzi.bsky.social · 31/08/2025
🚨 Our study investigating the relationship between evolutionary age and range size across plants and animals is out in @natcomms.nature.com! Delighted to be part of this great project led by @adrianaalzate.bsky.social www.nature.com/articles/s41... 🌐📈⏳️🐐🐋🐦🦎🐸🐠🌴🏝
nature.com
Evolutionary age correlates with range size across plants and animals - Nature Communications
Why are some species widespread while others are found only in small, isolated areas? This study shows that species with narrow ranges, and thus higher extinction risk, are often island-restricted, po...
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Joseph Tobias @josephtobias.bsky.social · 28/08/2025
🚨New paper led by @adrianaalzate.bsky.social showing that in most plant and animal groups the age of a species predicts its geographical range size, although the relationship is strongly mediated by dispersal ability and occurrence on islands 🧪🌐🪶 www.nature.com/articles/s41...
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Maxwell Shafer @maxshafer.bsky.social · 28/08/2025
Now published @natecoevo.nature.com with @annika-nichols.bsky.social, our latest on the evolution of 𝘴𝘭𝘦𝘦𝘱 across 𝟲𝟬 𝘀𝗽𝗲𝗰𝗶𝗲𝘀 of cichlid fishes! doi.org/10.1038/s415... with members of the @schierlab.bsky.social and Salzburger labs, as well as the burgeoning Shafer lab @uoftcellsysbiol.bsky.social
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Annals of Botany @annbot.bsky.social · 04/08/2025
🔥ADVANCE ACCESS🔥: Climatic oscillations, dispersibility and adaptability behind worldwide mountain radiations of the Helichrysum– Anaphalis—Pseudognaphalium (HAP) clade (Compositae) doi.org/10.1093/aob/...
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iDiv Biodiversity Research @idiv-research.bsky.social · 27/08/2025
To the paper: doi.org/10.1038/s414...
doi.org
Evolutionary age correlates with range size across plants and animals - Nature Communications
Why are some species widespread while others are found only in small, isolated areas? This study shows that species with narrow ranges, and thus higher extinction risk, are often island-restricted, po...
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iDiv Biodiversity Research @idiv-research.bsky.social · 27/08/2025
A new @natcomms.nature.com study led by iDiv alumna @adrianaalzate.bsky.social @naturalis.bsky.social uncovered that across >26,000 species evolutionary age is positively linked to range size, except in marine mammals. #Biodiversity #Evolution #iDivResearch www.idiv.de/older-specie...
idiv.de
Older species tend to have large ranges – unless they live on islands
New Nature Communication publications sheds light on how ecological, evolutionary, and geographical processes can simultaneously shape species’ vulnerability to extinction.
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Eawag Aquatic Research @eawag.bsky.social · 28/08/2025
An international study conducted in Eawag's experimental ponds demonstrates how indirect ecological effects influence the evolution of species. 👉 www.eawag.ch/en/info/port...
eawag.ch
Indirect effects drive evolution
An international study conducted in Eawag's experimental ponds demonstrates how indirect ecological effects influence the evolution of species.
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Thijs Janzen @thijsjanzen.bsky.social · 28/08/2025
This study by @hoehna.bsky.social and coauthors seems very reassuring: where we often pick partition specific models rather ad-hoc, it appears these do not influence divergence time estimations. (I would still love to see a densitree plot though!) www.biorxiv.org/content/10.1...
biorxiv.org
Impact of Partition Models on Phylogenetic Inference and Divergence Times of Lampyridae from Mitochondrial Genomes
Mitochondrial genomes are frequently used for phylogenetic inference due to their availability and cost-efficient sequencing. In most mitogenomic phylogenetic analyses, only the two ribosomal RNA and ...
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Prof Sam Illingworth @samillingworth.com · 25/08/2025
🌍 Age and extinction risk Analysing 26,000 species, researchers found older plants and animals usually have larger ranges, while younger species, island dwellers, and poor dispersers face greater extinction risk. 🔗 www.nature.com/articles/s41... #SciComm 🧪
nature.com
Evolutionary age correlates with range size across plants and animals - Nature Communications
Why are some species widespread while others are found only in small, isolated areas? This study shows that species with narrow ranges, and thus higher extinction risk, are often island-restricted, po...
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Alessio Capobianco @acapomorphic.bsky.social · 10/07/2025
We now have protein sequences from rhino enamel that are >20 million years old! I am extremely excited and grateful to have been part of this project. The incredible thing: these sequences are informative enough to place this ancient species in the rhino tree! www.nature.com/articles/s41...
nature.com
Phylogenetically informative proteins from an Early Miocene rhinocerotid - Nature
Protein sequences from fossil tooth enamel of a rhinocerotid from Canada’s High Arctic are used to develop phylogenetic frameworks from a specimen too old to preserve ancient DNA.
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