Sam von der Dunk
@derdunk.bsky.social
Studying the evolution of complexity through modelling and phylogenomics
Reposted by Sam von der Dunk
Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! 🎉🦠🧬
www.science.org/doi/10.1126/...
w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
www.science.org/doi/10.1126/...
w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.
www.science.org
June 1, 2026 at 8:26 AM
Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! 🎉🦠🧬
www.science.org/doi/10.1126/...
w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
www.science.org/doi/10.1126/...
w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
Reposted by Sam von der Dunk
Our study comparing promoter existence and emergence in random vs genomic DNA is finally published!!!
TLDR: the E. coli genome has more promoters than random DNA (even in intergenic regions), and promoters emerge ~3x more readily from random DNA than genomic DNA. (1/2)
TLDR: the E. coli genome has more promoters than random DNA (even in intergenic regions), and promoters emerge ~3x more readily from random DNA than genomic DNA. (1/2)
De novo promoters emerge more readily from random DNA than from genomic DNA
Promoters emerge three times more readily from random DNA than from genomic DNA.
www.science.org
May 29, 2026 at 8:08 PM
Our study comparing promoter existence and emergence in random vs genomic DNA is finally published!!!
TLDR: the E. coli genome has more promoters than random DNA (even in intergenic regions), and promoters emerge ~3x more readily from random DNA than genomic DNA. (1/2)
TLDR: the E. coli genome has more promoters than random DNA (even in intergenic regions), and promoters emerge ~3x more readily from random DNA than genomic DNA. (1/2)
Reposted by Sam von der Dunk
I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻
Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks!
www.uu.nl/en/organisat...
Please share! 🙏
Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks!
www.uu.nl/en/organisat...
Please share! 🙏
www.uu.nl
May 22, 2026 at 9:02 AM
I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻
Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks!
www.uu.nl/en/organisat...
Please share! 🙏
Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks!
www.uu.nl/en/organisat...
Please share! 🙏
Reposted by Sam von der Dunk
Our preprint on the 'Origins of Eukaryotic Metabolism' is out! Take a look at some of the new findings on the origin of eukaryotic membranes, metabolic integrations between archaeal and bacterial ancestors, and other fascinating prokaryotic interactions during eukaryogenesis.
doi.org/10.64898/202...
doi.org/10.64898/202...
doi.org
May 13, 2026 at 9:48 AM
Our preprint on the 'Origins of Eukaryotic Metabolism' is out! Take a look at some of the new findings on the origin of eukaryotic membranes, metabolic integrations between archaeal and bacterial ancestors, and other fascinating prokaryotic interactions during eukaryogenesis.
doi.org/10.64898/202...
doi.org/10.64898/202...
Reposted by Sam von der Dunk
@shrylishreekar.bsky.social and me wrote a commentary on Chunhui Hao's and @stuwest.bsky.social et al.'s recent paper
"Cooperation and the evolution of bacterial niche breadth"
in PNAS.
Please find our commentary here:
www.pnas.org/doi/10.1073/...
"Cooperation and the evolution of bacterial niche breadth"
in PNAS.
Please find our commentary here:
www.pnas.org/doi/10.1073/...
April 14, 2026 at 5:49 AM
@shrylishreekar.bsky.social and me wrote a commentary on Chunhui Hao's and @stuwest.bsky.social et al.'s recent paper
"Cooperation and the evolution of bacterial niche breadth"
in PNAS.
Please find our commentary here:
www.pnas.org/doi/10.1073/...
"Cooperation and the evolution of bacterial niche breadth"
in PNAS.
Please find our commentary here:
www.pnas.org/doi/10.1073/...
Very excited with the online publication of our modeling work on the evolution of sexual reproduction during obligate endosymbiosis: doi.org/10.1098/rstb.... The first publication of Alkmini Zania 🎉; together with Paulien Hogeweg.
doi.org
April 9, 2026 at 7:56 AM
Very excited with the online publication of our modeling work on the evolution of sexual reproduction during obligate endosymbiosis: doi.org/10.1098/rstb.... The first publication of Alkmini Zania 🎉; together with Paulien Hogeweg.
Reposted by Sam von der Dunk
In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨
Let me hit you with some highlights on why spatial structure matters. (and why you should care!)
Sharing is appreciated 🙏 🧵👇
doi.org/10.1093/fems...
Let me hit you with some highlights on why spatial structure matters. (and why you should care!)
Sharing is appreciated 🙏 🧵👇
doi.org/10.1093/fems...
February 25, 2026 at 1:06 PM
In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨
Let me hit you with some highlights on why spatial structure matters. (and why you should care!)
Sharing is appreciated 🙏 🧵👇
doi.org/10.1093/fems...
Let me hit you with some highlights on why spatial structure matters. (and why you should care!)
Sharing is appreciated 🙏 🧵👇
doi.org/10.1093/fems...
Reposted by Sam von der Dunk
Space is the place (for microbes 🦠)!
Delighted to have contributed to this review on spatial structure in microbial communities by @marcelbaecker.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others.
Delighted to have contributed to this review on spatial structure in microbial communities by @marcelbaecker.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others.
Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... 🧵👇
academic.oup.com/femsre/artic... 🧵👇
Spatial structure: shaping the ecology and evolution of microbial communities
Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up
academic.oup.com
February 13, 2026 at 1:04 PM
Space is the place (for microbes 🦠)!
Delighted to have contributed to this review on spatial structure in microbial communities by @marcelbaecker.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others.
Delighted to have contributed to this review on spatial structure in microbial communities by @marcelbaecker.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others.
Reposted by Sam von der Dunk
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?
Excited to share our latest work in @science.org on a new small polymerase.
1/n
Excited to share our latest work in @science.org on a new small polymerase.
1/n
A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
www.science.org
February 13, 2026 at 11:42 AM
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?
Excited to share our latest work in @science.org on a new small polymerase.
1/n
Excited to share our latest work in @science.org on a new small polymerase.
1/n
Reposted by Sam von der Dunk
Recently, a Hypothesis was posed in @jcellsci.bsky.social in which the root of eukaryotes was placed between kinetoplastids and all other eukaryotes. From this, it was implied that LECA did not have a kinetochore. We argue this is highly unlikely. A 🧵(1/12)
Read our reply here: tinyurl.com/n87myhpr
Read our reply here: tinyurl.com/n87myhpr
The LECA had a conventional kinetochore and the kinetoplastid kinetochore is a derived feature – a critical evaluation of Akiyoshi, 2025
Summary:Akiyoshi, 2025 presented a hypothesis with implications for the early evolution of eukaryotes and eukaryotic cell division machinery. In this Correspondence, the authors conclude that this hyp...
tinyurl.com
February 13, 2026 at 12:45 PM
Recently, a Hypothesis was posed in @jcellsci.bsky.social in which the root of eukaryotes was placed between kinetoplastids and all other eukaryotes. From this, it was implied that LECA did not have a kinetochore. We argue this is highly unlikely. A 🧵(1/12)
Read our reply here: tinyurl.com/n87myhpr
Read our reply here: tinyurl.com/n87myhpr
Reposted by Sam von der Dunk
Two more weeks to apply - come join us () in The Netherlands as a postdoctoral researcher on large-scale metagenomic exploration of new lineages!
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Please repost
Apply here: www.wur.nl/en/vacancy/p...
February 12, 2026 at 7:46 AM
Two more weeks to apply - come join us () in The Netherlands as a postdoctoral researcher on large-scale metagenomic exploration of new lineages!
Reposted by Sam von der Dunk
Meeting alert! EMBO workshop about molecular and physical principles in evolution in Portugal, 2-5 June 2026. Deadline for registration is March 1st. Check out the website it should be a fun and informative workshop bridging evolutionary biology and physics of life meetings.embo.org/event/26-cel...
The rules of the game: biophysical & molecular principles in cellular evolution
Cells are the fundamental units of life, shaped by evolution into a remarkable diversity of forms and functions. Much is known about the roles of genes and proteins, the regulation of molecular proce…
meetings.embo.org
February 12, 2026 at 1:37 PM
Meeting alert! EMBO workshop about molecular and physical principles in evolution in Portugal, 2-5 June 2026. Deadline for registration is March 1st. Check out the website it should be a fun and informative workshop bridging evolutionary biology and physics of life meetings.embo.org/event/26-cel...
Reposted by Sam von der Dunk
How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers
go.nature.com/4sEMwLH
go.nature.com/4sEMwLH
Genomic clues to the origin of eukaryotic cells
How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers.
go.nature.com
January 14, 2026 at 4:51 PM
How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers
go.nature.com/4sEMwLH
go.nature.com/4sEMwLH
Reposted by Sam von der Dunk
Less than two 2 weeks to apply for this PhD position in my group.
Please do not miss the opportunity to apply if the topic is of interest to you 👇
Please do not miss the opportunity to apply if the topic is of interest to you 👇
I am very excited to announce that a fully funded PhD position is available in my group.
Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia
Please RT or forward this information to interested candidates.
Deadline: 11.01.26
More info:
shorturl.at/f1TuF
Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia
Please RT or forward this information to interested candidates.
Deadline: 11.01.26
More info:
shorturl.at/f1TuF
December 30, 2025 at 10:36 AM
Less than two 2 weeks to apply for this PhD position in my group.
Please do not miss the opportunity to apply if the topic is of interest to you 👇
Please do not miss the opportunity to apply if the topic is of interest to you 👇
Reposted by Sam von der Dunk
@guyleonard.bsky.social et al. report a near-complete genome and transcriptome sequence dataset for green algae host Paramecium bursaria, an endosymbiotic model system.
🔗 doi.org/10.1093/gbe/evaf183
#genome #evolution
🔗 doi.org/10.1093/gbe/evaf183
#genome #evolution
De Novo Genome Sequence Assembly of the RNAi-Tractable Paramecium bursaria 186b: An Endosymbiotic Model System
Abstract. How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a use
doi.org
October 31, 2025 at 10:54 AM
@guyleonard.bsky.social et al. report a near-complete genome and transcriptome sequence dataset for green algae host Paramecium bursaria, an endosymbiotic model system.
🔗 doi.org/10.1093/gbe/evaf183
#genome #evolution
🔗 doi.org/10.1093/gbe/evaf183
#genome #evolution
Reposted by Sam von der Dunk
Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!
Hoe is al het complexe leven op aarde eigenlijk ontstaan?
Wat DNA uit slootwater ons vertelt over jouw onbekende voorouders | VPRO Tegenlicht
YouTube video by VPRO Tegenlicht
youtu.be
October 9, 2025 at 8:46 AM
Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!
Reposted by Sam von der Dunk
LMB PhD studentship available in the Baum lab to use informatics to infer cell structure from genomic data in collaboration with the brilliant Tom Williams. If you write to me and I don’t reply - try again - the spam filter is hungry…
October 2, 2025 at 9:04 AM
LMB PhD studentship available in the Baum lab to use informatics to infer cell structure from genomic data in collaboration with the brilliant Tom Williams. If you write to me and I don’t reply - try again - the spam filter is hungry…
Reposted by Sam von der Dunk
Oxford Biology is growing 📢
We’re appointing 3 Associate Professors in:
🌱 Plant Sciences
🦉 Animal Behaviour
🔬 Molecular Cell Biology
3 fields. 3 opportunities. One new home for Oxford Biology.
Learn more 👉 bit.ly/41S2Tc7
Apply now 👉 bit.ly/488CNW3
We’re appointing 3 Associate Professors in:
🌱 Plant Sciences
🦉 Animal Behaviour
🔬 Molecular Cell Biology
3 fields. 3 opportunities. One new home for Oxford Biology.
Learn more 👉 bit.ly/41S2Tc7
Apply now 👉 bit.ly/488CNW3
September 15, 2025 at 8:20 AM
Oxford Biology is growing 📢
We’re appointing 3 Associate Professors in:
🌱 Plant Sciences
🦉 Animal Behaviour
🔬 Molecular Cell Biology
3 fields. 3 opportunities. One new home for Oxford Biology.
Learn more 👉 bit.ly/41S2Tc7
Apply now 👉 bit.ly/488CNW3
We’re appointing 3 Associate Professors in:
🌱 Plant Sciences
🦉 Animal Behaviour
🔬 Molecular Cell Biology
3 fields. 3 opportunities. One new home for Oxford Biology.
Learn more 👉 bit.ly/41S2Tc7
Apply now 👉 bit.ly/488CNW3
Excited with two new preprints on evolution of molecular structure, in RNA (doi.org/10.1101/2025..., @n-martin.bsky.social) and proteins (doi.org/10.1101/2025...). Both RNA and protein structures are often conserved across evolution, but the underlying reasons are very different.
September 1, 2025 at 10:35 AM
Excited with two new preprints on evolution of molecular structure, in RNA (doi.org/10.1101/2025..., @n-martin.bsky.social) and proteins (doi.org/10.1101/2025...). Both RNA and protein structures are often conserved across evolution, but the underlying reasons are very different.
Reposted by Sam von der Dunk
And thanks to all poster presenters, including Moisès Bernabeu whose poster was in the top 5 of best posters at #ESEB2025. Congrats!
Great to see so many people at our symposium om the origin of eukaryotes. Thanks to all the speakers! #ESEB25 @julianvosseberg.bsky.social
August 22, 2025 at 2:27 PM
And thanks to all poster presenters, including Moisès Bernabeu whose poster was in the top 5 of best posters at #ESEB2025. Congrats!
Reposted by Sam von der Dunk
Sam von der Dunk: we know that RNA structure is robust to mutation yet evolvable. What about protein structure? Take advantage of ESMfold https://doi.org/10.1126/science.ade2574
Natural proteins are robust to mutations, whereas random amino-acid sequences are not. Even disordered natural […]
Natural proteins are robust to mutations, whereas random amino-acid sequences are not. Even disordered natural […]
Original post on ecoevo.social
ecoevo.social
August 22, 2025 at 9:53 AM
Sam von der Dunk: we know that RNA structure is robust to mutation yet evolvable. What about protein structure? Take advantage of ESMfold https://doi.org/10.1126/science.ade2574
Natural proteins are robust to mutations, whereas random amino-acid sequences are not. Even disordered natural […]
Natural proteins are robust to mutations, whereas random amino-acid sequences are not. Even disordered natural […]
Great to see so many people at our symposium om the origin of eukaryotes. Thanks to all the speakers! #ESEB25 @julianvosseberg.bsky.social
August 21, 2025 at 4:23 PM
Great to see so many people at our symposium om the origin of eukaryotes. Thanks to all the speakers! #ESEB25 @julianvosseberg.bsky.social
The exciting project of Alkmini Zania on the impact of sex on endosymbiosis reveals complex evolutionary dynamics. What could this mean for early eukaryotes? www.biorxiv.org/content/10.1...
The risk of sexual reproduction promotes the evolution of regulation between host and symbionts
Sexual reproduction is a widely spread feature of eukaryotes and was already present in the last eukaryotic common ancestor (LECA). Most extant eukaryotes inherit mitochondria from a single parent, bu...
www.biorxiv.org
August 5, 2025 at 9:35 AM
The exciting project of Alkmini Zania on the impact of sex on endosymbiosis reveals complex evolutionary dynamics. What could this mean for early eukaryotes? www.biorxiv.org/content/10.1...
