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Daniel Tamarit

@danieltamarit.bsky.social
1.9K followers 659 following 71 posts

Evolutionary biologist studying archaeal and bacterial genomes | Assistant Prof @BinfUtrecht.bsky.social 🇳🇱

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Reposted by Daniel Tamarit
Rasmus Jensen @rasmusjensen.bsky.social · 25/09/2026
🎉 Out today in Cell: the paper I've been looking forward to sharing for a long time 🎉 We used cryo-ET to find a molecular machine nobody knew existed on the surface of a minimal bacterium, and worked out what it does. 🧵(1/7) #TeamTomo #cryoET
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 01/06/2026
Application deadline coming up: June 7th 🔔 Interested in... 🧐 Fundamental biology? 🧩 Elucidating how evolution works? 🧬 Obtaining new insights from genome sequences? 🫥 Archaea, the least studied domain of life? Join us with an exciting PhD on archaeal genome evolution!
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Timothy Fuqua @timothyfuqua.bsky.social · 29/05/2026
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)
science.org
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.
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Rod Page @rdmpage.bsky.social · 27/05/2026
Interesting new tool to extract phylogenies from images (Tremble). It is crazy that this is still something we have to do. doi.org/10.1093/bioi...
doi.org
Treemble: a graphical tool to generate Newick strings from phylogenetic tree images
AbstractSummary. Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the ma
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Molecular Biology and Evolution @molbioevol.bsky.social · 27/05/2026
@joshnhamm.bsky.social @ndombrowski.bsky.social @greening.bsky.social @luisvalentin.bsky.social et al. provide the first investigation into the enigmatic Terrarchaeota and insights into the evolution of high salt adaptation in Archaea. 🔗 doi.org/10.1093/molbev/msag091 #evobio #molbio #microbeSky
doi.org
New lineages provide insights into the convergent evolution of extreme salt adaptation within symbiotic Archaea
Abstract. Environmental genomics has led to the discovery of many new lineages of archaea, including “DPANN” (or Nanobdellati), comprising organisms with s
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Daniel Tamarit @danieltamarit.bsky.social · 22/05/2026
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! 🙏
uu.nl
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Vivek Mutalik @vivekmutalik.bsky.social · 03/04/2026
📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
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Rob Edwards @linsalrob.bsky.social · 05/04/2026
Want to annotate a bacterial genome with structures? @oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures www.biorxiv.org/content/10.6... #phagesky #microsky #microbiomesky
biorxiv.org
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Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · 23/03/2026
Phd Position alert 🚨 Join our project ASTRAfun (Adaptation and Starship Traffic in Root-Associated fungi), in which we will use computational models to unveil the hidden dynamics of fungal evolution. It’s not going to be just regular fun. It’s going to ASTRAfun. 🤓 www.uu.nl/en/organisat...
uu.nl
PhD Position in Computational Modelling of Fungal Evolution
How do giant mobile elements called ‘Starships’ reshape fungal plant pathogens? Help us computationally model their spread and impact in nature and agriculture!
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Frank Melzner @frankmelzner.bsky.social · 19/03/2026
Come work with us in Vienna and along European coasts! We look for a creative Postdoc (4year contract) in Evolutionary Genomics to cooperate with physiologists, ecologists, see: jobs.univie.ac.at/job/Postdoc-... Please share! @univie.ac.at
jobs.univie.ac.at
Postdoc marine evolutionary genomics
Postdoc marine evolutionary genomics
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Eduardo Rocha @epcrocha.bsky.social · 17/03/2026
Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky
ecoevorxiv.org
From Trading Genes to Crafting New Tricks: How Horizontal Gene Transfer Potentiates the Emergence of Novel Functions
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Andrew Roger @andrewjroger.bsky.social · 18/03/2026
So you are using IQ-TREE to estimate a tree for "deep time" phylogenetics using amino acid alignments. There is a lot of confusion about how to test model fit. Here are some suggestions.
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Tobias Warnecke @tobiaswarnecke.bsky.social · 05/03/2026
Pls re-post: My department @oxfordbiochemistry.bsky.social are recruiting for several new faculty positions (links below). Broad search in molecular biology/biochemistry, across prokaryotes and eukaryotes. Interested in understanding life at the molecular level, this job might be for you! 1/n
my.corehr.com
Job Details
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Kassiani Panagiotou @kassipan.bsky.social · 05/03/2026
Just over ten years after the discovery of the first Asgard archaeal genomes, we revisit the rapid expansion of this remarkable archaeal lineage. From diverse genomes and metabolisms to eukaryotic signature proteins and the first cultured representatives. www.nature.com/articles/s41...
nature.com
Diversity, ecology, cell biology and evolution of the Asgard archaea - Nature Reviews Microbiology
The Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of th...
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Aileen Berasategui @berasymbionts.bsky.social · 05/03/2026
Excited to collaborate with @hassansalem.bsky.social and @tatsuyanobori.bsky.social on this new Postdoc opportunity! If you're interested in the developmental biology of symbiosis, apply and join us @johninnescentre.bsky.social and @thesainsburylab.bsky.social 🪲🦠🔬
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Stephan Köstlbacher @stephkoe.bsky.social · 05/03/2026
🧵 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! 🎉 How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us — so we used protein structure prediction to look deeper. 🧬 www.nature.com/articles/s41...
nature.com
Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling - Nature Microbiology
A structural catalogue of the Asgard archaeal pangenome reveals hundreds of eukaryotic-like proteins that suggest a higher degree of cellular complexity in the archaeal ancestor of eukaryotes.
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 05/03/2026
Finally out in @natmicrobiol.nature.com: Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling. Great work by @stephkoe.bsky.social @kassipan.bsky.social @jvhooff.bsky.social www.nature.com/articles/s41...
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Hassan Salem @hassansalem.bsky.social · 04/03/2026
Join @berasymbionts.bsky.social , @tatsuyanobori.bsky.social and us for a postdoc on the remarkable developmental biology of symbiosis! Applications are due March 25th 🪲🦠 @johninnescentre.bsky.social @thesainsburylab.bsky.social
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Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · 25/02/2026
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...
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Aldert Zomer @aldertzomer.bsky.social · 24/02/2026
Our faculty has a particularly interesting PhD position open on antimicrobial resistance, effects of antibiotics treatment on the microbiome and resistome, restoration of the equine microbiome using FMT. www.uu.nl/en/organisat... Please contact Mathijs Theelen, email address in the link below.
uu.nl
PhD candidate in Equine Intestinal Microbiome and Resistome
Join this PhD project to study how the equine gut microbiome and resistome can improve gastrointestinal health and combat antimicrobial resistance.
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Archaea Biology Vienna @archaea-vienna.bsky.social · 19/02/2026
Thank you @carlzimmer.com for sharing the excitement for our favorite organisms and introducing them to the broader audience! www.nytimes.com/2026/02/18/s...
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 18/02/2026
Finally out in @nature.com: a new piece of the puzzle of how complex life evolved. Lead by @archaeal.bsky.social & @katyappler.bsky.social. Great collab with @greening.bsky.social and @kassipan.bsky.social. More pieces to follow soon! www.nature.com/articles/s41...
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Kathryn (Katy) Appler @katyappler.bsky.social · 18/02/2026
Beyond thrilled to share that our study has been published! This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and @texasscience.bsky.social!!! #MicroSky #ArchaeaSky 1/12
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Brett Baker @archaeal.bsky.social · 18/02/2026
New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...
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Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · 13/02/2026
Please check out our review on the impact of spatial structure in microbial ecosystems! In it, we discuss how spatial patterns impact microbial ecology and evolution, eventually impacting everything we see around us! See @marcelbaecker.bsky.social's amazing summary below :) 🦠 𝚂𝙿𝙰𝙲𝙴 𝙼𝙰𝚃𝚃𝙴𝚁𝚂 ! 🦠
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Max Raas @maxraas.bsky.social · 13/02/2026
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
tinyurl.com
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...
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 16/02/2026
Our latest preprint: Together with the team of Jan Löwe, @danieltamarit.bsky.social and many others we discovered and characterized several Asgard tubulin genes and propose that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis www.biorxiv.org/content/10.6...
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 11/02/2026
Today we published a Correction on our 2023 @nature.com paper reporting the heimdallarchaeial ancestry of eukaryotes: www.nature.com/articles/s41... Corrected paper: www.nature.com/articles/s41... Importantly, the re-analyses of the corrected dataset are consistent with the original findings.
nature.com
Author Correction: Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes - Nature
Nature - Author Correction: Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
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Piotr Lukasik @sympiotr.bsky.social · 11/02/2026
Our new paper in @natcomms.nature.com is now online-early! We describe independent evolution of bacterial genomes of only ~50–52 kb — the smallest known outside cellular organelles — revealing striking convergence toward minimal gene sets. 🔗 doi.org/10.1038/s414...
The visualization of two bacterial genomes, of 50 and 52kb, representing independent instances of extreme genomic reduction in ancient heritable endosymbionts of planthoppers.
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 12/02/2026
Two more weeks to apply - come join us () in The Netherlands as a postdoctoral researcher on large-scale metagenomic exploration of new lineages!
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c0nc0rdance @c0nc0rdance.bsky.social · 17/12/2025
“A process which led from the amoeba to man appeared to the philosophers to be obviously a progress - though whether the amoeba would agree with this opinion is not known" - Bertrand Russell, 1976. Time-lapse video of Vampyrella lateritia eating Spirogyra algae from Science Source/Oliver Skibbe. 🦠
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Agathe Chaigne @agathechaigne.bsky.social · 18/12/2025
My lab is hiring a postdoc (ERC funded)! If you're interested, get in touch!
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Yamuna Krishnan @krishnanyamuna.bsky.social · 17/12/2025
Organelles do NOT have a single uniform pH. And if you think they must, because “protons diffuse fast,” this paper is for you. A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
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Buzz Baum @buzzbaum.bsky.social · 16/12/2025
Are you a long-time fan of Archaea, an extremophile-phile, or are you simply curious? Either way, we have good news. We’re delighted to announce the 2026 EMBO Workshop on Archaea, 6–10 July. Sign up: meetings.embo.org/event/26-arc... We look forward to seeing you in Cambridge, UK. Please repost!
meetings.embo.org
Molecular Biology of Archaea: Life Through the Prism of Archaea
In 1977, Woese and colleagues revealed Archaea as a distinct domain of life. Building on this insight, the discovery of Asgard archaea has strengthened the view that many hallmarks of eukaryotic cell…
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DEEMteam_Orsay @deemteam.bsky.social · 15/12/2025
With our old friends Sergey, Luis and Guifré, we have published a minireview in @currentbiology.bsky.social about aphelids, the sister group to fungi, including why we think they are not fungi but, nevertheless, key to understand early fungal evolution. authors.elsevier.com/a/1mH793QW8S...
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Stephen Royle @steveroyle.bsky.social · 16/12/2025
Vaults. They are cell biology's greatest puzzle! This preprint from Martin Beck's lab shows them docked on ER membranes with a ribosome inside. What on earth is going on there?? #CellBiology #WTFology www.biorxiv.org/content/10.6...
biorxiv.org
The vault associates with membranes in situ
The eukaryotic vault particle is a giant ribonucleoprotein complex that assembles into an iconic barrel-like cage. Its cellular function has remained elusive despite extensive characterization. Using ...
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Courtney Stairs @cstairs.bsky.social · 13/12/2025
Save the date! The next instalment of Comparative Genomics of Unicellular Eukaryotes is a GO! Join us next year for a programme of talks, posters, ECR/networking activities. Website and registration details to follow in the coming weeks. See you October 5-10 2026 in beautiful San Feliu!!
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Laura Eme @lauraeme.bsky.social · 13/12/2025
Microbial eukaryotes keep challenging assumptions about eukaryotic cell and genome biology. Our upcoming workshop explores the frontier of protist genomics and how it shapes cell biology, ecology and evolution. Please save the date! Talks, posters and ECR events Websites and details coming soon
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Elin Videvall @elinvidevall.bsky.social · 09/12/2025
Interested in applying for a postdoc on wildlife #microbiomes in my lab at Uppsala University, Sweden? The local Birgitta Sintring Foundation gives out generous 2-year postdoc scholarships to early-career researchers who apply with a PI at the department. Deadline Feb 9. www.uu.se/en/departmen...
uu.se
The Birgitta Sintring Foundation – Department of Ecology and Genetics – Uppsala University
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Qiyun Zhu @zhuqiyun.bsky.social · 11/12/2025
The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource
nature.com
Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods
Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis
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Daniel Tamarit @danieltamarit.bsky.social · 10/12/2025
Welcome to Bluesky, @pieterhart.bsky.social! Pieter just joined my group as a PhD student studying bacterial genome evolution—exciting years ahead! Here he is enjoying a chat about his MSc work (w/ @kassipan.bsky.social & @ettema.bsky.social) at Science4Life @utrechtuniversity.bsky.social 🧬🦠✨
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Andrew Roger @andrewjroger.bsky.social · 09/12/2025
Those interested in performing maximum likelihood phylogenomic analysis on data sets made up of eukaryotic nuclear genes using site heterogeneous mixture models like C60, I suggest you use the ELM model in IQ-TREE instead of the LG model /1
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Nicolas Mouquet @nmouquet.bsky.social · 09/12/2025
🔥 A lottery-first system 🎲 makes research grants allocation cheaper, faster, and boosts funding for women, while "traditional" (patriarcal?) peer review drags everyone down. 🤔 Maybe randomness is fairer than the experts. 🔄 Time to rethink the whole game! 💣 www.nature.com/articles/s41... 🧪
nature.com
Lottery before peer review is associated with increased female representation and reduced estimated economic cost in a German funding line - Nature Communications
The authors show evidence from a German funding line that a lottery-first approach followed by peer review is accompanied by increased female representation both at the submission stage and among fund...
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Emmanuele Severi @emmseveri.bsky.social · 09/12/2025
#microsky #phagesky More anti #phage systems in E. coli www.biorxiv.org/content/10.6...
biorxiv.org
Leveraging defense system modularity to discover anti-phage systems
Bacterial exposure to constant phage attack drives rapid diversification of anti-phage defense systems, often through the exchange of modular defensive domains. Here, we leverage this modularity signa...
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Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 09/12/2025
Now out in @currentbiology.bsky.social ! Screening over a thousand fungal genomes, @jromeijn.bsky.social, Iñigo Bañales Belaunde and @mfseidl.bsky.social find that horizontal transfer shapes the fungal mobilome 🍄🔄✈️🧬 @ubc-uu.bsky.social Don't miss Josje's thread for a summary of the findings! 👇
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Max Raas @maxraas.bsky.social · 01/12/2025
Our story on the kinetochore composition of the ciliate Tetrahymena thermophila is out now on bioRxiv! We find surprisingly many orthologs of conventional kinetochore components, but also components that have very different evolutionary origins. A 🧵 (1/11) Check it out here: tinyurl.com/4ectm9x4
tinyurl.com
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Alex Crits-Christoph @acritschristoph.bsky.social · 12/11/2025
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic. We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
Figure 2. PET screen results and RB-TnSeq gene fitness results
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Marta Lidia Sudo @martasu.bsky.social · 08/12/2025
It’s exciting to see converging evidence across systems! 😀 Alongside the new work on gutless worms, our study shows that organosulfur cycling is also essential in lucinid holobionts. Lucinid host provides DMSP to its symbionts, sulphur-oxidising Thiodiazotropha and, a new member, Endozoicomonas.
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Aldert Zomer @aldertzomer.bsky.social · 08/12/2025
MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 06/12/2025
Extensive horizontal transfer of transposable elements shapes fungal mobilomes @currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social www.cell.com/current-biol...
cell.com
Extensive horizontal transfer of transposable elements shapes fungal mobilomes
Romeijn et al. reveal that horizontal transposon transfer is widespread in fungi, contributing up to 70% of transposon content in some taxa. The authors uncover thousands of events across diverse line...
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