Tom Williams
@tweethinking.bsky.social
Computational evolutionary biologist - phylogenetics, molecular and microbial evolution. Lab website: tancata.github.io
Reposted by Tom Williams
The heatwave is finally over - just in time for our “Frosty Foci” to finally come online! ❄️🦠
We found that E. coli builds a transient nucleolus-like ribosome biogenesis compartment during cold adaptation, when RNA (mis)folding makes ribosome biogenesis challenging.
We found that E. coli builds a transient nucleolus-like ribosome biogenesis compartment during cold adaptation, when RNA (mis)folding makes ribosome biogenesis challenging.
September 18, 2026 at 4:46 PM
The heatwave is finally over - just in time for our “Frosty Foci” to finally come online! ❄️🦠
We found that E. coli builds a transient nucleolus-like ribosome biogenesis compartment during cold adaptation, when RNA (mis)folding makes ribosome biogenesis challenging.
We found that E. coli builds a transient nucleolus-like ribosome biogenesis compartment during cold adaptation, when RNA (mis)folding makes ribosome biogenesis challenging.
Reposted by Tom Williams
Big shoutout and thank you to our wonderful collaborators Nussi, @olivierduss.bsky.social, @kausthubh.bsky.social and @tweethinking.bsky.social. Thanks a lot also to @basler-lab.bsky.social, @ujenal.bsky.social & labs, who taught us how to get bacteria to behave for some beautiful cell biology!
September 18, 2026 at 4:46 PM
Big shoutout and thank you to our wonderful collaborators Nussi, @olivierduss.bsky.social, @kausthubh.bsky.social and @tweethinking.bsky.social. Thanks a lot also to @basler-lab.bsky.social, @ujenal.bsky.social & labs, who taught us how to get bacteria to behave for some beautiful cell biology!
Reposted by Tom Williams
Our paper is out in Nature Communications! 🌳🧬
We investigate the position of the archaeal root, the nature of the last archaeal common ancestor, and the evolution of DPANN archaea using state-of-the-art phylogenetic and gene-tree–species-tree reconciliation approaches. doi.org/10.1038/s414...
We investigate the position of the archaeal root, the nature of the last archaeal common ancestor, and the evolution of DPANN archaea using state-of-the-art phylogenetic and gene-tree–species-tree reconciliation approaches. doi.org/10.1038/s414...
Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages - Nature Communications
Key questions about the early evolution of archaea remain unanswered. Here, Huang et al. use improved methods of genome evolution to propose a euryarchaeal root for archaea, a methanogenic ancestor, a...
www.nature.com
August 14, 2026 at 8:10 AM
Our paper is out in Nature Communications! 🌳🧬
We investigate the position of the archaeal root, the nature of the last archaeal common ancestor, and the evolution of DPANN archaea using state-of-the-art phylogenetic and gene-tree–species-tree reconciliation approaches. doi.org/10.1038/s414...
We investigate the position of the archaeal root, the nature of the last archaeal common ancestor, and the evolution of DPANN archaea using state-of-the-art phylogenetic and gene-tree–species-tree reconciliation approaches. doi.org/10.1038/s414...
Reposted by Tom Williams
Ancestral genome reconstructions get noisier the deeper in time you go. The usual response: distrust them and joke about reading entrails. Ours is to train on the noise! The result is calibrated phenotype prediction back to the LBCA deep in the Archaean. New preprint
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Models trained with noisy genomes extend bacterial phenotype prediction into deep time
Predicting phenotype from genotype in extant organisms is increasingly tractable through the accumulation of genome sequences and the development of machine-learning algorithms. Here we show that mach...
www.biorxiv.org
July 4, 2026 at 6:33 AM
Ancestral genome reconstructions get noisier the deeper in time you go. The usual response: distrust them and joke about reading entrails. Ours is to train on the noise! The result is calibrated phenotype prediction back to the LBCA deep in the Archaean. New preprint
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Tom Williams
Very exciting to see this out at last, we use both sequence-based and structural phylogenetics to try and understand the pre-eukaryotic origins of the commander complex! Also some serious protein crystallography and cryo-EM, (five new pdb entries!)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
May 30, 2026 at 7:45 PM
Very exciting to see this out at last, we use both sequence-based and structural phylogenetics to try and understand the pre-eukaryotic origins of the commander complex! Also some serious protein crystallography and cryo-EM, (five new pdb entries!)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Tom Williams
Our paper examining the evolution of halophily in DPANN is out now in MBE!
academic.oup.com/mbe/advance-...
academic.oup.com/mbe/advance-...
May 19, 2026 at 1:36 PM
Our paper examining the evolution of halophily in DPANN is out now in MBE!
academic.oup.com/mbe/advance-...
academic.oup.com/mbe/advance-...
Reposted by Tom Williams
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.
March 18, 2026 at 12:00 AM
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.
Reposted by Tom Williams
MENI is back! Join us in Dublin this August 2026 for our 3rd Meeting for Microbial Evolution in Ireland. We are delighted to have @rachelmwheatley.bsky.social @drrebeccajhall.bsky.social @jpjhall.bsky.social and @tweethinking.bsky.social join us as keynote speakers this year. miniurl.com/MENI
February 18, 2026 at 12:16 PM
MENI is back! Join us in Dublin this August 2026 for our 3rd Meeting for Microbial Evolution in Ireland. We are delighted to have @rachelmwheatley.bsky.social @drrebeccajhall.bsky.social @jpjhall.bsky.social and @tweethinking.bsky.social join us as keynote speakers this year. miniurl.com/MENI
meetings.embo.org/event/26-mic... Announcing the 2026 EMBO course in Computational and Experimental Microbiomics, to be held at Bath. The course brings together experiments and bioinformatics to study host-microbe interactions and co-evolution. Register now, or at least by 11 May, if interested :)
Computational and experimental microbiomics
The critical contribution of microbiota to animal, plant and environmental health is now widely accepted. Progress has been driven by two parallel approaches: in silico analyses of large -omics data …
meetings.embo.org
February 6, 2026 at 4:37 PM
meetings.embo.org/event/26-mic... Announcing the 2026 EMBO course in Computational and Experimental Microbiomics, to be held at Bath. The course brings together experiments and bioinformatics to study host-microbe interactions and co-evolution. Register now, or at least by 11 May, if interested :)
Reposted by Tom Williams
Our analyses converge on a narrow archaeal root region at/near the base of the Euryarchaeota, supporting hypotheses in which the Last Archaeal Common Ancestor was a complex, free-living (hyper-)thermophilic methanogen.
November 13, 2025 at 7:28 PM
Our analyses converge on a narrow archaeal root region at/near the base of the Euryarchaeota, supporting hypotheses in which the Last Archaeal Common Ancestor was a complex, free-living (hyper-)thermophilic methanogen.
Reposted by Tom Williams
Reposted by Tom Williams
New PhD position in my lab at @uniofbath.bsky.social (with both @tweethinking.bsky.social & Dr Bethan Littleford-Colquhoun)!
We're looking for someone keen on bioinformatics and microbiome evolution.
Important info below on eligibility & URSA competition funding👇
www.findaphd.com/phds/project...
We're looking for someone keen on bioinformatics and microbiome evolution.
Important info below on eligibility & URSA competition funding👇
www.findaphd.com/phds/project...
The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath on FindAPhD.com
PhD Project - The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath, listed on FindAPhD.com
www.findaphd.com
November 12, 2025 at 1:20 PM
New PhD position in my lab at @uniofbath.bsky.social (with both @tweethinking.bsky.social & Dr Bethan Littleford-Colquhoun)!
We're looking for someone keen on bioinformatics and microbiome evolution.
Important info below on eligibility & URSA competition funding👇
www.findaphd.com/phds/project...
We're looking for someone keen on bioinformatics and microbiome evolution.
Important info below on eligibility & URSA competition funding👇
www.findaphd.com/phds/project...
Reposted by Tom Williams
I'm looking for a PhD student to dive into some protist genomes and maybe find some cool parasites like this (very flexible) apicomplexan.
www.findaphd.com/phds/project...
Please do reach out if you're interested. And APPLY EARLY! The advert will be taken down when a suitable candidate is found.🪱🦀🐟
www.findaphd.com/phds/project...
Please do reach out if you're interested. And APPLY EARLY! The advert will be taken down when a suitable candidate is found.🪱🦀🐟
October 9, 2025 at 4:02 PM
I'm looking for a PhD student to dive into some protist genomes and maybe find some cool parasites like this (very flexible) apicomplexan.
www.findaphd.com/phds/project...
Please do reach out if you're interested. And APPLY EARLY! The advert will be taken down when a suitable candidate is found.🪱🦀🐟
www.findaphd.com/phds/project...
Please do reach out if you're interested. And APPLY EARLY! The advert will be taken down when a suitable candidate is found.🪱🦀🐟
There's a PhD position now available with me in Bath, on the evolution of symbiosis. www.findaphd.com/phds/project.... The supervisory team also includes @anja1.bsky.social @phil-donoghue.bsky.social and others. NB, this is open both to UK-based students *and* to international students :)
The genomic basis of symbiotic integration at University of Bath on FindAPhD.com
PhD Project - The genomic basis of symbiotic integration at University of Bath, listed on FindAPhD.com
www.findaphd.com
October 9, 2025 at 9:39 AM
There's a PhD position now available with me in Bath, on the evolution of symbiosis. www.findaphd.com/phds/project.... The supervisory team also includes @anja1.bsky.social @phil-donoghue.bsky.social and others. NB, this is open both to UK-based students *and* to international students :)
Reposted by Tom Williams
❗️ Exciting review alert❗️focussing on the evolution and mechanism of prokaryotic ESCRT-III-like systems.. fun collaboration with Tom Williams @tweethinking.bsky.social!
doi.org/10.1016/j.sb...
doi.org/10.1016/j.sb...
July 14, 2025 at 5:19 PM
❗️ Exciting review alert❗️focussing on the evolution and mechanism of prokaryotic ESCRT-III-like systems.. fun collaboration with Tom Williams @tweethinking.bsky.social!
doi.org/10.1016/j.sb...
doi.org/10.1016/j.sb...
Reposted by Tom Williams
some thoughts on new methods to root a phylogenomic tree: the smart, the symbiotic, the violent
sishuowang2022.wordpress.com/2025/06/19/n...
#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social
sishuowang2022.wordpress.com/2025/06/19/n...
#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social
New Ways to Root Phylogenomic trees: the Smart, the symbiotic, the violent
To root a phylogenomic tree is very important to study the evolutionary relationship between species. However, typically the substitution models (say GTR, LG, etc.) people use are time-reversible m…
sishuowang2022.wordpress.com
July 11, 2025 at 9:18 AM
some thoughts on new methods to root a phylogenomic tree: the smart, the symbiotic, the violent
sishuowang2022.wordpress.com/2025/06/19/n...
#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social
sishuowang2022.wordpress.com/2025/06/19/n...
#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social
📣 We are proud of the publication of the second paper of @bbaker24.bsky.social PhD thesis. In collaboration with friends in Halifax we have studied the difficult question of the phylogeny of the DPANN archaea, composed of several phyla of highly reduced, fast-evolving epiparasites 🧵
rdcu.be/erkkU
rdcu.be/erkkU
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors
Nature Microbiology - Phylogenetic reconstructions with conserved protein markers from the 11 known DPANN phyla reveal their monophyletic placement within the Euryarchaeota.
rdcu.be
June 17, 2025 at 1:09 PM
Reposted by Tom Williams
#Asgard,#phylogeny
1/ 🧵 Does MAGs contamination affect the placement of Njord as suggested by Zhang et al, 2025? www.nature.com/articles/s41...
Our updated analysis suggests instead... www.biorxiv.org/content/10.1...
1/ 🧵 Does MAGs contamination affect the placement of Njord as suggested by Zhang et al, 2025? www.nature.com/articles/s41...
Our updated analysis suggests instead... www.biorxiv.org/content/10.1...
Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea within the Njordarchaeia
The Asgard archaea are a diverse archaeal phylum important for our understanding of cellular evolution because they include the lineage that gave rise to eukaryotes. Recent phylogenomic work has focus...
www.biorxiv.org
May 23, 2025 at 10:19 AM
#Asgard,#phylogeny
1/ 🧵 Does MAGs contamination affect the placement of Njord as suggested by Zhang et al, 2025? www.nature.com/articles/s41...
Our updated analysis suggests instead... www.biorxiv.org/content/10.1...
1/ 🧵 Does MAGs contamination affect the placement of Njord as suggested by Zhang et al, 2025? www.nature.com/articles/s41...
Our updated analysis suggests instead... www.biorxiv.org/content/10.1...
Reposted by Tom Williams
Dating Bacteria is hard due to the lack of maxima. Assuming aerobes likely postdated the GOE gave us better resolved ages, but also surprised us, but not Dr Dayhoff, showing O2 use predated its atmospheric rise by 900 Mys and helped oxygenic photosynthesis to evolve. www.science.org/doi/10.1126/...
April 4, 2025 at 1:20 AM
Dating Bacteria is hard due to the lack of maxima. Assuming aerobes likely postdated the GOE gave us better resolved ages, but also surprised us, but not Dr Dayhoff, showing O2 use predated its atmospheric rise by 900 Mys and helped oxygenic photosynthesis to evolve. www.science.org/doi/10.1126/...
Reposted by Tom Williams
Asgard archaea have actin - but what about microtubules? Where do they come from? 🧐 Our new paper www.cell.com/cell/fulltex... by @xujwet.bsky.social & @florianwollweber.bsky.social, in collaboration with the Schleper & Wieczorek labs, describes tiny Asgard microtubules! #TeamTomo #ArchaeaSky 1/6
March 21, 2025 at 3:16 PM
Asgard archaea have actin - but what about microtubules? Where do they come from? 🧐 Our new paper www.cell.com/cell/fulltex... by @xujwet.bsky.social & @florianwollweber.bsky.social, in collaboration with the Schleper & Wieczorek labs, describes tiny Asgard microtubules! #TeamTomo #ArchaeaSky 1/6
Very interesting indeed for enthusiasts of symbiotic integration...
Out today: Exciting intermediate between endosymbiont and organelle identified! Endosymbionts in Angomonas deanei lost nearly all bacterial cell division genes. Instead, we identified a host-encoded protein, ETP9, that became specialized for endosymbiont division. 1/2
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
March 20, 2025 at 7:49 PM
Very interesting indeed for enthusiasts of symbiotic integration...
Reposted by Tom Williams
Check out raxtax, our new open-source tool for taxonomic classification of barcoding sequences, it's 2.7-1000 times faster than competing tools and also implements fancy uncertainty scores: www.biorxiv.org/content/10.1...
raxtax: A k-mer-based non-Bayesian Taxonomic Classifier
Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) to a specific lineage using a reference database that contains named seq...
www.biorxiv.org
March 19, 2025 at 8:25 AM
Check out raxtax, our new open-source tool for taxonomic classification of barcoding sequences, it's 2.7-1000 times faster than competing tools and also implements fancy uncertainty scores: www.biorxiv.org/content/10.1...
www.pnas.org/doi/10.1073/... It's nice to see this study come out - genomic and evolutionary characterisation of deep soil-dwelling bacteria and their relatives, led by Xun Qian and colleagues.
Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone | PNAS
The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic
diversity and metabolic novelty, and the metabolic capab...
www.pnas.org
March 19, 2025 at 2:10 PM
www.pnas.org/doi/10.1073/... It's nice to see this study come out - genomic and evolutionary characterisation of deep soil-dwelling bacteria and their relatives, led by Xun Qian and colleagues.
www.nature.com/articles/s41... Exploring the root of the eukaryotic tree with new phylogenetic models (including extending branch-heterogeneous models to bigger datasets that previously). Very interesting stuff, nice to see the preprint published!
A robustly rooted tree of eukaryotes reveals their excavate ancestry - Nature
The root of the eukaryote Tree of Life is estimated from a new, larger dataset of mitochondrial proteins including all known eukaryotic supergroups, showing it lies between two multi-supergroup assemb...
www.nature.com
March 12, 2025 at 10:48 PM
www.nature.com/articles/s41... Exploring the root of the eukaryotic tree with new phylogenetic models (including extending branch-heterogeneous models to bigger datasets that previously). Very interesting stuff, nice to see the preprint published!