Tom Williams

Tom Williams

@tweethinking.bsky.social

Computational evolutionary biologist - phylogenetics, molecular and microbial evolution. Lab website: tancata.github.io

247 followers98 following16 posts

Tom Williams reposted

Maria Hondele
@mariahondele.bsky.social

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.

Tom Williams reposted

Wen-Cong Huang
@wentsunghwang.bsky.social

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...

nature.comPhylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages - Nature CommunicationsKey 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...

Tom Williams reposted

ssolo.bsky.social
@ssolo.bsky.social

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...

biorxiv.orgModels trained with noisy genomes extend bacterial phenotype prediction into deep timePredicting 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...

Tom Williams reposted

ERR_Moody
@emoody.bsky.social

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...

nature.comThe prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking - Nature CommunicationsCOMMD proteins assemble into a heterodecameric ring in the Commander complex, which plays a role in endosomal membrane trafficking and signalling in eukaryotes. Here, Liu et al. identify COMMD-like pr...
Brett Collins@brettcollins.bsky.social

After a slightly extended review process very happy to see our paper on COMMD protein evolution now online at Nature Comms.

nature.comThe prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking - Nature CommunicationsCOMMD proteins assemble into a heterodecameric ring in the Commander complex, which plays a role in endosomal membrane trafficking and signalling in eukaryotes. Here, Liu et al. identify COMMD-like pr...

Tom Williams reposted

Andrew Roger
@andrewjroger.bsky.social

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.

Tom Williams
@tweethinking.bsky.social

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 :)

meetings.embo.orgComputational and experimental microbiomicsThe 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 …

Tom Williams reposted

Wen-Cong Huang
@wentsunghwang.bsky.social

Replying to @wentsunghwang.bsky.social

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.

Tom Williams reposted

Wen-Cong Huang
@wentsunghwang.bsky.social

#Archaea, #DPANN, #phylogenetic_reconciliation New preprint online! www.biorxiv.org/content/10.1...

biorxiv.orgPhylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineagesThe phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...
Tom Williams
@tweethinking.bsky.social

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 :)

findaphd.comThe genomic basis of symbiotic integration at University of Bath on FindAPhD.comPhD Project - The genomic basis of symbiotic integration at University of Bath, listed on FindAPhD.com

Tom Williams reposted

Sishuo Wang
@sishuowang.bsky.social

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.comNew Ways to Root Phylogenomic trees: the Smart, the symbiotic, the violentTo 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…
Tom Williams
@tweethinking.bsky.social
DEEMteam_Orsay@deemteam.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.bePhylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestorsNature Microbiology - Phylogenetic reconstructions with conserved protein markers from the 11 known DPANN phyla reveal their monophyletic placement within the Euryarchaeota.

Tom Williams reposted

Wen-Cong Huang
@wentsunghwang.bsky.social

#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...

biorxiv.orgPhylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea within the NjordarchaeiaThe 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...
Tom Williams
@tweethinking.bsky.social

Very interesting indeed for enthusiasts of symbiotic integration...

Eva Nowack@evanowack.bsky.social

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/...

Tom Williams reposted

Alexis Stamatakis
@stamatak.bsky.social

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...

biorxiv.orgraxtax: A k-mer-based non-Bayesian Taxonomic ClassifierTaxonomic 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...
Tom Williams
@tweethinking.bsky.social

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.

pnas.orgDiversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone | PNASThe deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capab...
Tom Williams
@tweethinking.bsky.social

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!

nature.comA robustly rooted tree of eukaryotes reveals their excavate ancestry - NatureThe 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...

Tom Williams reposted

Carlos Santana Molina
@santanamolina.bsky.social

Asgardarchaea & Alphaproteobacteria: key players for the assembly eukaryotic central carbon metabolism! Our new study reveals their gene contributions to glycolysis & TCA cycle, supporting synthrophic scenarios of eukaryogenesis. rdcu.be/eb0aK

rdcu.beChimeric origins and dynamic evolution of central carbon metabolism in eukaryotesNature Ecology & Evolution - Analysis of the eukaryotic gene repertoires mediating central carbon metabolism identifies ancestral contributions from Alphaproteobacteria, Asgardarchaeota and...
Tom Williams
@tweethinking.bsky.social

The position will focus on phylogenomic and comparative genomic analyses of whole genome duplication and asynchronous rediploidization in eukaryotes. It's part of a wider large-scale grant (BBSRC sLOLA), with partners across the UK and further afield (e.g. Edinburgh, Oxford, Kew, Bristol, TCD, UCD).

Tom Williams
@tweethinking.bsky.social

Nice to see this out :)

Diorge Souza@diorgeps.bsky.social

Happy to share our paper’s final version on the evolution, structure, and membrane binding / remodeling of Asgard ESCRT-III proteins! And my first 🦋 post! www.science.org/doi/10.1126/...

science.orgAsgard archaea reveal the conserved principles of ESCRT-III membrane remodelingAsgard archaea have two ESCRT-III subunits with the conserved traits that drive stepwise membrane remodeling in eukaryotes.

Tom Williams reposted

Philip Donoghue
@phil-donoghue.bsky.social

Our LUCA study, led by @emoody.bsky.social has made it to #shortwave @NPR! Thanks to @jonlambert.bsky.social for indulging us @bristolpalaeo.bsky.social www.npr.org/2025/01/17/1...

npr.orgLife as we know it descended from a single cell. What do we know about LUCA? : Short WaveImagine the tree of life. The tip of every branch represents one species, and if you follow any two branches back through time, you'll hit an intersection. If you keep going back in time, you'll event...

Tom Williams reposted

Philip Donoghue
@phil-donoghue.bsky.social

Yay! Our LUCA study shorturl.at/09YR8 made into @quantamagazine.bsky.social list of 2024's biggest breakthroughs! Thanks to @emoody.bsky.social @tweethinking.bsky.social Davide Pisani @bristolpalaeo.bsky.social and the rest of our amazing team!

ERR_Moody@emoody.bsky.social

Wow! A real honour to be included on this year's list, thanks @quantamagazine.bsky.social and of course all the vital collaborators involved in the work youtu.be/p9XHI_26cPE?...

youtu.be2024's Biggest Breakthroughs in Biology and NeuroscienceYouTube video by Quanta Magazine

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