Tom Williams

@tweethinking.bsky.social

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

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...

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...

biorxiv.org

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.

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

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.

BildBild

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

findaphd.com

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

Chimeric origins and dynamic evolution of central carbon metabolism in eukaryotes

Nature Ecology & Evolution - Analysis of the eukaryotic gene repertoires mediating central carbon metabolism identifies ancestral contributions from Alphaproteobacteria, Asgardarchaeota and...

rdcu.be