Tom Williams
@tweethinking.bsky.social
Computational evolutionary biologist - phylogenetics, molecular and microbial evolution
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!
Reposted by Tom Williams
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.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
March 3, 2025 at 1:28 PM
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.be/eb0aK
Job announcement: a four-year postdoc position in phylogenomics at the Milner Centre for Evolution, Bath, with James Clark and me (I'm moving to Bath later in the year...). www.bath.ac.uk/jobs/Vacancy...
ED12442 Research Associate in Phylogenomics (fixed-term) - Jobs at Bath
www.bath.ac.uk
February 18, 2025 at 9:26 AM
Job announcement: a four-year postdoc position in phylogenomics at the Milner Centre for Evolution, Bath, with James Clark and me (I'm moving to Bath later in the year...). www.bath.ac.uk/jobs/Vacancy...
www.biorxiv.org/content/10.1... A new collaborative paper with Anja Spang, Wen-Cong Huang, @chrisrinke.bsky.social @ettema.bsky.social @ssolo.bsky.social Zheng-Shuang Hua Maraike Probst and Lenard Szantho. We investigated the phylogenetic position and metabolic evolution of Panguiarchaeum.
Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea
The Asgard archaea are a diverse archaeal phylum that includes the host lineage from which eukaryotes evolved. Due to the importance of the Asgard archaea for our understanding of cellular evolution a...
www.biorxiv.org
February 17, 2025 at 4:59 PM
www.biorxiv.org/content/10.1... A new collaborative paper with Anja Spang, Wen-Cong Huang, @chrisrinke.bsky.social @ettema.bsky.social @ssolo.bsky.social Zheng-Shuang Hua Maraike Probst and Lenard Szantho. We investigated the phylogenetic position and metabolic evolution of Panguiarchaeum.
Reposted by Tom Williams
New research on ancient Asgard archaeal ESCRT-III proteins reveals evolutionary secrets of membrane remodelling.
Diorge Souza, Javier Espadas and Sami Chaaban, investigated the ESCRT-III proteins with Buzz Baum and Aurelien Roux.
Read more: www2.mrc-lmb.cam.ac.uk/asgard-archa...
#LMBResearch (1/2)
Diorge Souza, Javier Espadas and Sami Chaaban, investigated the ESCRT-III proteins with Buzz Baum and Aurelien Roux.
Read more: www2.mrc-lmb.cam.ac.uk/asgard-archa...
#LMBResearch (1/2)
February 11, 2025 at 12:46 PM
New research on ancient Asgard archaeal ESCRT-III proteins reveals evolutionary secrets of membrane remodelling.
Diorge Souza, Javier Espadas and Sami Chaaban, investigated the ESCRT-III proteins with Buzz Baum and Aurelien Roux.
Read more: www2.mrc-lmb.cam.ac.uk/asgard-archa...
#LMBResearch (1/2)
Diorge Souza, Javier Espadas and Sami Chaaban, investigated the ESCRT-III proteins with Buzz Baum and Aurelien Roux.
Read more: www2.mrc-lmb.cam.ac.uk/asgard-archa...
#LMBResearch (1/2)
Nice to see this out :)
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/...
Asgard archaea reveal the conserved principles of ESCRT-III membrane remodeling
Asgard archaea have two ESCRT-III subunits with the conserved traits that drive stepwise membrane remodeling in eukaryotes.
www.science.org
February 8, 2025 at 9:43 AM
Nice to see this out :)
Reposted by Tom Williams
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...
www.npr.org/2025/01/17/1...
Life as we know it descended from a single cell. What do we know about LUCA? : Short Wave
Imagine 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...
www.npr.org
January 17, 2025 at 2:13 PM
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...
www.npr.org/2025/01/17/1...
Very interesting paper on the conservation of genes involved in fungal symbiosis in land plants! www.pnas.org/doi/full/10....
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
January 6, 2025 at 3:08 PM
Very interesting paper on the conservation of genes involved in fungal symbiosis in land plants! www.pnas.org/doi/full/10....
Reposted by Tom Williams
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!
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?...
2024's Biggest Breakthroughs in Biology and Neuroscience
YouTube video by Quanta Magazine
youtu.be
December 19, 2024 at 4:52 PM
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!
New short paper in GBE on the evolution of Pseudotrichomonas track.smtpsendmail.com/9032119/c?p=...
Transcriptome and evolutionary analysis of Pseudotrichomonas keilini, a free-living anaerobic eukaryote
Abstract. The early evolution of eukaryotes and their adaptations to low-oxygen environments are fascinating open questions in biology. Genome-scale data f
track.smtpsendmail.com
December 4, 2024 at 5:42 PM
New short paper in GBE on the evolution of Pseudotrichomonas track.smtpsendmail.com/9032119/c?p=...