Tom Williams
@tweethinking.bsky.social
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📥 81
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Computational evolutionary biologist - phylogenetics, molecular and microbial evolution
reposted by
Tom Williams
Corey Holt
about 1 month ago
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.🪱🦀🐟
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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 :)
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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
https://www.findaphd.com/phds/project/the-genomic-basis-of-symbiotic-integration/?p187773
about 1 month ago
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reposted by
Tom Williams
Harry Low’s Lab
4 months ago
❗️ 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...
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reposted by
Tom Williams
Sishuo Wang
4 months ago
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
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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…
https://sishuowang2022.wordpress.com/2025/06/19/new-ways-to-root-phylogenomic-trees-the-smart-the-symbiotic-the-violent/
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add a skeleton here at some point
5 months ago
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reposted by
Tom Williams
Wen-Cong Huang | 黄文聪
6 months ago
#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...
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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...
https://www.biorxiv.org/content/10.1101/2025.02.13.637844v2
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reposted by
Tom Williams
ssolo.bsky.social
7 months ago
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/...
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reposted by
Tom Williams
Pilhofer Lab 🦠❄️🔬
8 months ago
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
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Very interesting indeed for enthusiasts of symbiotic integration...
add a skeleton here at some point
8 months ago
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reposted by
Tom Williams
Alexis Stamatakis
8 months ago
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.03.11.642618v1.abstract
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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.
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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...
https://www.pnas.org/doi/10.1073/pnas.2424463122
8 months ago
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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!
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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...
https://www.nature.com/articles/s41586-025-08709-5
8 months ago
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reposted by
Tom Williams
Carlos Santana Molina
8 months ago
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
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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...
https://rdcu.be/eb0aK
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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...
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ED12442 Research Associate in Phylogenomics (fixed-term) - Jobs at Bath
https://www.bath.ac.uk/jobs/Vacancy.aspx?ref=ED12442
9 months ago
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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.
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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...
https://www.biorxiv.org/content/10.1101/2025.02.13.637844v1
9 months ago
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reposted by
Tom Williams
MRC Laboratory of Molecular Biology
9 months ago
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
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Nice to see this out :)
add a skeleton here at some point
9 months ago
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reposted by
Tom Williams
Philip Donoghue
10 months ago
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...
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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...
https://www.npr.org/2025/01/17/1225172117/life-species-luca-ancestors
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Very interesting paper on the conservation of genes involved in fungal symbiosis in land plants!
www.pnas.org/doi/full/10....
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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...
https://www.pnas.org/doi/full/10.1073/pnas.2408539121
10 months ago
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reposted by
Tom Williams
Philip Donoghue
11 months ago
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!
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New short paper in GBE on the evolution of Pseudotrichomonas
track.smtpsendmail.com/9032119/c?p=...
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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
https://track.smtpsendmail.com/9032119/c?p=ibTwahYS8FKqpMetpwanyC_b5Rp9ibiB26CVC-l6l9HtMzakYxGlaEkm4PQuBgk7VSsmlPSpupl5avribwmm7n4zsPJ_ukZAKv0YSKwE-2B-Spt1JKRX8FKetapB61k4gjVHtAT_SQqMl80f0-CKO-PrkG8_EtBnTOljlbGBe08NAak6BdfK7DW4VhOnkRWTgdSGN2rr4l9wZ-wadbtlCgT351kEk0kQFU78tDIGQO2wMJeRUScqPzUvISsyrpLdLcSRF-94bpYIAMXRJiy3Ke8f2DlyTXyzGOKz5voRQnpaPiPLT0GYGIwONrNfRdhr
11 months ago
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