@tweethinking

Phylogenetics, bioinformatics, molecular and microbial evolution.

 University of Bristol, England
research-information.bris.ac.uk/en/persons/tom-williams
Joined October 2017
  • Tweets606
  • Following452
  • Followers1.1K
2Media
Tom Williams (tweethinking.bsky.social) retweeted
Hend Abu-Elmakarem@Hypatia_EG30 Sep 2024
Microbial #eukaryotes have a fascinating evolutionary history and are our windows to learning about early eukaryotic life. 👇 First peek into our #preprint on the #transcriptome of a free-living relative of trichomonas and analysis of how/if they differ! Tinyurl.com/pkeilini
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Tom Williams (tweethinking.bsky.social) retweeted
Georg Hochberg@KaHochberg20 Sep 2024
Our latest preprint: @Sriramgarg calculate a general substitution matrix for structural phylogenetics and used it to root the tree of life. biorxiv.org/content/10.1101/… 1/n

A general substitution matrix for structural phylogenetics.

Sequence-based maximum likelihood (ML) phylogenetics is a widely used method for inferring evolutionary relationships, which has illuminated the evolutionary histories of proteins and the organisms...

biorxiv.org
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Tom Williams (tweethinking.bsky.social) retweeted
Julian Vosseberg@JulianVosseberg11 Sep 2024
Many novel Asgard genomes, cultivated Lokiarchaeia, new phylogenetic analyses: what insights do these and other recent studies provide into the enigmatic origin of eukaryotes? In this review in @Nature , we discuss the latest findings and open questions: nature.com/articles/s41586-0…
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biorxiv.org/content/10.1101/… This looks interesting --- a meaty paper on a difficult question. Congratulations to all the authors!
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Tom Williams (tweethinking.bsky.social) retweeted
Bacille Diderm Beaud@BasileBeaud28 Aug 2024
Happy to share a chapter of my PhD thesis🐣! We review the diversity of the cell envelope in Terrabacteria which tell us a lot about outer membrane biogenesis and the diderm-to-monoderm transition. Thanks to my co-authors Najwa Taib @ChrisBel70 @SGribaldo nature.com/articles/s41579-0…
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Tom Williams (tweethinking.bsky.social) retweeted
Andrew J. Roger (@andrewjroger.bsky.social)@andrewjroger9 Aug 2024
Can free-living eukaryotes exist without mitochondria? In a new paper from my group led by @retortacarp, we show that the answer is probably yes! nature.com/articles/s41467-0…

Extreme mitochondrial reduction in a novel group of free-living metamonads

Nature Communications - Mitochondria are essential cellular components that are found in animals, plants, fungi, and protists. This study reports what is believed to be the first example of...

nature.com
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Tom Williams (tweethinking.bsky.social) retweeted
Alistair Hetherington@NP_EiC23 Jul 2024
Plants growing in extreme conditions – like algae on ice – can provide insights into the evolution of alternative solutions to old problems, like responses to UV stress. An excellent Commentary by Cäcilia F. Kunz et al. on recent work by Bowles et al.: nph.onlinelibrary.wiley.com/…
Genomes sampled from the Zygnematophyceae, the closest algal relatives of land plants. A cladogram based on Hess et al. (2022) depicts the phylogenetic relationships within Zygnematophyceae, divided into a five-order system.

ALT Genomes sampled from the Zygnematophyceae, the closest algal relatives of land plants. A cladogram based on Hess et al. (2022) depicts the phylogenetic relationships within Zygnematophyceae, divided into a five-order system.

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Tom Williams (tweethinking.bsky.social) retweeted
Phil Donoghue@glpcjd22 Jul 2024
Registration open for free meeting @royalsociety Nov 11-12 "Chance and purpose in the evolution of biospheres" on the coevolution of Life and Earth - as well as other planets. Organised by @glpcjd @anjspa1 @gramolius Samir Okasha and Tim Lenton. Register: royalsociety.org/science-eve…
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Our review article about phylogenetic (gene tree-species tree) reconciliation is out. We make the case that reconciliation methods provide a natural framework for modelling/studying microbial evolution, summarise some previous work... academic.oup.com/ismej/advan…

Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and...

Abstract. In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is t

academic.oup.com
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...and provide some pointers for trying out the methods. Many thanks to co-authors @sllsi @PhilHugenholtz @anjspa1 @eme_laura @Paul__Sheridan Adrian Davin @AlexisCompBio @wwood @micecoevo @drenal_eu @RochelleSoo1 Noah Wahl
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Tom Williams (tweethinking.bsky.social) retweeted
Akos T. Kovacs@EvolvedBiofilm14 Jul 2024
Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution @ISMEJournal from @sllsi with @PhilHugenholtz @anjspa1 @micecoevo @Paul__Sheridan @eme_laura @RochelleSoo1 @wwood @drenal_eu academic.oup.com/ismej/advan…
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Very happy to have been part of this project!
Diorge Souza@diorge_souza2 Jul 2024
We're thrilled to share our new preprint: "Evolutionarily Conserved Principles of ESCRT-III-Mediated Membrane Remodeling Revealed by a Two-Subunit Asgard Archaeal System." biorxiv.org/content/10.1101/…

Evolutionarily conserved principles of ESCRT-III-mediated membrane remodelling revealed by a...

ESCRT-III proteins assemble into composite polymers that undergo stepwise changes in composition and structure to deform membranes across the tree of life. Here, using a phylogenetic analysis we...

biorxiv.org
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Tom Williams (tweethinking.bsky.social) retweeted
Chris Greening@greeninglab11 Jun 2024
In our new paper at Cell (@CellCellPress), we reveal secrets of how the third form of life, archaea, make energy. We uncover new lineages of hydrogen-using enzymes, both minimal and complex. These help archaea thrive in all sorts of extreme environments. sciencedirect.com/science/ar…
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Tom Williams (tweethinking.bsky.social) retweeted
Alex Bowles@_AlexBowles6 Jun 2024
Delighted to see the work from my postdoc at @BristolUni on algal evolution on ice and land out in @NewPhyt @tweethinking | @glpcjd | Doug Campbell | @MicroLabBristo1 @Bristol_Glac | @BristolPalaeo nph.onlinelibrary.wiley.com/… 1/6
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Tom Williams (tweethinking.bsky.social) retweeted
C Santana Molina@carlosSantanaMS2 Jun 2024
Happy to share our preprint about the evolution of Glycolysis and TCA cycle, demonstrating that eukaryotic metabolism also have archaeal origins and underwent a highly dynamic evolution. Special thanks to Anja Spang and Berend Snel for promoting this interesting project! @anjspa1
bioRxiv Evobio@biorxiv_evobio1 Jun 2024
Chimeric Origins and Dynamic Evolution of Central Carbon Metabolism in Eukaryotes biorxiv.org/cgi/content/shor… #biorxiv_evobio
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Tom Williams (tweethinking.bsky.social) retweeted
Tanja Stadler@TanjaStadler_CH28 May 2024
DECODING GENOMES - from sequences to phylodynamics: We are proud to present our book on how to analyse genomic sequences with an evolutionary perspective. See decodinggenomes.org for a free pdf, Amazon links for print orders, and further information. Great team effort 1/2
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Tom Williams (tweethinking.bsky.social) retweeted
Conor Meehan@con_meehan13 May 2024
Our oral microbiome evolution from ancient DNA data review is out! Led by @GDahlquistAxe and @fstandeven193 with @DrATedder and Camilla Speller, published in MGEN @MicrobioSoc and of interest to @spaam_community and others in microbiome evolution or aDNA. microbiologyresearch.org/con…

Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes

microbiologyresearch.org
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Tom Williams (tweethinking.bsky.social) retweeted
Joanne Boden@ColoradoJo1913 May 2024
Proud to see my latest research published! With help from Rika, Eva & Juntao we traced the evolution of phosphorus uptake enzymes to see how ancient microbes sourced the nutrients they needed to grow billions of yrs ago, when days were shorter & the Moon looked larger in the sky
Nature Communications@NatureComms10 May 2024
Phosphorus may have influenced Earth's early biosphere. Boden et al. interrogate genomic records, finding potentially phosphate depleted conditions toward the end of the Archean. @ColoradoJo19 @EarthSciStA @univofstandrews nature.com/articles/s41467-0…

Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics

Nature Communications - Phosphorus is an essential nutrient which may have influenced Earth’s early biosphere. This study interrogates genomic records, finding potentially phosphate depleted...

nature.com
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Tom Williams (tweethinking.bsky.social) retweeted
Gergely J Szöllősi@sllsi22 Mar 2024
The AleRax paper with @AlexisCompBio, @tweethinking and Benoit Morel leading is now out in Bioinformatics! academic.oup.com/bioinformat…
Gergely J Szöllősi@sllsi9 Oct 2023
AleRax is 10x faster 🚀 than ALE, but just as accurate. It can also infer a species tree 🌲 and, most importantly, process gene families in parallel to estimate lineage specific DTL parameters 🎄 for genome-scale datasets with 100s of taxa. bit.ly/3PG32s8
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