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.

MENI is back! Join us in Dublin this August 2026 for our 3rd Meeting for Microbial Evolution in Ireland. We are delighted to have @rachelmwheatley.bsky.social @drrebeccajhall.bsky.social @jpjhall.bsky.social and @tweethinking.bsky.social join us as keynote speakers this year. miniurl.com/MENI

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 :)

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.

Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages The 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...

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

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

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...

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.🪱🦀🐟

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

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 :)

❗️ 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...

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…

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

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...

#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...

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/...

Credit: Margot Riggi (@margotriggi.bsky.social), Max-Planck Institute of Biochemistry (@mpibiochem.bsky.social)

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...

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...

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...

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/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.

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/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!

Mosaic evolution of eukaryotic carbon metabolism - Nature Ecology & Evolution A comparative genomic investigation of metabolism across the tree of life supports the hypothesis that syntrophy — metabolic exchange between symbiotic partners — had a key role in the evolution of eu...

John Archibald also wrote an accessible summary of the work here: www.nature.com/articles/s41...

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...

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

The position will involve developing pipelines and collaborating with other postdocs working on specific case studies of WGD across these different locations. See project website here www.rediploidisation.org. Feel free to contact James (jc493@bath.ac.uk) or me for inquiries, or see the ad.

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).

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...

Tagging @anja1.bsky.social and @wentsunghwang.bsky.social 🤣

These are Asgard archaea that have evolved by genome reduction from a more complex ancestor, perhaps due to evolving a symbiotic lifestyle … not the only Asgards that have trodden that path…

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/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.

Evolution, structure and membrane remodelling function of the ESCRT-III superfamily in eukaryotes and their closest relatives Asgard archaea. The two subfamilies, B-type and A-type, have distinct structural properties to perform sequential steps of the membrane remodelling pathway.

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)

Nice to see this out :)

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...

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...