Andrew Roger
@andrewjroger.bsky.social
deep-time evolution, phylogenetics, anaerobic protists, the tree of Life. Science depends on vigorous respectful debate and evidence-based reasoning. I like cats. This is my personal page and what I post here has nothing to do with my employer.
From MBoC A new localization atlas maps more than 600 Giardia proteins, revealing the locations of hundreds of previously uncharacterized proteins and creating a valuable resource for functional discovery. https://www.molbiolcell.org/doi/10.1091/mbc.E25-12-0590
Záhonová et al. tested whether hydrogenosomes and mitosomes in Metamonada originated from an independent endosymbiosis, finding instead that these organelles originated from an Alphaproteobacterium during a single common endosymbiosis. 🔗 doi.org/10.1093/molbev/msag175 #societyjournal #compbio
Phylogenetic ancestry of Metamonada proteins points to a common origin of mitochondria in all eukaryotes
Abstract. Hypotheses concerning eukaryogenesis, the evolution of eukaryotic cells, differ in the relative timing of mitochondrial acquisition. Recently, a
doi.org
Our new paper introduces a fast & Bayesian state-dependent OU model in RevBayes that implements joint inference, to test adaptive macroevolutionary hypotheses. Congrats @prilau.bsky.social! Be sure to give her a follow & give her original tweet some love! Many more exciting PCMs in her future!
Priscilla Lau@prilau.bsky.social · 6d agoOur paper (also, my first first-author paper) is now available in MEE early view! In this study, we introduced a state-dependent Ornstein-Uhlenbeck model we implemented in RevBayes to test adaptive hypotheses in macroevolution. (1/3) besjournals.onlinelibrary.wiley.com/doi/10.1111/...
Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social
Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models
Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig
academic.oup.com
Joanna Masel@joannamasel.bsky.social · 8mo agoSequence alignments are notoriously prone to error. Our latest preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. www.biorxiv.org/content/10.6... @phylowheeler.bsky.social 1/10
New review out in Nat Rev Genet: Emergence & evolution of protein-coding de novo genes by Erich and Lars Eicholt @lacholt.bsky.social. How non-coding DNA becomes translated, persists or is lost in populations, and can yield structured/functional proteins—plus methods & open questions! rdcu.be/e09SM
Emergence and evolution of protein-coding de novo genes
Nature Reviews Genetics - De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes...
rdcu.be
1/ Deep-time phylogenetics is hard: overly simplistic substitution models can mislead tree estimation at the billion year timescale. Our new preprint introduces GTRspmix, a protein modeling framework designed to more realistically model site-to-site heterogeneity in amino acid replacement. 🧵
Where are mutations most likely to happen in the genome? @mattjago.bsky.social has answers! This paper is also a masterclass in simple visualizations of complicated ideas. I really enjoyed getting deep into these results as a middle author 🧬
Matt Jago@mattjago.bsky.social · 2mo agoOur work characterizing how mutational bias is influenced by the local sequence context beyond trinucleotides is out now @pnas.org! We also showed which motifs are most prone to mutations caused by strand misalignment, revealing several new hotspots! 🧬 www.pnas.org/doi/10.1073/...
New #ISEPpapers! Diversity and evolution of DNA polymerase θ in eukaryotes and the origin of mitochondrion-localized DNA polymerase PolIA in euglenozoa www.sciencedirect.com/science/arti... #Protists #Microbes #Evolution #Mitochondria
How ancient are the building blocks of animal sensory systems? Key components of animal sensory systems evolved before animals. We find that choanoflagellates possess diverse & spatially segregated TRP channels, pointing to ancient origins of sensory specialization. doi.org/10.64898/202...
🎄 Just published 🎉! Our ongoing genome sequencing of the basal dinoflagellate Oxyrrhis marina uncovered a new lineage of endogenized Polinton-like viruses, OmPLV. Notably, OmPLV encodes ... [cont] #VirEvol #MicroSky #Mevosky #SymbioSky #ProtistsOnSky
Endogenized polinton-like viruses in the dinoflagellate Oxyrrhis marina uncover novel PolB fusion
Marine viruses are ubiquitous entities that impact the biology of a large fraction of prokaryotic and eukaryotic diversity. Dinoflagellates are heterotrophic, mixotrophic and photosynthetic eukaryotes...
doi.org
Very important work!
Leigh Anne Riedman@fossils.bsky.social · 3mo agoExcited to say that my new paper with @maxlechte.bsky.social (and others not on bluesky) has come out in @nature.com! Study of sediments, geochemistry and fossils from rocks 1.75 to 1.4 billion years old indicate that the oldest known #eukaryotes were aerobic and benthic! #protists rdcu.be/fjNgL
New #ISEPpapers by @deemteam.bsky.social! Reversal to osmotrophy in eukaryotes www.nature.com/articles/s41... "Distant eukaryotic lineages convergently reverted from predation to osmotrophy through co-option of bacterial genes and their mobilization via eukaryote-to-eukaryote HGT" #Protists
Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...
biorxiv.org
I'm reposting this because I want to make a correction. In the thread below I mention using the -mset flag for testing site profile mixture models. But in fact you should use -madd flag. I'm sorry for this mistake.
Andrew Roger@andrewjroger.bsky.social · 5mo agoSo 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.
Pisani, @elpiratavell.bsky.social et al. dissipate doubts about the utility of models accounting for compositional heterogeneity across sites and identify CAT-GTR as one of the most flexible models in the phylogenomic arsenal. 🔗 doi.org/10.1093/molbev/msag090 #evobio #molbio #phylogenomics
Phylogenomic mixture models outperform homogeneous and partitioned models
Abstract. Significant advances have been made in resolving the tree of life, but many nodes remain debated. The last two decades saw the emergence of mixtu
doi.org
1/ Our new paper in Systematic Biology "Modeling Site-and-Branch-Heterogeneity with GFmix" led by @cgpmcc.bsky.social describes improved ways to model compositional heterogeneity across both sites and branches—an important source of error in deep phylogenomics. doi.org/10.1093/sysb...
Modeling Site-and-Branch-Heterogeneity with GFmix
Abstract. Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino a
doi.org
Just saw a meme that said something like: "Yeah but would your thesis defend you?" which made me laugh...😂
We have a thread explaining it here: bsky.app/profile/joan...
Joanna Masel@joannamasel.bsky.social · 8mo agoSequence alignments are notoriously prone to error. Our latest preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. www.biorxiv.org/content/10.6... @phylowheeler.bsky.social 1/10
A new method to filter alignment errors! CLOAK from @joannamasel.bsky.social 's group and collaborators: www.biorxiv.org/content/10.6...
biorxiv.org
Very interesting and useful thread.
Ashar Malik@proteinmechanic.bsky.social · 3mo agoNew work: Our earlier work showed that Foldseek characters could be adapted for phylogenetic alignment, treating each character as an evolutionary state. That part holds but there's a hidden assumption baked in that needed unpacking. So lets do that.🧵 #StructuralPhylogenetics #Evolution #Protein
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
academic.oup.com
I am begging people looking to make major donations to universities to either 1) care as much about academics as they do sports, or 2) make unrestricted gifts instead. Signed, A faculty member at a university with brand new athletic facilities and crumbling teaching and research infrastructure
RFK Jr. just said that immigration is to blame for the outbreaks of vaccine-preventable diseases in the U.S., not him.
The media’s failure to cover Trump’s son-in-law Jared Kushner’s ongoing conflicts of interest as he gets billions from the Middle East while being Trump’s negotiator is insane. (Especially after what they did with Hunter Biden) popular.info/p/the-media-...
Wrote a fun little thing on gene tree discordance: authors.elsevier.com/a/1mzPI3QW8S...
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This will be really interesting!
Caroline Puente-Lelievre@cpuentelelievre.bsky.social · 4mo agoLooking forward to presenting our work on bacterial flagella and structural phylogenetics at @biologyanu.bsky.social Protein structure+evolutionary analyses is a powerful yet underexplored combination. Come along or join on Zoom. Always happy to connect. Thanks @corrylab.bsky.social for hosting me!
New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9
New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga). 🔗 DOI: www.biorxiv.org/content/10.6...
