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ssolo.bsky.social

@ssolo.bsky.social
189 followers 193 following 24 posts

Physicist turned Evolutionary Biologist, Model-Based Evolutionary Genomics Research Unit @oistedu.bsky.social phylogenomics, HGT, somatic evolution (ssolo.bsky.social)

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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 01/09/2026
1 month left to apply!
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ssolo.bsky.social @ssolo.bsky.social · 04/07/2026
Ancestral genome reconstructions get noisier the deeper in time you go. The usual response: distrust them and joke about reading entrails. Ours is to train on the noise! The result is calibrated phenotype prediction back to the LBCA deep in the Archaean. New preprint www.biorxiv.org/content/10.6...
biorxiv.org
Models trained with noisy genomes extend bacterial phenotype prediction into deep time
Predicting phenotype from genotype in extant organisms is increasingly tractable through the accumulation of genome sequences and the development of machine-learning algorithms. Here we show that mach...
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 02/07/2026
Faculty Positions Open! OIST is now inviting applications for tenure-track assistant professor positions in two broad areas: - Chemistry & Materials Science - Life Sciences & Neuroscience Learn more and apply by October 1st: www.oist.jp/careers/facu... #FacultySearch
Open Faculty Positions at OIST
Image of a modern campus with a blue sea in the background, accompanied by images of scientists at work in the labs. 

Text describes we are looking for faculty in the fields of chemistry & materials science and life sciences & neuroscience.
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 11/06/2026
Decomposers are nature’s recyclers, keeping Earth habitable. Now, a new Nature Ecology & Evolution study reveals that gene swapping between species helped eukaryotic decomposers evolve some of their common traits, adding new insights into how complex life evolves. www.oist.jp/news-center/...
oist.jp
Gene swapping helped build the planet's decomposers
A new study reveals that horizontal gene transfer contributed to the repeated evolution of fungi-like, absorption-feeding life across eukaryotes.
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Alexis Stamatakis @stamatak.bsky.social · 03/06/2026
We can now also predict the difficulty of the multiple sequence alignment task with our new ALDiScore tool www.biorxiv.org/content/10.6... The plot shows MSA difficulty prediction performance on completely unseen data
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Megan Sorensen @messorensen.bsky.social · 30/04/2026
Interested in working on the evolution of photosynthetic endosymbioses? Come join us! I have 2 open positions in my new group @cemess.bsky.social in Vienna 3yr postdoc info: tinyurl.com/4emkjpn4 4yr PhD info: tinyurl.com/mtxmsjpy Apply by 1st June! Please share/repost #Protists #Symbiosis #PhD
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Hoyaboya @hoyaboya1.bsky.social · 10/04/2026
Pisani et al. (2026-04, Molecular Biology and Evolution)(オープンアクセス open access) 「ゲノム系統学的混合モデルは,均質モデルと分割モデルよりも優れている」 Phylogenomic mixture models outperform homogeneous and partitioned models academic.oup.com/mbe/advance-...
academic.oup.com
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
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Hoyaboya @hoyaboya1.bsky.social · 10/04/2026
“Our results 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.”
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Philip Donoghue @phil-donoghue.bsky.social · 06/04/2026
Our latest: Conflict in ant phylogeny results from complex interaction between multiple evolutionary signals and tree reconstruction artifacts.
academic.oup.com
Conflict in ant phylogeny results from complex interaction between multiple evolutionary signals and tree reconstruction artifacts
Abstract. Ants, Formicidae, are a group of small social insects that inhabit nearly all terrestrial environments. Three competing hypotheses of ant relatio
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 31/03/2026
Limited fossil records and genomic information has made it difficult to determine the evolutionary history of squid and cuttlefish, until now. Published in @natecoevo.nature.com, @cephagus.bsky.social and team identify the ‘long fuse’ that led to today’s diversity: www.oist.jp/news-center/...
oist.jp
100 million years ago, an ‘evolutionary fuse’ was lit in the deep ocean, sparking squid diversification
New evolutionary mapping suggests deep sea origins and mass extinction triggered diversification of modern squid and cuttlefish.
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Ben J Woodcroft @benjwoodcroft.bsky.social · 23/03/2026
New paper in mSystems! 🧵 - how much of your metagenome is actually bacterial/archaeal DNA? For many samples, nobody knows. We built SingleM prokaryotic_fraction (SPF) to answer this, then ran it on >100,000 public metagenomes. 🧬🖥️🦠 Here's what we found 👇 doi.org/10.1128/msystems.01062-25
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Nature @nature.com · 23/02/2026
Nature research paper: Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor go.nature.com/4rSfRRw
go.nature.com
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature
Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgardarchaeota, in conditions that may have given rise to early eukaryotes.
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 26/11/2025
Come join us! Soon I will be advertising a postdoc vacancy in my group as part of my @erc.europa.eu AdG project 'DARK ROOTS'. Focus of the project will be on phylo- and metagenomic mining of novel prokaryotic lineages. I will soon post a link here - stay tuned, and please repost! #asgardarchaea
media.tenor.com
a man walking in a field with an umbrella
ALT: a man walking in a field with an umbrella
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 05/01/2026
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻 Please repost Apply here: www.wur.nl/en/vacancy/p...
wur.nl
Postdoctoral researcher Phylogenomics and metagenomics
Are you just as excited as we are about the fascinating world of microorganisms? Do you want to contribute to exploring and genomically characterize novel prokaryotic lineages? Do you have a PhD degre...
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 15/12/2025
In @currentbiology.bsky.social, scientists crack ambiguities in trees of life by using ‘jumping genes’. The new method can transform the way we evaluate evolutionary relationships in deep time. Learn more www.oist.jp/news-center/... Or read the full paper doi.org/10.1016/j.cu...
oist.jp
'Jumping genes’ help scientists resolve tree of life
Termite study provides researchers with template to solve ancient evolutionary mysteries.
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 12/12/2025
The rare, mushroom-like Balanophora plant surprises researchers with their genetic makeup and unconventional role of plastids in biosynthesis, despite being entirely parasitic of a select few trees. New study in @newphyt.bsky.social 👇 www.oist.jp/news-center/...
oist.jp
The evolutionary mysteries of a rare parasitic plant
New study maps the strange genomes of Asia-Pacific Balanophora species, giving new insights into the evolution of parasitic plants and an unconventional role of plastids.
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Andrew Roger @andrewjroger.bsky.social · 09/12/2025
Why? Because ELM was optimized by ML for use with C60 on a large pan-eukaryotic data set and fits much better than LG. See this paper: academic.oup.com/mbe/article/... /2
academic.oup.com
GTRpmix: A Linked General Time-Reversible Model for Profile Mixture Models
Abstract. Profile mixture models capture distinct biochemical constraints on the amino acid substitution process at different sites in proteins. These mode
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Andrew Roger @andrewjroger.bsky.social · 09/12/2025
Those interested in performing maximum likelihood phylogenomic analysis on data sets made up of eukaryotic nuclear genes using site heterogeneous mixture models like C60, I suggest you use the ELM model in IQ-TREE instead of the LG model /1
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 04/12/2025
Read the study here, which featured researchers from OIST, @bristoluni.bsky.social, @niozsearesearch.bsky.social and @uniofbath.bsky.social 👇https://www.nature.com/articles/s41586-025-09808-z
nature.com
Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature
Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex archaea that already possessed an elaborated cytoskeleton, membrane trafficking, endomembrane, phagocytotic machinery and a nucleus.
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 04/12/2025
New evidence-based model of the evolution stretches out the differentiation of eukaryotes from prokaryotes over billions of years and places development of mitochondria much later than other cell structures. New @nature.com study 👇 @ssolo.bsky.social www.oist.jp/news-center/...
oist.jp
Complex life developed earlier than previously thought
New evidence-based evolutionary model provides access to the beginning of complex life with unprecedented accuracy.
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Philip Donoghue @phil-donoghue.bsky.social · 03/12/2025
Our latest, led by the inimitable Chris Kay "Dated gene duplications elucidate the evolutionary assembly of eukaryotes" in which we used gene duplications to test hypotheses of eukaryogenesis. TLDR? They're all wrong. With @tweethinking.bsky.social @anya1.bsky.social @ssolo.bsky.social Davide Pisani
nature.com
Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature
Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex ar...
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Henry Gee 亨利·纪 @endofthepier.bsky.social · 03/12/2025
Eukaryogenesis was a billion year spree, but the acquisition of mitochondria happened when the party was winding down www.nature.com/articles/s41...
nature.com
Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature
Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex ar...
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Wen-Cong Huang @wentsunghwang.bsky.social · 13/11/2025
#Archaea, #DPANN, #phylogenetic_reconciliation New preprint online! www.biorxiv.org/content/10.1...
biorxiv.org
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...
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 31/10/2025
Applications are now open for the Buribushi Fellowship 2026! OIST is offering a unique opportunity for early-career, theory-focused researchers to lead their own projects with full funding support. Learn more & Apply by November 30th: www.oist.jp/research/buribushi #Fellowship
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Philip Donoghue @phil-donoghue.bsky.social · 07/10/2025
Our latest, led by Edu Ocaña-Pallarès and @ssolo.bsky.social, a timescale for fungal phylogeny that wrangles calibration from the unstructured fossil record of fungi and a history of horizontal gene transfers www.nature.com/articles/s41...
nature.com
A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution
Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 02/10/2025
In @natecoevo.nature.com , our researchers describe a new fungal family tree reaching back over a billion years, and the importance of fungi in setting the stage for ancient life on land. Read more at www.oist.jp/news-center/...
oist.jp
Fungi set the stage for life on land hundreds of millions of years earlier than thought
From fossils and rare genetic ‘gene-swap’ clues, researchers reconstruct fungi’s deep timeline and reveal how they helped shape early Earth ecosystems.
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 02/10/2025
Alternatively, read the full article at doi.org/10.1038/s415...
doi.org
A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution
Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 12/09/2025
Out now in @science.org, OIST researchers and collaborators find 79% of endemic ant species in Fiji in decline, highlighting the vulnerability of island biodiversity to ecosystem changes: www.oist.jp/news-center/...
oist.jp
Island ant communities show signs of ‘insect apocalypse’
79% of endemic species show signs of decline, highlighting the vulnerability of island biodiversity to ecosystem changes.
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 24/09/2025
New @nature.com study: Prof. Oleg Sitsel (OIST) and collaborators uncover how PMCA calcium pumps use PIP2 lipids for ultra-fast transport at cell membranes — a discovery that may pave the way for new therapies. 🧬 dx.doi.org/10.1038/s415...
dx.doi.org
Molecular mechanism of ultrafast transport by plasma membrane Ca2+-ATPases - Nature
Structural insights into ultrafast Ca2+ transport by plasma membrane Ca2+-ATPases are provided, highlighting an essential role for PtdIns(4,5)P2 dynamics.
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 12/09/2025
“Insects are essential for the environment,” emphasizes Prof. Evan Economo. “As scientists, we need to play our part in their protection, and provide and analyze the relevant data to ensure the long-term integrity of our ecosystems”. Read the full study @science.org www.science.org/doi/10.1126/...
science.org
Genomic signatures indicate biodiversity loss in an endemic island ant fauna
Insect populations have declined worldwide, but the extent and drivers of these declines are debated. Most studies rely on field surveys performed in the past century, leaving gaps in our understandin...
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 04/09/2025
OIST PhD & Research Internship Program - Call for Applications! 🔗Research Internship: shorturl.at/EJMGe (Deadline: 15 October 2025) 🔗 PhD program: shorturl.at/lhheq (Deadline: 15 November 2025)
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 19/08/2025
📢 #FacultyHiring: OIST is hiring! We invite exceptional scientists to apply for faculty positions in: - Ecology, Environmental Science, Earth Science, and Oceanography - Physics and Quantum Science (including related fields) 🔗: www.oist.jp/careers/facu...
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 18/08/2025
Understanding plant-microbe symbiosis is essential in tackling global challenges like food security and ecosystem restoration. In ISME Journal, OIST researchers describe the unique symbiosis between T. azollae cyanobacteria and Azolla ferns: www.oist.jp/news-center/...
oist.jp
Fern leaf pockets hide secrets of plant-microbe symbiosis
Comparison of symbiotic bacteria to free-living relatives shows the genomic effects of host adaptation.
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Wen-Cong Huang @wentsunghwang.bsky.social · 23/05/2025
4/ 🧵 This project is with @anja1.bsky.social, @tweethinking.bsky.social, @ssolo.bsky.social , @ettema.bsky.social,@chrisrinke.bsky.social, Zheng-Shuang Hua Maraike Probst and Lenard Szantho.
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ERR_Moody @emoody.bsky.social · 12/08/2025
Very happy to announce our new paper on the evolution of metabolism is out now! royalsocietypublishing.org/doi/10.1098/... With @tweethinking.bsky.social @sabifo4.bsky.social @ssolo.bsky.social Davide Pisani, Tim Lenton and @phil-donoghue.bsky.social (1/2)
royalsocietypublishing.org
The emergence of metabolisms through Earth history and implications for biospheric evolution | Philosophical Transactions of the Royal Society B: Biological Sciences
We investigate the evolution of microbial metabolisms from the last universal common ancestor to the extant biota through comparative phylogenomics, reconciling the evolution of the genes that underpi...
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Geula Hanin @geula.bsky.social · 24/07/2025
🚨 I’m looking for two enthusiastic scientists to join our team at Cambridge to explore the molecular mechanisms of lactation, early nutrition, and their long-term impact on health. Apply here: 👉 RA: www.jobs.cam.ac.uk/job/51988/ 👉 Postdoc: www.jobs.cam.ac.uk/job/51984/ Please share 🔬👩‍🔬
jobs.cam.ac.uk
Research Assistant (Fixed Term) - Job Opportunities - University of Cambridge
Research Assistant (Fixed Term) in the Department of Physiology, Development and Neuroscience at the University of Cambridge.
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Daniel Tamarit @danieltamarit.bsky.social · 14/05/2025
New vacancy in my team! PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture. Please repost and share with talented MSc students in #evobio, bioinformatics or related :) www.uu.nl/en/organisat... #MEvoSky #MicroSky
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Alex Rubinsteyn @alexr.bsky.social · 04/06/2025
Lyft driver picked me up from UNC, turned out he was a medicinal chemistry post-doc in a building near mine, until his grant got cut last month. Worked on novel antivirals.
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Andrea Ganna @andganna.bsky.social · 01/06/2025
We have 2-3 group leader positions opening @fimm-uh.bsky.social !! We are looking for outstanding candidates in human genetics and precision medicine. This time we have a focus on population health data science. E.g. AI for EHR/health data        Generous starting package 💰 shorturl.at/FAk6n
jobs.helsinki.fi
FIMM-EMBL Group Leaders in Molecular Medicine
FIMM-EMBL Group Leaders in Molecular Medicine
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Roland Hatzenpichler @environmicrobio.bsky.social · 31/05/2025
The biggest gift the US can give to its global rivals is to ideologically motivated slashing investment in scientific, biomedical and technological research and innovation and driving away talent abroad.
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Nancy Moran @nancy-moran.bsky.social · 29/05/2025
Looking for a postdoc on bacterial-insect symbiosis, combining evolution and molecular mechanisms? I'll have one open in my lab starting Sept 2025. If interested contact me (or find me at the GRC on Animal-microbe symbiosis if you'll be there). #SymbioSky
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European Research Council (ERC) @erc.europa.eu · 16/05/2025
Today, the ERC formally adopted a decision to increase its support for researchers moving to Europe. On top of its normal grants, the ERC offers 'start-up' funding to help PIs establish laboratories / research teams in Europe. This extra funding is now x2 (up to €2 million!) europa.eu/!6Vdgmp
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Mike Sowden @mikeachim.bsky.social · 12/05/2025
OK, this is wild. In September 2023, geophysicists across the world started monitoring a very odd signal coming from the ground under them. It was picked up in the Arctic. And Antarctica. It was detected everywhere, every 90 seconds, as regular as a metronome, for *nine days*. What the HELL? 1/
Unsplash image of the Earth, mostly the nightside with a tracery of city lights on every continent.
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Paola Laurino @paolalaurino.bsky.social · 28/04/2025
Great to see our paper on SAR11 SBPs, published in Nature, selected as a 2025 national Frontiers Planet Prize champion!
frontiersplanetprize.org
SAR11 Bacteria’s Role in Carbon Cycling and Climate Solutions — Frontiers Planet Prize
Paola Laurino from the Okinawa Institute of Science and Technology, National Champion for Japan, reveals groundbreaking insights into SAR11 bacteria, the most abundant microbes on Earth. Her study unc...
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OIST (Okinawa Institute of Science and Technology) @oistedu.bsky.social · 24/04/2025
The ‘fuel’ of our cells, ATP, has been found to regulate the viscosity of the cytoplasm in axons 🧠 This influences the rate of harmful aggregation of proteins in neurodegenerative diseases like Parkinson’s and ALS. New discovery in #ScienceAdvances 👇
oist.jp
ATP prevents harmful aggregation of proteins associated with Parkinson’s and ALS
ATP, the ‘fuel’ of our cells, has been found to make the cytosol in axons more liquid, stopping proteins from clustering and causing harm.
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Buzz Baum @buzzbaum.bsky.social · 11/04/2025
With a heavy heart I have decided not to attend a meeting in the US this June. I can’t act as if things are normal when science, universities, dissent & truth are all under threat. And I feel I can’t attend when there are scientists who are not able to travel to the US without fear of arrest.
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Fabien Burki @fburki.bsky.social · 11/04/2025
This is important
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Andrea Telatin @telatin.bsky.social · 10/04/2025
Hello binfies 👋! There is an open position for a senior bioinformatician to join our fab **core bioinformatics** team at @quadraminstitute.bsky.social. jobs.quadram.ac.uk/Details.asp?...
Core Bioinformatics team at QIB -- job offer to join the team as bioinformatics programmer as per link
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Zamin Iqbal @zaminiqbal.bsky.social · 09/04/2025
So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu
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Philip Donoghue @phil-donoghue.bsky.social · 04/04/2025
Really pleased to be part of this project which shows that aerobic bacteria arose in the Archaean, long before the GOE - after which aerobes proliferated through HGT. Fun @bristolpalaeo.bsky.social collab including @tweethinking.bsky.social @sabifo4.bsky.social @emoody.bsky.social Davide Pisani
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