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-...

“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.”

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

Our latest: Conflict in ant phylogeny results from complex interaction between multiple evolutionary signals and tree reconstruction artifacts.

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.

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/...

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

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.

Nature research paper: Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor

go.nature.com/4rSfRRw

a man walking in a field with an umbrella ALT: a man walking in a field with an umbrella

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

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...

'Jumping genes’ help scientists resolve tree of life Termite study provides researchers with template to solve ancient evolutionary mysteries.

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...

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.

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/...

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

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

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

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.

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

Complex life developed earlier than previously thought New evidence-based evolutionary model provides access to the beginning of complex life with unprecedented accuracy.

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/...

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...

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

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...

Eukaryogenesis was a billion year spree, but the acquisition of mitochondria happened when the party was winding down www.nature.com/articles/s41...

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...

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: https://www.oist.jp/research/buribushi
#Fellowship

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).

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...

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.

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/...

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).

Alternatively, read the full article at doi.org/10.1038/s415...

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.

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/...

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.

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...

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...

“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/...

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)

📢 #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...

Fern leaf pockets hide secrets of plant-microbe symbiosis Comparison of symbiotic bacteria to free-living relatives shows the genomic effects of host adaptation.

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/...

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.

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...

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

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🚨 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/

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