Ryo Harada

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...

Pleased to share our new preprint: "Plasmodium ARK1 regulates spindle formation during atypical mitosis and forms a divergent chromosomal passenger complex". Many thanks to our collaborators.
@ritatewari.bsky.social @eelcotromer.bsky.social @davidguttery.bsky.social

www.biorxiv.org/content/10.1...

Modeling site-and-branch-heterogeneity with GFmix Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino acid sequences may be heterogeneous across both sites an...

Our paper describing our new improved GFmix models for phylogenetic inference that capture site-and-branch heterogeneity in amino acid composition.
www.biorxiv.org/content/10.1...

Modeling site-and-branch-heterogeneity with GFmix https://www.biorxiv.org/content/10.1101/2025.08.07.669136v1

Phylogenetic dissection provides insights into the incongruity in the tree of Archaeplastida between the analyses of nucleus- and plastid-encoded proteins. https://www.biorxiv.org/content/10.1101/2025.05.06.652364v1

Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data | mBio Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from various environments. Th...

Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data | mBio journals.asm.org/doi/10.1128/...

New paper out!
We discovered a tiny archaeon with the smallest known archaeal genome — only 238 kbp!
Candidatus Sukunaarchaeum mirabile has almost no recognizable metabolic pathways and may rely heavily on a host to survive.
It also represents a novel, deep-branching lineage in the archaeal tree.

A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome https://www.biorxiv.org/content/10.1101/2025.05.02.651781v1