Ryo Harada

Ryo Harada

@ryoharada.bsky.social

Postdoc at Ryoma’s lab, Kyoto University Phylogenomics, Eukaryotic Evolution, Symbiosis Tsukuba -> Dalhousie -> Kyoto

54 followers25 following3 posts

Ryo Harada reposted

Andrew Roger
@andrewjroger.bsky.social

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. 🧵

Ryo Harada reposted

Andrew Roger
@andrewjroger.bsky.social

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...

doi.orgModeling Site-and-Branch-Heterogeneity with GFmixAbstract. Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino a

Ryo Harada reposted

Wen-Cong Huang
@wentsunghwang.bsky.social

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

biorxiv.orgPhylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineagesThe 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...

Ryo Harada reposted

Andrew Roger
@andrewjroger.bsky.social

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...

biorxiv.orgModeling site-and-branch-heterogeneity with GFmixPhylogenetic 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...

Ryo Harada reposted

Andrew Roger
@andrewjroger.bsky.social

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

journals.asm.orgEukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data | mBioAdvancements 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...
Ryo Harada
@ryoharada.bsky.social

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.

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social

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

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