New #ISEPpapers! Single‐Cell Transcriptomes and Phylogenomic Analysis of Uncultivated #Oxymonads: Morelia Trznadel et al. https://pmc.ncbi.nlm.nih.gov/articles/PMC13002328/

"Oxymonads are divided into five families in a classification that has remained more or less unchanged for 35 years, but the relationships of these families are unknown... Here, we carry out the first phylogenomic analysis of oxymonads that includes all five families."

#Protists #Microbes #Evolution #TreeOfLife #Phylogeny

A major #update to my #collection of #morphological #matrices worthy to infer #networks:
a bunch of matrices we generated and reanalysed for a paper by S. Renner, D. Sokoloff, and me dealing with ancestors, hard polytomies and seed plant evolution; depicted not as the usual cladograms (where ancestor-descendant pairs must trigger unsolvable hard trichotomies) but as a "Romerogram" (or spindle graph) that shows #dichotomy as well as #buddingEvolution, i.e., #phylogeny

https://doi.org/10.6084/m9.figshare.7067369

#PhylogeneticConservatism sustains stable associations across #Pinaceae genera (#Ectomycorrhiza), while environmental filtering drives species-specific community differentiation at local scales on the #Qinghai_TibetanPlateau.

#CommunityAssembly | #Phylogeny

https://doi.org/10.1093/jpe/rtaf159

Single-blind #PeerReview strikes again. Reviewer revealing himself to the coauthors of a paper 1 week after submission threatening to reject it, unless he becomes a coauthor.

Now they are negotiating a deal to avoid having to redo everything.

Wondering also, why a method-focussed paper (new approach) submitted to a journal dedicated to molecular #phylogeny is reviewed by somebody who knows the organism but has very little experience in (phylo)genetics

Have to love single blind.
#FightTheFog

New #ISEPpapers! Single-cell #phylogenomics identifies major groups of marine eugregarine endosymbionts (Apicomplexa) https://www.sciencedirect.com/science/article/abs/pii/S1055790326000187

#protists #microbes #parasites #evolution #phylogeny #symbiosis

So much for strict #OpenData policies. Paper published in 2021 in New Phytologist, data matrix: "... is accessible to readers in #Morphobank, project # 3917. We have enabled anonymous login."

https://www.morphobank.org/myprojects/3917/overview

Anonymous login works (first pic), "Project disc usage: 0 bytes". Which happens to be exactly the number of linked matrices under the project (2nd pic)

Deleted the data after review? Avoid anyone else can (mis)use it.

#paleobotany #phylogeny #FightTheFog #transparency in #science

Congrats to Vincent Garot for his first PhD #preprint on #machinelearning in #phylodynamics (supported by #dim1health, cosupervised by @alizon @laurentjacob and Anna Zhukova ).

His #TEDDY software package can learn epidemiological parameters, e.g. #R0 or infection duration, directly from multiple sequence alignments of #virus genomic data thanks to simulation-based #inference.

No need to for a #phylogeny, which opens many perspectives for the field!

https://www.biorxiv.org/content/10.64898/2026.01.05.697728v1

@biorxivpreprint

New #ISEPpapers #preprint! Environmental #phylogenetics supports a steady diversification of crown #eukaryotes starting from the mid Proterozoic https://www.biorxiv.org/content/10.64898/2025.12.12.693929v1.full

#Protists #Microbes #Evolution #Phylogeny #Proterozoic #Eukaryogenesis