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

🍄The #fungal genus Phaeolus is a major #conifer #pathogen.
🌲Cui et al. explore its #phylogeny, #divergence times, and #biogeography, laying the foundation for future pathogen control and #ecological #conservation.
🔗https://doi.org/10.1111/jse.13187 @WileyEcolEvol #JSE #forestry #trees #botany

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

Ok I'd actually love to hear people's take on this one. Vigorous skepticism about inferred trees (based on alignments) that eventually also require manual adjustment, and what that means for phylogeny is a curiously often encountered conversation for me these days.

https://arxiv.org/abs/1808.07717

#phylogeny #bioinformatics #evolution

Zhang et al. present NeuralNJ, an accurate and efficient approach to phylogenetic inference whose innovation lies in its learnable neighbor joining mechanism, which iteratively joins neighbors guided by learned priority scores for tree reconstruction.

🔗 https://doi.org/10.1093/molbev/msaf260

#evobio #molbio #phylogeny

#Sponges are back at the root of the animal tree! I knew the cnidarians-as-root hypothesis was just too hard justify given the sum total of evidence.
https://www.science.org/doi/10.1126/science.adw9456

#evolution #phylogeny

200 isn't really a #milestone (wouldn't that be 1000?), but not a bad number of reads for a #preprint of a paper deemed not fit for publication.

https://www.researchgate.net/profile/Guido-Grimm/achievement/691574d72d8b361441dbb9bb

Currently processing the data to please the editor (more P.R.Chinese samples), nothing unexpected came up but all analyses will have to be updated and streamlined.
So enjoy the original, the final product will have more tips but not more content 😅
#Fagus #beech #phylogeny

【🎉Latest accepted article】
Evolutionary history and environmental filtering jointly structure ectomycorrhizal fungal communities across Qinghai-Tibetan #Pinaceae forests

#Ectomycorrhiza | #CommunityAssembly | #Phylogeny | #Qinghai_TibetanPlateau

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

🚨UPDATE!
Yao et al. provide an updated plastome #phylogeny and #molecular dating of Apocynaceae, with emphasis on the #histories of #flora #biogeography and #diversification in tropical and subtropical #Asia.

⭐️ https://doi.org/10.1111/jse.70014
@WileyEcolEvol
#systematics #evolution #botany

Kilara Waris et al. estimated global spatiotemporal patterns of #WoodDensity and their relationships with #ModernClimate and #Paleoclimate.

#Angiosperms | #Cenozoic | #GlobalVariation | #Phylogeny | #TraitEvolution

https://doi.org/10.1093/jpe/rtaf003

Who Stays, Who Goes: Predicting Community Dynamics From Evolutionary History
Summary & analysis by Deepika Gunasekaran of “Effects of Phylogeny on Coexistence in Model Communities” by Serván et al.

Read here!
https://www.amnat.org/an/newpapers/Feb-2025-Servan.html

#CommunityDynamics #EvolutionaryHistory #EEB #Phylogeny

New #ISEPpapers #preprint! Modeling site-and-branch-heterogeneity with GFmix https://www.biorxiv.org/content/10.1101/2025.08.07.669136v1.full

#Evolution #Bioinformatics #Phylogeny #TreeOfLife

Tree of life
Vs
Network of life

Am enjoying David Mindell book in gene movements and biodiversity

#networkoflife #mindell #hgt #plasmids #Introgression #biodiversity #ecology #evolution #tree #phylogeny #book #bookstadon

How did #wolf #spiders go from vagrant hunting to web building and burrowing?
Let's dive into this phylogenomic analysis of the higher-level #phylogeny and #evolution of mitogenomes and the evolution of lycosid prey-capture strategies!
https://doi.org/10.1111/jse.13198
@WileyEcolEvol
#JSE

#Fungal genus Phaeolus is a significant #conifer #pathogen. Cui et al.'s analysis of its #phylogeny, #divergence times, and #biogeography sets the foundation for future pathogen control and #ecological #conservation.
https://doi.org/10.1111/jse.13187
@WileyEcolEvol
#JSE #forestry #trees #botany