SatuTe by Manuel et al. is a new tool to quantify phylogenetic signal and saturation between subtrees. Applied to the Tree of Life, SatuTe shows that most ribosomal proteins support a eukaryotic clade.

doi.org/10.1093/molbev/msaf090

SQUIRREL is a fast, consistent algorithm for inferring phylogenetic networks from sequence data. It can capture reticulate evolution more accurately than trees. New Methods paper in MBE by Holtgrefe et al.

https://doi.org/10.1093/molbev/msaf067

Phyloformer by Nesterenko et al. is a deep learning method for phylogenetic inference that estimates evolutionary trees directly from sequence alignments, often outperforming traditional methods in speed and accuracy.

@laurentjacob.bsky.social

https://doi.org/10.1093/molbev/msaf051

PhyloSIB, our annual workshop about molecular evolution, phylogenetics, and comparative phylogenomics took place Wednesday in Lausanne as a satellite event preceding Biology25.

15 SIB Groups gave presentations on recent developments in the field. We had a full house with 80 participants. A lively and fruitful open discussion forum concluded the workshop.

@richardneher, @marcrr, @dessimoz, @mariedangles, @rmwaterhouse

CAGEE 1.2 is now available!

CAGEE analyzes changes in global or sample- or clade-specific gene expression taking into account phylogenetic history, and provides a statistical foundation for evolutionary inferences. The new version supports likelihood estimation as a gamma curve and input data that is expressed as ratios.

#phylogenetics @3rdreviewer

Download from here: https://github.com/hahnlab/CAGEE/releases/tag/1.2

Really fascinating paper on the evolution of fruit colour
#Evolution #PlantScience #Phylogenetics #Agriculture

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.19849

I'm hiring a #postdoc, for #bioinformatics work on amino acid substitution models. I think they are key for understanding biophysics of selection on #proteins, #mutation patterns, and #AncientLife, as well as improving #phylogenetics methods. https://evol.mcmaster.ca/brian/evoldir/PostDocs//UArizona.AminoAcidSubstitutionModels #ScienceJobs #evolution @jobsecoevo

New #OpenAccess paper on evolution of root-nodule symbiosis (key in nitrogen fixation), including rate heterogeneity and both gains and losses. https://www.nature.com/articles/s41467-024-48036-3 . Team effort by multiple research groups; important for the cool #evolution and #ecology but could also have implications for agriculture (understanding how nitrogen fixation evolves and is lost)

Still so much undescribed oyster diversity in Australia!

Molecular identification of intertidal rock oyster species in north-eastern Australia reveals new candidates for aquaculture:
https://doi.org/10.1016/j.aquaculture.2024.740838

Come explore the frontier of PCM with us! Mariana P. Braga (https://www.marianapbraga.com) and I host the symposium “What we can and cannot know through current and upcoming Phylogenetic Comparative Methods” at the joint​@evol_mtg in Montréal and want your views in that discussion!

https://ecoevo.social/@evol_mtg/111976003905981068

#Evol2024 #evolution #macroevolution #phylogenetics

1/X

Always stunning to see advances in #science.
Key figures in a paper about history of signing alphabets from five years ago vs the two figures from a paper just published in flagship journal Science in which "Computational #phylogenetics reveal histories of sign languages"
Guess, which one is which
#Linguistics #Phylogeny
(1/2)

Shamelessly boosting this again for #fossilfriday #Palaeontology #paleontology #dinosaurs #dinosaur #phylogenetics #evolution #EvolutionaryBiology #newpaper #academia

Elevated evolutionary rates of biting biomechanics reveal patterns of extraordinary craniodental adaptations in some herbivorous dinosaurs
Callum Kunz, Manabu Sakamoto
https://doi.org/10.1111/pala.12689

In my reading list:

AleRax: A tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.

https://www.biorxiv.org/content/10.1101/2023.10.06.561091v2

Like phylogenies? This paper may be of interest - we use simulations show that timescaling of phylogenies is not severely hampered by inaccuracies in placement of fossils on the tree of life.

https://onlinelibrary.wiley.com/doi/full/10.1111/pala.12680

Led by Nicolás Mongiardino Koch.

I'm seeking grad students this round of admissions: see more at https://brianomeara.info/opportunities.html#grad-students .

Like other good ecology and evolutionary biology programs, students making adequate progress are fully funded (through TA lines), we practice holistic admissions, and students are in a community.

Some of the topics folks in my lab have worked on:

#Phylogenetics
#Evolution
#Conservation
#Systematics
#TraitEvolution
#Diversification
#Dating
#Fish, #Birds, #Insects, #Plants, and more

I wrote a short blog post on the rationale for @SystBiol's proposed code of ethics: https://brianomeara.info/posts/codeofethics/ . Members, look for an email with subject "SSB Code of Ethics" and vote!

Applications of machine learning in phylogenetics

"Supervised machine learning approaches that rely on simulated training data have been used to infer tree topologies and branch lengths, to select substitution models, and to perform downstream inferences of introgression and diversification...We review how researchers have used several promising machine learning approaches to make phylogenetic inferences."

#MachineLearning #Phylogenetics

https://ecoevorxiv.org/repository/view/6096/

Another phylogenetic controversy: are Arachnida actually monophyletic?

I am puzzled by this Ballesteros et al 2022 article:
https://academic.oup.com/mbe/article/39/2/msac021/6522129

Traditionally, horseshoe crabs (Xiphosura) are viewed as the closest parent of arachnids, but here they find that they are nested within, when coping for artefacts (saturation, taxon occupancy)...

I'm not expert of arachnids, but this does not seem in line with the fossil record, so what's wrong, #orthology again?