phylogeny

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I wish I could get a large enough print of this that I could actually read it. It's a phylogeny of flowering plants along with examples of typical flowers from each genus. Mind blown. #NativePlants #Phylogeny

Marveling about this beautiful #wasp #phylogeny visualization from the great book "Wasps" by Eric R. Eaton. I'd so love to have that (with timeline approximations) for EVERY taxon.

Now in IOB issue !

Variation in Molar Size and Proportions in the #hominid Lineage: An Inter- and Intraspecific Approach
L A D'Addona et al

https://doi.org/10.1093/iob/obae041

#evolution #biology #fossils #Phylogeny #allometric #science

@dantheclamman Naked (kind-of) shell-less clams with an agile foot read like a proto-cephalopod. Are they close at all to the phylogenetic branch that took off with squids, octopus and cuttlefish, or is "cephalopodness" a trait that can re-evolve from an ancestral clam base?
#evolution #phylogeny #cephalopods

Some ancient divergences in #Opisthokonta (animals, fungi & their unicellular pals) remain contentious. Hongyue Liu @RokasLab Yuanning Li &co present a genome-scale #phylogeny & establish the geological timeline of #opisthokont diversification #PLOSBiology https://plos.io/3XrOD6U

New fossil #fish species scales up evidence of Earth's evolutionary march https://phys.org/news/2024-09-fossil-fish-species-scales-evidence.html

A Late #Devonian coelacanth reconfigures actinistian #phylogeny, disparity, and evolutionary dynamics: Alice Clement et al. https://www.nature.com/articles/s41467-024-51238-4

"The discovery of an exceptionally well preserved ancient primitive Devonian #coelacanth fish in remote Western #Australia has been linked to a period of heightened tectonic activity, or movement in the Earth's crust"

Literally every time I google #Phylogeny stuff: 'shit, I forgot just how long the Cretaceous was'. It's like half the Mesozoic!

#Time #Paleontology #Palaeontology #Mesozoic

There Are Only 7 Sea Turtles, But You Don't Know Them All! - Phylogeny of Sea Turtles

https://www.youtube.com/watch?v=7GhBgNd8yUw

#Phylogeny
#ClintsReptiles

Two #Jurassic #mammaliaforms from China shed light on mammalian #evolution
https://phys.org/news/2024-04-jurassic-mammaliaforms-china-mammalian-evolution.html

"The studies provide key information about the evolutionary shift from reptilian jaw bones to early mammalian middle ear ossicles, presenting new perspectives on the early diversity of mammaliaforms and reshaping the early mammalian #phylogeny."

New #preprint out looking at structural causes and mitigation of #identifiability problems when reconstructing past evolutionary change, inspired by the problems in phylogenetic inference.
It's quite technical, and unfortunately I don't have time/funding to continue working on this in the near future but maybe these thoughts are helpful to the #EvolutionaryBiology community
#Phylogeny #MathematicalBiology
https://arxiv.org/abs/2403.03000

New #research #software now out
https://mindthegap-erc.github.io/admtools/
You can use it to estimate age depth models from stratigraphic and sedimentological data (nonparametrically) and transform complex data such as phylogenetic trees with it.

Check this neat example, isn't it nice how branching events align with gaps in the rock record? #geology #paleontology #Phylogeny

A new look at our linguistic roots
https://knowablemagazine.org/content/article/society/2024/origin-spread-indo-european-languages #linguistics #archaeology #IndoEuropean #languages #pastoralists #farmers #Computational #phylogeny

New Research Sheds Light on Evolutionary History of Tardigrade Extremotolerance
https://www.sci.news/biology/tardigrade-extremotolerance-12643.html #tardigrade #Extremotolerance #genetics #phylogeny #genefamilies

We posted this cool preprint between Xmas and new year, now time for a thread about the results: Begum et al "Phylogenetic modeling provides evidence for sudden shifts in expression after small-scale duplication in vertebrates and strong support for the ortholog conjecture"
https://www.biorxiv.org/content/10.1101/2023.12.29.571877v1
#paralog #ortholog #GeneDuplication #GenomeDuplication #MolecularEvolution #phylogeny #ohnolog

A new preprint from the lab on the distribution of ancient whole-genome duplications across the angiosperm phylogeny. Great work led by PhD student Michael McKibben! We used a variety of methods and different species trees to infer and place WGDs across the phylogeny. Overall, similar results to our past work, but species tree had a large impact on WGD inferences. Check it out here:

https://www.biorxiv.org/content/10.1101/2024.01.04.574202v1

#WGD #polyploidy #phylogeny #angiosperms

#Paleontologists Find New #Fossils of Enigmatic North American Primate
https://www.sci.news/paleontology/ekgmowechashala-12425.html

#Phylogeny and #paleobiogeography of the enigmatic North American #primate #Ekgmowechashala illuminated by new #fossils https://www.sciencedirect.com/science/article/pii/S0047248423001318

"Ekgmowechashala is a poorly documented but very distinctive species of ancient primate that lived in western North America during the Early #Oligocene epoch, some 30 million years ago."

Today we publish a new paper on a molecular #phylogeny of true #crabs. We find crabs transitioned from marine to non-marine environments 7-17x over 100+ myr! This culminates 15+ years(!) of effort from an international team! 1/4
https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syad066/7370615

Interesting study of the performance of phylogenetic models for gene expression evolution, although they seem to have only investigated single-optimum OU models, which IMO limits conclusions on datasets with orthologs and paralogs. (Indeed they find poor performance for our 2016 dataset testing the ortholog conjucture.)
https://www.biorxiv.org/content/10.1101/2023.02.09.527893v2
#phylogeny #GeneExpression #MolecularEvolution #bioinformatics #phylogenetics

PhylteR: efficient identification of outlier sequences in phylogenomic datasets.

PhylteR can automatically identify sequences likely to be hidden paralogs or horizontally transferred genes in very large datasets. Removing those sequences therefore reduces noise in downstream analyses.

Available as an R package on CRAN or as docker and singularity images.

Package:

https://cran.r-project.org/web/packages/phylter/index.html

Paper:

https://doi.org/10.1093/molbev/msad234

#Phylogeny #Genomics #bioinformatics #Phylogenomics