#phylogenetics

Does anyone know of a good tanglegram/cophylogram generator in Python? The only option I see is pretty minimal - not really up to par against the R version in features or visual quality.

#phylogenetics #dataviz #bioinformatics

Januario et al. found no correlation between sexual selection intensity & speciation rates or proxy traits. Because sexual selection intensity has high intraspecific variation and low phylogenetic signal, its macroevolutionary impacts are weak. Read now!
https://www.journals.uchicago.edu/doi/10.1086/734457

#sexualSelection #speciation #intraspecificVariation #phylogenetics #macroevolution

Analyses of #phylogenetics, natural #selection, and #protein structure of clade 2.3.4.4b #H5N1 #Influenza A reveal that recent viral lineages have evolved promiscuity ..., https://etidiohnew.blogspot.com/2025/03/analyses-of-phylogenetics-natural.html

A question while writing up a study proposal:

What are characters of a good prokaryotic gene alignment?

The way I learned it from no-one is a good alignment gives well-scoring inferred tree later, but that feels a bit iffy and takes too long to confirm. Any great articles/insights on this would be appreciated!

#bioinformatics #microbiology #phylogenetics

Pipeline release! nf-core/phyloplace v2.0.0 - Phylosearch release!

Please see the changelog: https://github.com/nf-core/phyloplace/releases/tag/2.0.0

#evolution #evolutionarytree #phylogeneticplacement #phylogenetics #sequenceclassification #taxonomyassignment #nfcore #openscience #nextflow #bioinformatics

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

#PhyloSIB #Bioinformatics #Phylogenetics #Phylogenomics #Biology25

The study provides a clearer evolutionary framework for Kalanchoe, but more work is needed to refine its classification. (8/8)

https://doi.org/n5ck

#AoBpapers #Botany #Phylogenetics #Kalanchoe

@planetaryecologist
For everyone willing to go down the rabbit hole of concepts for non-trivial #phylogenetics; here's the links for the pics (and more)

Who published the first phylogenetic tree?
https://phylonetworks.blogspot.com/2012/08/who-published-first-phylogenetic-tree.html

The dilemma of evolutionary networks and Darwinian trees
https://phylonetworks.blogspot.com/2014/01/the-dilemma-of-evolutionary-networks.html

Clades, cladograms, cladistics, and why networks are inevitable
https://phylonetworks.blogspot.com/2017/10/clades-cladograms-cladistics-and-why.html

Let's see the magic of @Mastodon

Is there a way to plot a dated phylogeny with a log-scale time axis? If possible, using R

#phylogenetics #phylo #rstats @rstats @ecology @plants @botany @plantscience @nature @biodiversity @evolution

#Computational tool streamlines #genetic analysis for #evolutionary biologists

#PsiPartition #genomics #phylogenetics #Bayesian

https://phys.org/news/2025-01-tool-genetic-analysis-evolutionary-biologists.html

New review: How is the living world organized and classified? Encyclopaedic in scope yet compelling to read, the deeply researched Kingdoms, Empires, & Domains is an 851-page behemoth that surveys 26 centuries of our changing understanding.

https://inquisitivebiologist.com/2025/01/17/book-review-kingdoms-empires-domains-the-history-of-high-level-biological-classification/

#Books #BookReview #Bookstodon #Scicomm #Classification #Genetics #HistoryOfScience #ScienceHistory #HistSci #Microbiology #Phylogenetics #ScalaNaturae #Taxonomy #Zoophyta @bookstodon

Understanding the evolution of orchids is essential for uncovering the secrets behind their incredible diversification and ecological success across the globe. (8/8)
https://doi.org/nzqf

#OrchidEvolution #PlantScience #Botany #Orchids #Phylogenetics #Genomics #Ecology #PlantDiversification

23 days this bad boy took me, all the way over Christmas and New Years to this weekend. (Yes, that's my idea of having a good time)

Review coming soon https://inquisitivebiologist.com

#Books #BookReview #Bookstodon #Scicomm #Classification #Genetics #HistoryOfScience #ScienceHistory #HistSci #Microbiology #Phylogenetics #ScalaNaturae #Taxonomy #Zoophyta

Borstein et al., 2024 “The macroevolutionary dynamics of pharyngognathy in fishes fail to support the key innovation hypothesis”

https://www.nature.com/articles/s41467-024-53141-4

Added to my reading list!

#Phylogenetics #SciArticleScreening

Our new #preprint is out
Cardoni et al. Pruning the tree: Comparing OTUs and ASVs for processing HTS 5S-IGS data
https://doi.org/10.22541/au.173437938.80481043/v1

Organising 100k of reads per studied sample (5S #rDNA intergenic spacers) into a handier amount of tips (~100) for #phylogenetic inferences and assessing #biodiversity

#phylogenetics #taxonomy #genetics #NGS

@EVDHmn @academicchatter
@academia
#phylogenetics

“There's a maximum likelihood that I'm doing phylogenetics wrong,” he writes elsewhere. | xkcd by Randall Munroe, shared by Meredith Yeager. #evolution #phylogenetics https://xkcd.com/3010/

A classic, my first paper on #beech #genetics getting a RG-#milestone: 1000 reads for "The #evolutionary history of #Fagus in western Eurasia: Genes, morphology and the #fossil record" RG added #reticulate #evolution, suppressed #speciation, could say that.

http://dx.doi.org/10.1007/s006060200044

Low impact? Enduring research still (obviously) worth a read over 20 yrs later

PS Still happy with it. But wouldn't just use a tree anymore for #phylogenetics

Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution

https://doi.org/10.1093/ismejo/wrae129

#phylogenetics #phylogenomics #MicrobialEcology #evolution

Unifying statistical #genetics & #phylogenetics. @jgschraiber @DocEdge85 & @mwpen show that the distinct ways of mapping phenotypes while controlling for ancestry in these two fields are actually special cases of the same general approach #PLOSBiology https://plos.io/4eZvKiv