#phylogenetics — Public Fediverse posts

Cool work on slow evolving lineages, aka "living fossils". I like the contrast between the morphologically conserved lineages and control species-poor lineages.
Sad not to see amphioxus included though.
https://www.biorxiv.org/content/10.64898/2026.10.03.756400v1
#EvoDevo #Phylogenetics

https://www.europesays.com/ie/714601/ Evolution of terrestrial anatomy revealed by a derived stem tetrapod #Éire #Evolution #HumanitiesAndSocialSciences #IE #Ireland #multidisciplinary #Palaeoecology #palaeontology #Phylogenetics #Science #XRayTomography

Evolution of terrestrial anatomy revealed by a derived stem tetrapod

Ahlberg, P. E. Elginerpeton pancheni and the earliest tetrapod clade. Nature 373, 420–425 (1995). Article  ADS  CAS  Google…
#NewsBeep #News #US #USA #UnitedStates #UnitedStatesOfAmerica #Science #evolution #HumanitiesandSocialSciences #multidisciplinary #Palaeoecology #Palaeontology #phylogenetics #X-raytomography
https://www.newsbeep.com/us/866625/

Evolution of terrestrial anatomy revealed by a derived stem tetrapod

Ahlberg, P. E. Elginerpeton pancheni and the earliest tetrapod clade. Nature 373, 420–425 (1995). Article  ADS  CAS  Google…
#NewsBeep #News #Science #Evolution #GB #HumanitiesandSocialSciences #multidisciplinary #Palaeoecology #Palaeontology #Phylogenetics #UK #UnitedKingdom #X-raytomography
https://www.newsbeep.com/uk/788094/

https://www.europesays.com/uk/1229678/ Evolution of terrestrial anatomy revealed by a derived stem tetrapod #evolution #HumanitiesAndSocialSciences #multidisciplinary #Palaeoecology #Palaeontology #phylogenetics #Science #UK #UnitedKingdom #XRayTomography

🦇 NEW: A recent #Nature study analyzed #genomes from 103 bat species across all 21 living families, plus physical traits from dozens of species and #fossils.

The results place bat origins in #Europe around 65 million years ago, with later spread to #Africa, #Asia, the Americas and #Australia. The timeline for #echolocation’s emergence is still unsolved.

👉 https://www.smithsonianmag.com/smart-news/where-did-bats-originate-huge-genetic-study-may-have-settled-the-longstanding-debate-and-rewritten-the-creatures-evolutionary-tree-180989568/

#bats #evolution #phylogenetics #echolocation #flight #mammals #conservation #paleontology #research #science #education

https://www.europesays.com/news/81621/ Reference genomes and fossils revise bat family phylogeny and biogeography #Biogeography #Chromosomes #Genomics #Headlines #HumanitiesAndSocialSciences #multidisciplinary #News #Palaeontology #Phylogenetics #Science #TopStories

Reference genomes and fossils revise bat family phylogeny and biogeography

Senckenberg-Leibniz Institution for Biodiversity and Earth System Research, Senckenberganlage, Frankfurt, Germany Ariadna E. Morales, Evgeny V. Leushkin, Alexander Ben Hamadou, Alejandro…
#NewsBeep #News #Science #Biogeography #Chromosomes #GB #Genomics #HumanitiesandSocialSciences #multidisciplinary #Palaeontology #Phylogenetics #UK #UnitedKingdom
https://www.newsbeep.com/uk/780544/

https://www.europesays.com/ie/703392/ Reference genomes and fossils revise bat family phylogeny and biogeography #Biogeography #Chromosomes #Éire #genomics #HumanitiesAndSocialSciences #IE #Ireland #multidisciplinary #palaeontology #Phylogenetics #Science

https://www.europesays.com/uk/1219665/ Reference genomes and fossils revise bat family phylogeny and biogeography #Biogeography #Chromosomes #Genomics #HumanitiesAndSocialSciences #multidisciplinary #Palaeontology #phylogenetics #Science #UK #UnitedKingdom

Pipeline release! nf-core/phyloplace v2.3.0 - v2.3.0 - 2026-09-23!
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Please see the changelog: https://github.com/nf-core/phyloplace/releases/tag/2.3.0

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

my features published in @CurrentBiology this year, issue 18: Where do we draw the line defining our genus, #Homo? Progress in molecular and morphological insights into human #evolution give a complex picture.

https://proseandpassion.blogspot.com/2026/09/being-homo.html

#science #neanderthal #ancientDNA #Australopithecus #paranthropus #HomoErectus #humans #phylogenetics #denisovans

Shan et al.'s work on medicinal floras across #China's ethnic groups reveals how #environmental barriers and cultural exchange interact to shape the #biogeographic structure of traditional #medicine.
https://doi.org/10.1111/jipb.70334
@WileyLifeSci
#JIPB #PlantScience #phylogenetics

Tiny DNA fragments reveal two extinct Galápagos tortoise lineages

DNA from museum tortoise…
#NewsBeep #News #Science #AdalgisaCaccone #AlexanderOchoa #AncientDNA #AU #Australia #conservationgenetics #extinctGalápagostortoiseDNA #Galápagosgianttortoises #genomesequencing #GlobalGoodNews #historicalDNA #museumspecimens #NewDiscoveries #Phylogenetics #research #SanCristóbaltortoise #SantaFetortoise #ultra-low-coveragegenomes #wildlifeconservation #YaleUniversity
https://www.newsbeep.com/au/888718/

Pipeline release! nf-core/phyloplace v2.2.0 - v2.2.0 - 2026-09-11!
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Please see the changelog: https://github.com/nf-core/phyloplace/releases/tag/2.2.0

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

https://www.europesays.com/africa/415766/ Multiple bursts of speciation in Madagascar’s endangered lemurs #ConservationBiology #EvolutionaryBiology #HumanitiesAndSocialSciences #Madagascar #MolecularEvolution #multidisciplinary #Phylogenetics #science #zoology

What I would most like eyes on. What none of those three frameworks covers is the alphabet *with* weights: induction to irreducibles of dimension above one of a space group that is not abelian, and recombination of conjugate pairs over real or quaternionic ground. That is the sector the physics actually needs, and it is where our own contributions sit.

It is adjacent to — and I am careful not to identify it with — the non-abelian direction Sturmfels and Sullivant raised in 2005 with a single computed data point.

Two things I would genuinely like to be told:

— has the mixed-order case been treated anywhere, where the cone orders of a group-based model differ?

— is there a name for what the \(\mathbb{Z}_4\) tripod does: a complete intersection on the Zariski-open set the phylogenetics literature works in, and not one globally?

Code, gates and every archived output:
https://github.com/karlesmarin/orbifold-alphabet
https://github.com/karlesmarin/orbifold-semigroup

#AlgebraicStatistics #Phylogenetics

Pipeline release! nf-core/phyloplace v2.1.0 - v2.1.0 - 2026-08-03!
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Please see the changelog: https://github.com/nf-core/phyloplace/releases/tag/2.1.0

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

Exceptional brain and ecological diversity in the earliest snakes

Caldwell, M. W. The Origin of Snakes: Morphology and the Fossil Record (CRC Press, 2019). Gower, D. J.…
#NewsBeep #News #Science #GB #herpetology #HumanitiesandSocialSciences #multidisciplinary #Palaeontology #Phylogenetics #UK #UnitedKingdom
https://www.newsbeep.com/uk/706304/

https://www.europesays.com/uk/1105727/ Exceptional brain and ecological diversity in the earliest snakes #Herpetology #HumanitiesAndSocialSciences #multidisciplinary #Palaeontology #phylogenetics #Science #UK #UnitedKingdom

https://www.europesays.com/uk/1101375/ Rates of passerine body plan evolution in time and space #biodiversity #BiologicalAndPhysicalAnthropology #Ecology #EvolutionaryBiology #general #LifeSciences #Macroecology #Palaeontology #paleontology #phylogenetics #Science #UK #UnitedKingdom #Zoology

Rates of passerine body plan evolution in time and space

Jablonski, D., Roy, K. & Valentine, J. W. Out of the tropics: evolutionary dynamics of the latitudinal diversity…
#NewsBeep #News #Science #Biodiversity #BiologicalandPhysicalAnthropology #Ecology #EvolutionaryBiology #GB #general #LifeSciences #Macroecology #Palaeontology #paleontology #Phylogenetics #UK #UnitedKingdom #Zoology
https://www.newsbeep.com/uk/702155/

https://www.europesays.com/uk/1053610/ Complex multicellularity is linked with expanded specialized metabolite production in microorganisms #EvolutionaryGenetics #general #Health #InfectiousDiseases #LifeSciences #MedicalMicrobiology #MicrobialGenetics #Microbiology #NaturalProducts #Parasitology #phylogenetics #UK #UnitedKingdom #Virology

Pipeline release! nf-core/phyloplace v2.0.1 - Documentation improvements, software updates!
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Please see the changelog: https://github.com/nf-core/phyloplace/releases/tag/2.0.1

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

Gene ancestries reveal diverse microbial associations during eukaryogenesis

Data retrieval, curation and proteome database reconstructioneTOLDB construction To guide dataset selection and LECA reconstruction, we used the…
#NewsBeep #News #Science #Evolutionarygenetics #GB #HumanitiesandSocialSciences #multidisciplinary #Phylogenetics #UK #UnitedKingdom
https://www.newsbeep.com/uk/631748/

https://www.europesays.com/uk/1018179/ Gene ancestries reveal diverse microbial associations during eukaryogenesis #EvolutionaryGenetics #HumanitiesAndSocialSciences #multidisciplinary #phylogenetics #Science #UK #UnitedKingdom

Hey IQTree3 paper is out. Bread and butter for tree building anything in my workflow. They have a pretty standout documentation too.

#bioinformatics #phylogenetics

https://academic.oup.com/mbe/article/43/5/msag117/8669857

New paper: "The Tree and Its Echo" — ultrametric organization from pre-numeric first principles.

Before numbers: marks on a bone. Three primitives: correspondence, order, nesting. Hierarchy without metrics.

The independence assumption is the fallacy. Baseline convergence: similarity is the default, not the exception. Tree = residual. P0 PASSED (p<0.001).

DOI: 10.5281/zenodo.20348370

#Mathematics #Physics #ComplexSystems #SpinGlasses #Ultrametric #Phylogenetics #Science

Predictable evolution is bad news for toads, good news for their predators

"Under certain circumstances, the process of evolution can be highly predictable, especially when there are limited solutions to a particular problem, such as resistance to dangerous toxins"

#SciComm by @grrlscientist

#evolution #poisons #phylogenetics #Australia https://grrlscientist.medium.com/predictable-evolution-is-bad-news-for-toads-good-news-for-their-predators-7260c33dc54c

Predictable evolution is bad news for toads, good news for their predators

"Under certain circumstances, the process of evolution can be highly predictable, especially when there are limited solutions to a particular problem, such as resistance to dangerous toxins"

#SciComm by @GrrlScientist

#evolution #poisons #phylogenetics #Australia https://grrlscientist.medium.com/predictable-evolution-is-bad-news-for-toads-good-news-for-their-predators-7260c33dc54c

Predictable evolution is bad news for toads, good news for their predators

"Under certain circumstances, the process of evolution can be highly predictable, especially when there are limited solutions to a particular problem, such as resistance to dangerous toxins"

#SciComm by @grrlscientist

#evolution #poisons #phylogenetics #Australia https://grrlscientist.medium.com/predictable-evolution-is-bad-news-for-toads-good-news-for-their-predators-7260c33dc54c

https://www.europesays.com/ie/453730/ Gram-negative-staining Bacillaceae with thick cell wall and monoderm architecture uncover evolutionary diversity and challenge Gram-based classification #Bacteriology #Éire #general #IE #Ireland #LifeSciences #Phylogenetics #Science #TransmissionElectronMicroscopy

MBE is excited to launch our newest Call for Papers on the Major Transitions of Life, covering all aspects of phylogenomic research.

🔗 academic.oup.com/mbe/pages/call-for-papers-on-the-major-transitions-of-life

Guest Editors:
Davide Pisani
Anja Spang

Accepted manuscripts will receive a 20% discount on the APCs, on top of the SMBE membership discount.

Toward a genomic understanding of the tree of life
🔗 https://doi.org/10.1093/molbev/msag043

#evobio #molbio #phylogenetics

RE: https://mastodon.green/@plazi_species/116260383338896477

#Endemic #species are always interesting from different perspectives, e.g. from an #evolutionary and #ecological point of view. This also applies to #skinks of the genus
#Madascincus, being with several known species endemic to #Madagascar.
A. Miralles et al. (2026) described based on #multilocus #phylogenetics and #morphology two #newspecies:
M. #irery and M.
#minotaurus, with restricted distributions to limited areas of Madagascar only.
© this text #StefanFWirth

Could the shape of phylogenetic trees contain hidden information? Siqi Liu, Sarah Svensson & Daniel Falush show that the "backboned" shape of the phylogenetic tree of #Klebsiella pneumoniae may reveal a history of diversifying selection on an unknown trait.
#microbiology #phylogenetics
https://plos.io/4bgI3qz

Is there something analogous to #ClintReptiles but for #botany? I want someone to explain me the #plant branch of the tree of life while telling how much they love it, clade by clade.

#systematics #treeOfLife #cladistics #phylogenetics

Fresh WIP piece of #Archaea #phylogenetics data for a collaborator.

Those barplot margins are driving me crazy - it's actually throwing off the immediate impression of the data! (pink bars are essentially all 1/2 or less of the orange bars, which is pretty important in context) I really need to buckle down and get to hand-coding my trees from scratch using #rlang or #julialang soon.

Hmm. How's Julia ecosystem for phylogenetic trees these days?

#microbiology #bioinformatics

Our first preprint of 2026 is online:

Phylogenetic based dissection of eukaryotic Mo-insertase functionality: From mechanism to complex assembly
https://doi.org/10.64898/2025.12.12.693926

#Evolution #Phylogenetics
@PuckerLab

Lineages of carnivorous mammals that established on new continents diversified faster— even before they moved into new territory. That suggests those lineages have diversified specifically because they're better competitors https://doi.org/10.1086/738413

#science #evolution #mammals #paleontology #phylogenetics

#SequenceAlignment is notoriously prone to error. Our latest #preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. https://www.biorxiv.org/content/10.64898/2025.12.01.691663v1 1/10 #MSA #alignment #phylogenetics

Sharma & Kumar present the Net Bootstrap Support (NBS) approach that accounts for phylogenetic variation in the estimates of bootstrap confidence.

🔗 https://doi.org/10.1093/molbev/msaf296

#evobio #molbio #phylogenetics

Tabatabaee et al. introduce CASTLES-Pro for estimating species tree branch lengths while accounting for both gene duplication and loss and incomplete lineage sorting.

🔗 https://doi.org/10.1093/gbe/evaf200

#genome #evolution #phylogenetics

"Clint's Reptiles | Not All Dogs Have Bones"

#Phylogenetics is Phun!

Clint's Reptiles is my new favorite #Youtube channel. It's not just #educational and informative, it's high art.

https://www.youtube.com/watch?v=YerdELZuEhY

And low art, but definitely high art. You know, self-referential, culturally aware and, but subtly so.

Just posting again, but I've got two PhD positions on offer through the CROCUS-DLA at the University of Reading. One on the phylogenetics and evolution of dragonflies with Dr Jamie Thompson, and another on the evolution of gastropods (Polystira) in response to changing climate with Prof Chris Venditti and Dr Jon Todd (NHM UK).

https://blogs.reading.ac.uk/crocus-dla/cr2026_43_evolutionary/

https://blogs.reading.ac.uk/crocus-dla/cr2026_28_ocean/

#PhD #phdStudentship #science #zoology #evolution #evolutionaryBiology #phylogenetics #palaeontology

Derkarabetian et al. developed a metazoan ultraconserved element probe set, providing a resource for multiple research groups working on vastly different animal lineages.

🔗 https://doi.org/10.1093/gbe/evaf193

#genome #evolution #compbio #phylogenetics

Gámbaro et al. use simulations to evaluate an adjusted Bayes factor for discrete phylogeography that accounts for sampling bias, which lowers false positives and improves root inference.

🔗 https://doi.org/10.1093/molbev/msaf253

#evobio #molbio #phylogenetics