Description languages as modelling decisions: A comment on Wheeler and Varón (2025) Wheeler and Varón (2025) proposed phylogenetic minimum description length (PMDL) as a phylogenetic optimality criterion grounded in algorithmic (Kolmogorov) complexity. PMDL applies the minimum descr...

No such thing as a free lunch: a note on what 'natural' means in the Phylogenetic Minimum Description Length optimality criterion and how PMDL relocates substantive assumptions into the chosen description language onlinelibrary.wiley.com/doi/full/10....

Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism:

merenlab.org/2026/04/15/u...

Observation.org Biodiversity Citizen Science & Monitoring

That moth definitely looks like a Garden Tiger! observation.org/species/1730

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To resolve the history of these large-sized #mammals, we integrate a dependency-coded matrix of 54 discrete characters and 42 morphogeometric and 5 continuous characters, across a sample of 37 taxa.
✅ 5 major lineages recovered
✅ Character weight ranking
✅ Ancestral reconstructions

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What makes South American Ungulates so unique?🦏🍃 #FossilFriday
Check out our new comprehensive combined-evidence #phylogeny of #Toxodontidae!!! #Paleontology #Evolution #Fossils #Argentina #CONICET

doi.org/10.1111/cla....

A weird phrase is plaguing scientific papers – and we traced it back to a glitch in AI training data Once errors creep into the AI knowledge base, they can be very hard to get out.

AI perpetuates knowledge artefacts. Mind you, a look at PubMed will tell you that humans are pretty good at perpetuating these too.. theconversation.com/a-weird-phra... ht @cyrilpedia.bsky.social

A new morphological phylogeny of Malacostraca comparing the application of character dependencies and implied weighting Using a new character matrix composed of revised matrices of previous analyses and new morphological findings, the phylogeny of Malacostraca (Pancrustacea) is analysed anew with 207 characters for 35...

A new morphological phylogeny of Malacostraca comparing the application of character dependencies and implied weighting - Grams - Cladistics - Wiley Online Library onlinelibrary.wiley.com/doi/10.1111/...

Cladistic estimates of evolutionary rates focused on palaeontological datasets using TNT We describe a protocol for estimating evolutionary rates from phylogenetic trees based on parsimony character optimization. The rate estimation is conducted through a TNT script and the results are a...

In onlinelibrary.wiley.com/doi/full/10.... Pol & Ezcurra present a fully scripted (TNT & R, incl. publication-ready graphics) #parsimony based workflow for estimating rates. It deals with ambiguous optimizations and multiple MPTs and can use different calibration approaches. Nice work! #phylogeny

If you see this quote with flowers from your gallery.
We can all use some beauty right now (Quercus robur L., pedunculate oak, in Belgium; www.plantsystematics.org/imgs/jdelaet...)

A reconsideration of inapplicable characters, and an approximation with step‐matrix recoding Evidence for phylogenetic analysis comes in the form of observed similarities, and trees are selected to minimize the number of similarities that cannot be accounted for by homology (homoplasies). Th...

We also provide additional discussion and background of the onlinelibrary.wiley.com/doi/full/10.... step matrix approach to #inapplicables that is used in our recent onlinelibrary.wiley.com/doi/10.1111/... paper on #phylogenetic methods to incorporate different types of character dependence.

An unrooted tree in which all terminal nodes have a head but the inner nodes are reconstructed as headless. Wheeler's approach considers this the optimal tree for the data at hand.

We show how and why Wheeler's proposal can lead to artefacts such optimal trees where every every terminal has a head but all inner nodes are reconstructed as headless.

Nothing to it: a reply to Wheeler's “much ado about nothing” Wheeler (Cladistics 2023, 39, 475) recently suggested that the issues with inapplicable characters in phylogenetic analysis can be dealt with directly by treating observed absences of a feature not i...

In onlinelibrary.wiley.com/doi/10.1111/... we examine Wheeler's proposal starting from the premise that #parsimony analysis aims at finding the trees that maximize secondary #homology.

Much ado about nothing: inapplicable data as insertion–deletion events The treatment of inapplicable characters has proved especially vexing to systematists. Investigators have wrestled with alternative coding scenarios to capture both the presence and absence of a feat....

Wheeler (onlinelibrary.wiley.com/doi/10.1111/...) recently proposed to deal with inapplicable characters in #morphology and #phylogeny by concatenating morphological characters into morphological sequences that are, in a next step, to be analyzed using #phylogenetic tree alignment algorithms.

Nothing to it: a reply to Wheeler's “much ado about nothing” Wheeler (Cladistics 2023, 39, 475) recently suggested that the issues with inapplicable characters in phylogenetic analysis can be dealt with directly by treating observed absences of a feature not i....

2/ In onlinelibrary.wiley.com/doi/10.1111/... we examine Wheeler's proposal starting from the premise that #parsimony analysis aims at finding the trees that maximize secondary #homology.

2/ In https://onlinelibrary.wiley.com/doi/10.1111/cla.12571 we examine Wheeler's proposal starting from the premise that #parsimony analysis aims at finding the trees that maximize secondary #homology.

2/ In https://onlinelibrary.wiley.com/doi/10.1111/cla.12571 we examine Wheeler's proposal starting from the premise that #parsimony analysis aims at finding the trees that maximize secondary #homology.

Permineralized rhizome of Osmundacaulis (Osmundales)

Alternative phylogenies showing different relationships and ancestral character states upon considering dependencies (right tree)

Our new paper on the #phylogeny of Osmundales is out. We reviewed the phylogeny of the group by taking into account character dependence and found that most of the recognised groups are hardly when dependencies are ignored. Check it out

#ferns #fossilfriday

onlinelibrary.wiley.com/doi/abs/10.1...