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Alessio Capobianco @acapomorphic.bsky.social · 13/05/2026

We also show the impact that the number of fossils included in the unresolved FBD analysis has on node ages. Turns out that you need a substantial number of fossils (in our croc example, >20 in total) to have effective priors that are more informative than those induced by flat node calibrations.

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Alessio Capobianco @acapomorphic.bsky.social · 13/05/2026

We looked at two study cases (crocodylians and fireflies), comparing effective prior and posterior distributions on node ages. We show that effective priors induced by unresolved FBD are extremely similar to those induced by flat node calibrations when only one fossil per calibrated clade is used.

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Alessio Capobianco @acapomorphic.bsky.social · 13/05/2026

In the unresolved FBD (fossilized birth-death), extinct species (fossils) are treated as tips in the tree, providing chronostratigraphic data to the analysis. No morphological data is included, so fossils are constrained based on expert knowledge, similarly to how node calibrations are designed.

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Alessio Capobianco @acapomorphic.bsky.social · 04/03/2026

- Shifts in diversification rate happen more frequently in younger phylogenies - Groups with faster diversification overall also show higher variability in diversification rates - Flowering plants appear to experience larger (and more frequent) shifts than any other group we analyzed

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Alessio Capobianco @acapomorphic.bsky.social · 04/03/2026

A few key findings: - Shifts in diversification rate are ubiquitous across the Tree of Life: the process of diversification is highly heterogeneous - Upshifts are way more common than downshifts (but this is likely due to lack of power in detecting downshifts with extant phylogenies)

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Alessio Capobianco @acapomorphic.bsky.social · 04/03/2026

New paper out from @hoehna.bsky.social Lab, led by the brilliant @bjorntko.bsky.social! We applied the Pesto software (Kopperud & Höhna, 2025) to look at lineage-specific shifts in diversification rate on large, densely-sampled phylogenies across the Tree of Life doi.org/10.1093/evle...

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Alessio Capobianco @acapomorphic.bsky.social · 15/10/2025

Overall, between 100 and 500 variable characters are necessary to reach sufficient accuracy and precision of phylogenetic estimates for as low as 20 taxa. This is relevant not only for morphological phylogenetics, but also for gene trees and SNP-based estimates, and for Bayesian phylolinguistics.

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Alessio Capobianco @acapomorphic.bsky.social · 15/10/2025

Three different metrics of accuracy and precision were used to evaluate how good was the phylogenetic inference. General resulting patterns: more characters are better; more states are better (but this has little effect for >50 taxa); more taxa are worse for short trees, but better for long trees.

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Alessio Capobianco @acapomorphic.bsky.social · 15/10/2025

I designed this simulation study in RevBayes to perfectly match the models used for sim and inference. Any differences between the true tree generating data and the inferred tree(s) are due to dataset size. Parameters that varied across sims are: # characters, # taxa, tree length, and # states.

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Alessio Capobianco @acapomorphic.bsky.social · 15/10/2025

Out now in Biology Letters, my latest paper tackles an apparently simple question: how many characters are needed to reconstruct a phylogeny? TL;DR: in most cases between 100 and 500, more than a substantial portion of morphological datasets, but the story is more complex... doi.org/10.1098/rsbl...

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Alessio Capobianco @acapomorphic.bsky.social · 25/09/2025

Non-exhaustive list of things you can find in our paper: - A survey of all fossil tip-dating studies published until 2023 - A flowchart with all the steps to set up a tip-dating analysis - Detailed discussion of all the elements making up a tip-dating analysis, from molecular alignment to FBD models

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Alessio Capobianco @acapomorphic.bsky.social · 25/09/2025

I am extremely happy to see that our review on fossil tip-dating is out in early view in Systematic Biology! A huge thanks to all the authors of this massive project (@heckeberg.bsky.social, @basantakhakurel.bsky.social, Gustavo Darlim, and @hoehna.bsky.social)! academic.oup.com/sysbio/advan...

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