Alessio Capobianco

Alessio Capobianco

@acapomorphic.bsky.social

Vertebrate paleontologist and evolutionary biologist, currently postdoc at LMU Munich. In a love-hate relationship with phylogenies :D

239 followers255 following34 posts

Alessio Capobianco reposted

Rodrigo Figueroa
@rodrigoichthys.bsky.social

Just learned this masterpiece got published today and couldn’t be more excited about it!! During my first PhD semester at UMich back in 2019 Willy gave an amazing talk about this project, setting the bauplan of the kind of research I have tried to do since! scholarlypress.si.edu/store/all/co...

scholarlypress.si.eduComparative Anatomy of Ocean Sunfishes (Tetraodontiformes: Molidae) | Smithsonian Institution Scholarly Press

Alessio Capobianco reposted

Laura Mulvey
@lauramulvey.bsky.social

📣 Introducing MorphSim: an R package for simulating discrete morphological data along phylogenetic trees, built for fossil-inclusive phylogenetics, with all the complexity of real morphological data baked in 🪨🌿 besjournals.onlinelibrary.wiley.com/doi/10.1111/...

besjournals.onlinelibrary.wiley.comMorphSim: An R package for simulating discrete morphological dataMorphological data are essential for reconstructing evolutionary histories, particularly for fossil taxa, as they represent the primary source of information for integrating extinct lineages into ...

Alessio Capobianco reposted

Rodrigo Figueroa
@rodrigoichthys.bsky.social

Very well-timed publication of my most recent work at @royalsociety.org Proc B showcasing the backbone of my future research at @stonybrooku.bsky.social! There is still much to learn about ray-finned fish neurocranial evolution and the diversity of ways brain and endocasts interact in this lineage!

royalsocietypublishing.orgThe ray-finned fish blackbox: unprecedented morphological diversity and the interplay between brain and endocastAbstract. Vertebrates are unique among animals as they bear a neurocranium, which almost completely encapsulates the brain. Thus, within vertebrates, the e

Alessio Capobianco reposted

gdarlim.bsky.social
@gdarlim.bsky.social

Check out our new paper comparing node calibrations and unresolved FBD for dating molecular phylogenies using crocs and firefly datasets as case studies 🐊

Alessio Capobianco@acapomorphic.bsky.social

My new paper with @gdarlim.bsky.social and @hoehna.bsky.social is now out in Proceedings B! We set out to compare two different approaches to time-calibrate a molecular phylogeny: traditional node calibrations, and unresolved FBD... @royalsocietypublishing.org doi.org/10.1098/rspb...

doi.orgHow to date a molecular phylogeny: comparison of effective priors between node calibration and fossilized birth–deathAbstract. Time-calibrating a phylogenetic tree is a fundamental step in phylogenetic inference, as it allows the study of macroevolutionary processes such
Alessio Capobianco
@acapomorphic.bsky.social

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.

Alessio Capobianco
@acapomorphic.bsky.social

Ultimately, to time-calibrate a molecular phylogeny, we recommend using the unresolved FBD approach when several extinct species are sampled in the focal group, or sampled fossils are taxonomically uncertain. In other cases (e.g. few fossils), we favor the use of classic node-dating approaches.

Alessio Capobianco
@acapomorphic.bsky.social

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.

Alessio Capobianco
@acapomorphic.bsky.social

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.

Alessio Capobianco reposted

Matt Friedman
@friedmanlab.bsky.social

Out now in Contributions from me and @gilespalaeo.bsky.social, a deep dive into an early member of the sturgeon and paddlefish lineage. Bear with me, but there’s a long backstory highlighting uncertainty about the anatomy of living species and how well-studied fossils can still yield new insights.

Alessio Capobianco reposted

Matt Friedman
@friedmanlab.bsky.social

Osteichthyans--the bony fishes--are by far the most diverse group of living jawed vertebrates. Two papers out today in @nature.com feature remarkable new Chinese fossils that paint a picture of substantial morphological diversity among stem osteichthyans.

Alessio Capobianco reposted

Dr John Clarke
@jclarkepaleo.bsky.social

Our new paper revealing major patterns of diversification across the Tree of Life is here! doi.org/10.1093/evle... Congratulations to @bjorntko.bsky.social for leading this ambitious effort, it was a pleasure to contribute alongside @acapomorphic.bsky.social, @hoehna.bsky.social & Luis Palazzesi.

Alessio Capobianco@acapomorphic.bsky.social

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

- 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

Alessio Capobianco
@acapomorphic.bsky.social

We hope that our study will provide the foundations for understanding the nature of diversification rate shifts in exceptionally species-rich clades. You can read it open access in Evolution Letters: doi.org/10.1093/evle... @bjorntko.bsky.social @jclarkepaleo.bsky.social @hoehna.bsky.social

doi.orgThe nature and prevalence of diversification rate shifts across the Tree of LifeAbstract. Strong disparity in species richness among organisms is well documented, but heterogeneity in the underlying diversification process is less unde
Alessio Capobianco
@acapomorphic.bsky.social

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)

Alessio Capobianco reposted

𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
@basantakhakurel.bsky.social

Our new paper 'A covarion model for phylogenetic estimation using discrete morphological datasets,' is out in SysBio! We introduce the "covariomorph" model in RevBayes to capture character and lineage specific rates of morphological traits. 🔗 doi.org/10.1093/sysb...

doi.orgA covarion model for phylogenetic estimation using discrete morphological datasetsAbstract. The rate of evolution of a single morphological character is not homogeneous across the phylogeny and this rate heterogeneity varies between morp
Alessio Capobianco
@acapomorphic.bsky.social

I'll be presenting a poster at #2025SVP #SVP2025 about my recently published work on how many characters are needed to reconstruct a phylogeny. Come by at the poster session this Thursday if you want to chat about it! royalsocietypublishing.org/doi/abs/10.1...

royalsocietypublishing.orgHow many characters are needed to reconstruct a phylogeny? | Biology LettersDespite increased recent attention towards Bayesian phylogenetics and its applications in understanding macroevolutionary processes, it remains unclear how many discrete characters are needed to accur...
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Alessio Capobianco
@acapomorphic.bsky.social

An important point: the 100-500 chars threshold refers to an ideal scenario where we know under which model the data evolved (no model misspecification), this model is relatively simple (few parameters to infer), and there is no missing data. Thus, this should be taken as a very minimum number.

Alessio Capobianco
@acapomorphic.bsky.social

Problem: a lot of empirical morphological datasets have fewer than 100 characters, and way fewer than 500. Possible solutions? Continuous characters; total-evidence datasets; more funding, hiring, training targeted towards characterization and digitization of interspecific morphological diversity.

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Alessio Capobianco
@acapomorphic.bsky.social

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.

Alessio Capobianco
@acapomorphic.bsky.social

One intriguing empirical application of these findings is that, for more than 50 taxa, characters that change multiple times independently across the tree (homoplastic characters) improve tree reconstruction compared to characters that change only once (synapomorphies and autapomorphies).

Alessio Capobianco
@acapomorphic.bsky.social

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.

Alessio Capobianco
@acapomorphic.bsky.social

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.

Alessio Capobianco reposted

𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
@basantakhakurel.bsky.social

Ever wondered how to incorporate fossils as tips in a phylogenetic tree? Our new paper provides a comprehensive guide! #EarlyFossilFriday #FossilFriday #TipDating #Phylogeny #EvolutionaryBiology

Alessio Capobianco@acapomorphic.bsky.social

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...

Alessio Capobianco
@acapomorphic.bsky.social

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

Alessio Capobianco
@acapomorphic.bsky.social

We hope that our contribution will not only be a useful reference for all researchers wanting to perform a tip-dating analysis on their favorite group of organisms, but also a starting point of discussion to further improve this class of methods and its application to empirical data!

Alessio Capobianco
@acapomorphic.bsky.social

We (me, @barankarapunar.bsky.social, @sinjinis.bsky.social and @harriedrage.bsky.social) organized a symposium for the next IPC (Cape Town 2026!) on evolution, diversity and ecology in marine ecosystems throughout the Phanerozoic. Contact us if you would like to participate or to know more about it!

IPC7@ipc7.bsky.social

Symposia 🔍 Among our 29 themed symposia + 1 open symposium, we are pleased to feature: ✨ Life in the Phanerozoic Oceans: Evolution, diversity and ecology in deep time marine ecosystems✨ 📩 To participate in this symposium or get more information, contact the conveners: 👇

Alessio Capobianco reposted

CPEG & CPB Symposium 2025
@cpeg-cpb25.bsky.social

The CPEG & CPB meeting is officially underway! 🎉 We kicked things off with two fantastic workshop sessions: 📊 R-based open data science in palaeobiology and ecology 🧠 Deep learning for macroevolutionary analyses Big thanks to all our speakers and participants - spot yourself below! #CPEGCPB25

Alessio Capobianco
@acapomorphic.bsky.social

We now have protein sequences from rhino enamel that are >20 million years old! I am extremely excited and grateful to have been part of this project. The incredible thing: these sequences are informative enough to place this ancient species in the rhino tree! www.nature.com/articles/s41...

nature.comPhylogenetically informative proteins from an Early Miocene rhinocerotid - NatureProtein sequences from fossil tooth enamel of a rhinocerotid from Canada’s High Arctic are used to develop phylogenetic frameworks from a specimen too old to preserve ancient DNA.
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Alessio Capobianco
@acapomorphic.bsky.social

According to our analysis, Elasmotherium (the "Siberian unicorn") and modern rhinos share a common ancestor in the Oligocene (more recently than previously thought), and they are more closed related to each other than to our aceratherine from the High Arctic.

Alessio Capobianco
@acapomorphic.bsky.social

We now have protein sequences from rhino enamel that are >20 million years old! I am extremely excited and grateful to have been part of this project. The incredible thing: these sequences are informative enough to place this ancient species in the rhino tree! www.nature.com/articles/s41...

nature.comPhylogenetically informative proteins from an Early Miocene rhinocerotid - NatureProtein sequences from fossil tooth enamel of a rhinocerotid from Canada’s High Arctic are used to develop phylogenetic frameworks from a specimen too old to preserve ancient DNA.
Alessio Capobianco
@acapomorphic.bsky.social

Our protein-based tip-dated phylogenetic analysis (a combination of words that would have been totally absurd until recently) shows that this aceratherine ("hornless rhino") belonged to an early-diverging lineage in the rhino family tree.

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