Sign in

Alessio Capobianco

@acapomorphic.bsky.social
236 followers 255 following 34 posts

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

PostsRepliesMedia
Reposted by Alessio Capobianco
Rodrigo Figueroa @rodrigoichthys.bsky.social · 11/08/2026
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.edu
Comparative Anatomy of Ocean Sunfishes (Tetraodontiformes: Molidae) | Smithsonian Institution Scholarly Press
0135
Reposted by Alessio Capobianco
Laura Mulvey @lauramulvey.bsky.social · 27/05/2026
📣 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.com
MorphSim: An R package for simulating discrete morphological data
Morphological data are essential for reconstructing evolutionary histories, particularly for fossil taxa, as they represent the primary source of information for integrating extinct lineages into ...
14217
Reposted by Alessio Capobianco
April Wright @wrightam.bsky.social · 26/05/2026
Oh, this looks quite convenient, especially the filtering and mimicking empirical matrices.
0299
Reposted by Alessio Capobianco
Rodrigo Figueroa @rodrigoichthys.bsky.social · 06/05/2026
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.org
The ray-finned fish blackbox: unprecedented morphological diversity and the interplay between brain and endocast
Abstract. Vertebrates are unique among animals as they bear a neurocranium, which almost completely encapsulates the brain. Thus, within vertebrates, the e
02817
Reposted by Alessio Capobianco
gdarlim.bsky.social @gdarlim.bsky.social · 13/05/2026
Check out our new paper comparing node calibrations and unresolved FBD for dating molecular phylogenies using crocs and firefly datasets as case studies 🐊
052
Alessio Capobianco @acapomorphic.bsky.social · 13/05/2026
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.
040
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.
120
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.
130
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.
120
Alessio Capobianco @acapomorphic.bsky.social · 13/05/2026
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.org
How to date a molecular phylogeny: comparison of effective priors between node calibration and fossilized birth–death
Abstract. Time-calibrating a phylogenetic tree is a fundamental step in phylogenetic inference, as it allows the study of macroevolutionary processes such
15736
Reposted by Alessio Capobianco
Evolution Letters @evolletters.bsky.social · 10/03/2026
Diversification rate shifts are everywhere. Analyses of phylogenies covering >300k species reveal widespread changes in speciation dynamics across the Tree of Life. @bjorntko.bsky.social @hoehna.bsky.social @acapomorphic.bsky.social ‬ academic.oup.com/evlett/advan...
0158
Reposted by Alessio Capobianco
Matt Friedman @friedmanlab.bsky.social · 07/03/2026
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.
Photograph of a fossil fish skull in right lateral view. The bone is dark brown/black against a gray matrix.
28130
Reposted by Alessio Capobianco
Matt Friedman @friedmanlab.bsky.social · 04/03/2026
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.
Cover of the journal Nature, featuring the head of a large fish with its mouth open.  A smaller fish is swimming into its mouth. The cover reads "Caught in Time: Early fossils shed light on the origins of bony fish."
19133
Reposted by Alessio Capobianco
Dr John Clarke @jclarkepaleo.bsky.social · 04/03/2026
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.
0163
Alessio Capobianco @acapomorphic.bsky.social · 04/03/2026
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.org
The nature and prevalence of diversification rate shifts across the Tree of Life
Abstract. Strong disparity in species richness among organisms is well documented, but heterogeneity in the underlying diversification process is less unde
091
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
140
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)
140
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...
15026
Reposted by Alessio Capobianco
𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻 @basantakhakurel.bsky.social · 25/02/2026
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.org
A covarion model for phylogenetic estimation using discrete morphological datasets
Abstract. The rate of evolution of a single morphological character is not homogeneous across the phylogeny and this rate heterogeneity varies between morp
23720
Reposted by Alessio Capobianco
Matt Friedman @friedmanlab.bsky.social · 15/11/2025
Michigan paleontology family portrait, Birmingham edition #2025SVP
A group of smiling paleontologists standing in front of signs reading "REGISTRATION" and "SVP 2025." Photo credit: Sam Giles.
0517
Alessio Capobianco @acapomorphic.bsky.social · 15/11/2025
#2025SVP #SVP2025 Final Banquet loading... ⏳⏳⌛
0152
Alessio Capobianco @acapomorphic.bsky.social · 11/11/2025
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.org
How many characters are needed to reconstruct a phylogeny? | Biology Letters
Despite increased recent attention towards Bayesian phylogenetics and its applications in understanding macroevolutionary processes, it remains unclear how many discrete characters are needed to accur...
0166
Alessio Capobianco @acapomorphic.bsky.social · 16/10/2025
Ah, I see! That is definitely true, but that same character discretized vs in its continuous form carries a very different quantity of information. If modeled properly (maybe a big if), one continuous character should have more information content to estimate a phylogeny than its discretized version
110
Alessio Capobianco @acapomorphic.bsky.social · 16/10/2025
I like the optimism there! I guess what would be good to know is: given the amount of "perturbation" from the true phylogeny that I can expect based on the size of my data, are the main patterns I'm interested in (diversification, biogeography, phenotypic evolution) robust to that much perturbation?
120
Alessio Capobianco @acapomorphic.bsky.social · 16/10/2025
Continuous characters are not that commonly used in Bayesian morphological phylogenetics though. I want to believe that those can be a mostly unexplored source of information to infer evolutionary relationships, although I'm very aware that they come with their own set of issues and limitations
120
Alessio Capobianco @acapomorphic.bsky.social · 16/10/2025
In my simulation, a phylogeny inferred for 50 taxa with 50 binary characters on average has 50% of the nodes wrong (and this is with no model misspecification and no missing data). What can we do about it? I don't have any clear/easy solution, but at the same time I don't want to be too pessimistic
120
Alessio Capobianco @acapomorphic.bsky.social · 16/10/2025
I totally agree, for some systems there is possibly an intrinsic limit on the number of (more or less) independent variable characters that can be defined and scored that is lower than 100. Then the question is: what can we do for those? Do we just accept that our phylo estimates will always be off?
220
Alessio Capobianco @acapomorphic.bsky.social · 16/10/2025
Thank you! I would expect that adding rate heterogeneity to the model (which means adding parameters) would require at least the same minimum number of characters, if not more.
040
Alessio Capobianco @acapomorphic.bsky.social · 15/10/2025
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.
2150
Alessio Capobianco @acapomorphic.bsky.social · 15/10/2025
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.
180
Alessio Capobianco @acapomorphic.bsky.social · 15/10/2025
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).
2100
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.
160
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.
150
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.
170
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...
19148
Reposted by Alessio Capobianco
Kenneth De Baets @djbirddanerd.bsky.social · 26/09/2025
Just in time for #FossilFriday 🦖 What are the big questions in #paleontology today? dx.doi.org/10.1017/pab.2025.10042 Nearly 200 scientists worldwide came together to map where our field is headed. Here’s the story 👇
dx.doi.org
Identifying the Big Questions in paleontology: a community-driven project | Paleobiology | Cambridge Core
Identifying the Big Questions in paleontology: a community-driven project
12920
Reposted by Alessio Capobianco
Alessandro Chiarenza @macroecoevoale.bsky.social · 26/09/2025
What are the biggest questions in #paleontology? New paper out today in Paleobiology led by Smith & Kiessling with ~200 coauthors on the relevance of our field, methods, & museum collections to climate & biodiversity research🦖 #FossilFriday @paleosoc.bsky.social 🔗: www.cambridge.org/core/journal...
02414
Alessio Capobianco @acapomorphic.bsky.social · 26/09/2025
I'm afraid we forgot to mention any lemurs there... 😅 But I hope you're still using them for Analytical Paleo! 😁
010
Alessio Capobianco @acapomorphic.bsky.social · 25/09/2025
Thanks Jeff! The VP lecture slides definitely left an impression, I had to use the bird somewhere 😅
010
Reposted by Alessio Capobianco
𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻 @basantakhakurel.bsky.social · 25/09/2025
Ever wondered how to incorporate fossils as tips in a phylogenetic tree? Our new paper provides a comprehensive guide! #EarlyFossilFriday #FossilFriday #TipDating #Phylogeny #EvolutionaryBiology
074
Alessio Capobianco @acapomorphic.bsky.social · 25/09/2025
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!
031
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
141
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...
35338
Alessio Capobianco @acapomorphic.bsky.social · 19/09/2025
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!
084
Reposted by Alessio Capobianco
Catalina Pimiento 🆓🇵🇸 @pimientoc.bsky.social · 01/08/2025
No, it is not a dream. This actually happened!!! We had a *fantastic* #CPEGCPB26 meeting and I cannot articulate any other adjective to describe it until I recover from it. Thanks to everyone who attended and everyone who helped making this happen. @kristinakocakova.bsky.social
1196
Reposted by Alessio Capobianco
CPEG & CPB Symposium 2025 @cpeg-cpb25.bsky.social · 27/07/2025
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
0158
Alessio Capobianco @acapomorphic.bsky.social · 10/07/2025
Here is a Nature News writeup on our work, covering also another remarkable new paper on extremely old enamel proteins by Daniel Green and colleagues. www.nature.com/articles/d41...
nature.com
Ancient proteins rewrite the rhino family tree — are dinosaurs next?
Molecules from 20-million-year-old teeth are among the oldest ever sequenced.
000
Alessio Capobianco @acapomorphic.bsky.social · 10/07/2025
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.
100
Alessio Capobianco @acapomorphic.bsky.social · 10/07/2025
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.
110
Alessio Capobianco @acapomorphic.bsky.social · 10/07/2025
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.com
Phylogenetically informative proteins from an Early Miocene rhinocerotid - Nature
Protein 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.
1126