Alessio Capobianco
@acapomorphic.bsky.social
Vertebrate paleontologist and evolutionary biologist, currently postdoc at LMU Munich. In a love-hate relationship with phylogenies :D
November 15, 2025 at 5:17 PM
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...
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...
royalsocietypublishing.org
November 11, 2025 at 7:51 PM
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...
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
October 16, 2025 at 1:56 PM
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
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?
October 16, 2025 at 1:48 PM
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?
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
October 16, 2025 at 10:16 AM
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
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
October 16, 2025 at 10:11 AM
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
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?
October 16, 2025 at 10:01 AM
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?
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.
October 16, 2025 at 9:56 AM
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.
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.
October 15, 2025 at 9:29 AM
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.
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.
October 15, 2025 at 9:29 AM
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.
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).
October 15, 2025 at 9:29 AM
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).
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.
October 15, 2025 at 9:29 AM
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.
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.
October 15, 2025 at 9:29 AM
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.
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.
October 15, 2025 at 9:29 AM
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.
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...
October 15, 2025 at 9:29 AM
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...
Reposted by Alessio Capobianco
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/10.1017/pab.2025.10042
Nearly 200 scientists worldwide came together to map where our field is headed. Here’s the story 👇
Identifying the Big Questions in paleontology: a community-driven project | Paleobiology | Cambridge Core
Identifying the Big Questions in paleontology: a community-driven project
dx.doi.org
September 26, 2025 at 1:59 PM
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/10.1017/pab.2025.10042
Nearly 200 scientists worldwide came together to map where our field is headed. Here’s the story 👇
Reposted by Alessio Capobianco
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...
September 26, 2025 at 11:53 AM
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...
I'm afraid we forgot to mention any lemurs there... 😅 But I hope you're still using them for Analytical Paleo! 😁
September 26, 2025 at 8:42 AM
I'm afraid we forgot to mention any lemurs there... 😅 But I hope you're still using them for Analytical Paleo! 😁
Thanks Jeff! The VP lecture slides definitely left an impression, I had to use the bird somewhere 😅
September 25, 2025 at 9:29 PM
Thanks Jeff! The VP lecture slides definitely left an impression, I had to use the bird somewhere 😅
Reposted by Alessio Capobianco
Ever wondered how to incorporate fossils as tips in a phylogenetic tree?
Our new paper provides a comprehensive guide!
#EarlyFossilFriday
#FossilFriday
#TipDating
#Phylogeny
#EvolutionaryBiology
Our new paper provides a comprehensive guide!
#EarlyFossilFriday
#FossilFriday
#TipDating
#Phylogeny
#EvolutionaryBiology
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...
September 25, 2025 at 1:21 PM
Ever wondered how to incorporate fossils as tips in a phylogenetic tree?
Our new paper provides a comprehensive guide!
#EarlyFossilFriday
#FossilFriday
#TipDating
#Phylogeny
#EvolutionaryBiology
Our new paper provides a comprehensive guide!
#EarlyFossilFriday
#FossilFriday
#TipDating
#Phylogeny
#EvolutionaryBiology
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!
September 25, 2025 at 12:40 PM
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!
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
- 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
September 25, 2025 at 12:40 PM
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
- 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
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...
September 25, 2025 at 12:40 PM
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...
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!
Contact us if you would like to participate or to know more about it!
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: 👇
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: 👇
September 19, 2025 at 2:39 PM
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!
Contact us if you would like to participate or to know more about it!