Levi Yoder Raskin
@leviyoderraskin.bsky.social
Integrative biology PhD candidate @ UC Berkeley and member of the Huelsenbeck Lab. Interested in morphological phylogenetics, fossils, and especially hominins. DOE CSGF fellow.
Thanks so much for sharing! To add, we don't necessarily think shape is poor data for phylogenetic inference. Instead, we think PCA is inherently a poor method for phylogenetic inference! My dissertation research focuses on Bayesian inference of phylogeny from shape data; hope to share more soon!
November 8, 2025 at 10:09 PM
Thanks so much for sharing! To add, we don't necessarily think shape is poor data for phylogenetic inference. Instead, we think PCA is inherently a poor method for phylogenetic inference! My dissertation research focuses on Bayesian inference of phylogeny from shape data; hope to share more soon!
Despite its widespread use in paleoanthropology, PCA is ill-suited and unreliable for inferring hominin evolutionary relationships from morphological data. Studies of hominin systematics that rely on PCA as a means of inferring morphological and phylogenetic affinity should be revisited. end/
Principal Components Analysis fails to recover phylogenetic structure in hominins
Objectives: Paleoanthropologists often utilize geometric morphometrics and principal components analysis (PCA) to interpret shape variation within the hominin fossil record. It is common practice to i...
doi.org
November 1, 2025 at 3:36 PM
Despite its widespread use in paleoanthropology, PCA is ill-suited and unreliable for inferring hominin evolutionary relationships from morphological data. Studies of hominin systematics that rely on PCA as a means of inferring morphological and phylogenetic affinity should be revisited. end/
Much of what we know about hominin diversity comes from studies which make phylogenetic claims from PCA. Here, we simulated datasets analogous to the hominin fossil record and found that PCA vastly underperformed, recovering topology in 0-2.4% of simulated datasets. 2/
November 1, 2025 at 3:36 PM
Much of what we know about hominin diversity comes from studies which make phylogenetic claims from PCA. Here, we simulated datasets analogous to the hominin fossil record and found that PCA vastly underperformed, recovering topology in 0-2.4% of simulated datasets. 2/
We came across your Sys Bio paper a few days ago and are absolutely including it in our revisions!! So sorry we missed it the first time around-- finding it was really reassuring to us! I'm hoping to keep working on character analysis throughout my PhD, so hopefully more interesting results to come!
January 25, 2025 at 4:33 PM
We came across your Sys Bio paper a few days ago and are absolutely including it in our revisions!! So sorry we missed it the first time around-- finding it was really reassuring to us! I'm hoping to keep working on character analysis throughout my PhD, so hopefully more interesting results to come!
I'm interested!!
November 17, 2024 at 5:33 PM
I'm interested!!
I am interested! I haven’t done any sci comm but will be posting more both here and on Twitter and trying do hominin/phylogenetics sci comm.
November 12, 2024 at 11:35 PM
I am interested! I haven’t done any sci comm but will be posting more both here and on Twitter and trying do hominin/phylogenetics sci comm.
Awesome, thanks! I'll start with the twitter threads as a way to practice/get in a habit with it and see what works. Thank you!
November 11, 2024 at 5:16 PM
Awesome, thanks! I'll start with the twitter threads as a way to practice/get in a habit with it and see what works. Thank you!
Do you have any suggestions for scientists trying to reach broader audiences?
I’m a PhD student in evolutionary biology (formerly studied Paleolithic archaeology) and would love to try and reach audiences that aren’t primed for evo bio, but don’t know where to start.
Thanks!
I’m a PhD student in evolutionary biology (formerly studied Paleolithic archaeology) and would love to try and reach audiences that aren’t primed for evo bio, but don’t know where to start.
Thanks!
November 11, 2024 at 4:31 PM
Do you have any suggestions for scientists trying to reach broader audiences?
I’m a PhD student in evolutionary biology (formerly studied Paleolithic archaeology) and would love to try and reach audiences that aren’t primed for evo bio, but don’t know where to start.
Thanks!
I’m a PhD student in evolutionary biology (formerly studied Paleolithic archaeology) and would love to try and reach audiences that aren’t primed for evo bio, but don’t know where to start.
Thanks!
Hi, not sure if I'm too late on this. I just swapped over from twitter and I'm hoping it would be possible to join the Science feed! I'm an Integrative Biology PhD student at UC Berkeley and I study phylogenetic methods development.
Here's my orcid for proof:
orcid.org/0009-0001-26...
Here's my orcid for proof:
orcid.org/0009-0001-26...
ORCID
orcid.org
November 9, 2024 at 7:35 PM
Hi, not sure if I'm too late on this. I just swapped over from twitter and I'm hoping it would be possible to join the Science feed! I'm an Integrative Biology PhD student at UC Berkeley and I study phylogenetic methods development.
Here's my orcid for proof:
orcid.org/0009-0001-26...
Here's my orcid for proof:
orcid.org/0009-0001-26...
November 9, 2024 at 7:22 PM
Preprint: biorxiv.org/content/10.1...
#paleoanthropology, #hominins, #humanevolution, #phylogenetics, #morphology, #parsimony, #characteranalysis, #methods, #BrynMawrCollege, #HaverfordCollege, #UCBerkeley
#paleoanthropology, #hominins, #humanevolution, #phylogenetics, #morphology, #parsimony, #characteranalysis, #methods, #BrynMawrCollege, #HaverfordCollege, #UCBerkeley
The effects of trait redundancy and information content on hominin phylogenetic inference
Paleoanthropological phylogenetic inference is based on characters assumed to be phylogenetically informative and mutually independent, but our understanding of which traits fulfill these requirements...
biorxiv.org
November 7, 2024 at 4:44 PM
4) Informative traits are informative to the most parsimonious topology and not necessarily to the correct topology, which may never be known. When we say informative we mean that the most parsimonious consensus hominin topology is dependent on the inclusion of an unaltered trait
November 7, 2024 at 4:43 PM
4) Informative traits are informative to the most parsimonious topology and not necessarily to the correct topology, which may never be known. When we say informative we mean that the most parsimonious consensus hominin topology is dependent on the inclusion of an unaltered trait
3) While Mongle et al. (2023) have expanded the dataset we used, we decided to use the 2019 matrix for easy comparison to other methodological papers (e.g., Gautney, 2023)
November 7, 2024 at 4:43 PM
3) While Mongle et al. (2023) have expanded the dataset we used, we decided to use the 2019 matrix for easy comparison to other methodological papers (e.g., Gautney, 2023)
2) We also only measured the information content in traits and bony elements in Mongle et al. (2019)’s character matrix; our results are limited to traits in this character matrix and operationalized in this way
November 7, 2024 at 4:43 PM
2) We also only measured the information content in traits and bony elements in Mongle et al. (2019)’s character matrix; our results are limited to traits in this character matrix and operationalized in this way
Limitations: 1) we inferred topologies using parsimony, as that method is still widely used in morphological phylogenetics (follow for updates on novel Bayesian approaches as my PhD progresses!)
November 7, 2024 at 4:43 PM
Limitations: 1) we inferred topologies using parsimony, as that method is still widely used in morphological phylogenetics (follow for updates on novel Bayesian approaches as my PhD progresses!)
A better understanding of missing data, informative data, and what traits are driving the cladistics seen both in our paper and many other hominin phylogenetic papers is crucial to understanding the uncertainty inherent in the record
November 7, 2024 at 4:43 PM
A better understanding of missing data, informative data, and what traits are driving the cladistics seen both in our paper and many other hominin phylogenetic papers is crucial to understanding the uncertainty inherent in the record
For example, below is (left) the MP consensus topology using all taxa and traits and (right) the MP consensus topology inferred from the character matrix missing Kenyanthropus platyops. Purple diamonds indicate changes in relation to the topology including all the taxa
November 7, 2024 at 4:42 PM
For example, below is (left) the MP consensus topology using all taxa and traits and (right) the MP consensus topology inferred from the character matrix missing Kenyanthropus platyops. Purple diamonds indicate changes in relation to the topology including all the taxa
We also find that isolated cranial bones (e.g., isolated fossil mandible) contain insufficient information to closely resolve the hominin topology and demonstrate that the baseline hominin topology is potentially biased by the inclusion of dubious taxa
November 7, 2024 at 4:42 PM
We also find that isolated cranial bones (e.g., isolated fossil mandible) contain insufficient information to closely resolve the hominin topology and demonstrate that the baseline hominin topology is potentially biased by the inclusion of dubious taxa
We find that only 21% of the characters in that matrix contribute unique phylogenetic information and at least 22 traits (and perhaps up to 76) contribute no information whatsoever to the inferred topology under a maximum parsimony framework
November 7, 2024 at 4:42 PM
We find that only 21% of the characters in that matrix contribute unique phylogenetic information and at least 22 traits (and perhaps up to 76) contribute no information whatsoever to the inferred topology under a maximum parsimony framework
We use a combination of permutation of trait values and removal of traits, sets of traits composing anatomical units, and operational taxonomic units
November 7, 2024 at 4:42 PM
We use a combination of permutation of trait values and removal of traits, sets of traits composing anatomical units, and operational taxonomic units