A phylogenetic tree of plasmodial slime molds & their common features
October 21, 2025 at 6:28 AM
A phylogenetic tree of plasmodial slime molds & their common features
My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore.
August 25, 2026 at 1:32 PM
My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore.
Hi all. I am very excited that after 6 years I finally got my phylogenetic comparative methods book and online exercises online. Feel free to use and share. The book is here: nhcooper123.github.io/pcm-primer/. Note that it is not finished, we had to abandon it before the sunk costs fallacy broke us
Phylogenetic Comparative Methods
Phylogenetic Comparative Methods
nhcooper123.github.io
March 25, 2026 at 2:32 PM
Hi all. I am very excited that after 6 years I finally got my phylogenetic comparative methods book and online exercises online. Feel free to use and share. The book is here: nhcooper123.github.io/pcm-primer/. Note that it is not finished, we had to abandon it before the sunk costs fallacy broke us
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
rdcu.be/eg4OA
1/
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.
rdcu.be
April 9, 2025 at 9:07 PM
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
rdcu.be/eg4OA
1/
Phylogenetic broccoli
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🧪 ⚒️
August 12, 2024 at 12:57 PM
Phylogenetic broccoli
🧪 ⚒️
🧪 ⚒️
I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
PhyloWeaver – Interactive phylogenetic tree editor
Edit and visualize phylogenetic trees directly in your browser. PhyloWeaver lets you interactively rearrange tree topologies and export high-quality figures for publications and presentations.
yawak.jp
November 18, 2025 at 1:59 AM
I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
Phylogenetic biodiversity is a DEI initiative
I received a heartbreaking email today: A paper in a special issue I’m editing is being retracted because one of its authors is afraid of losing their job and their legal status in the U.S. if they publish a scientific study on evolution. Yes, on evolution, nature's engine of diversity.
March 30, 2025 at 6:36 AM
Phylogenetic biodiversity is a DEI initiative
not now babe I’m memorizing the cutthroat trout phylogenetic tree
December 12, 2024 at 8:02 PM
not now babe I’m memorizing the cutthroat trout phylogenetic tree
Phylogenetic parallelograms: visual comparison of discordant phylogenetic trees https://www.biorxiv.org/content/10.64898/2026.09.18.752558v1
September 25, 2026 at 2:40 AM
Phylogenetic parallelograms: visual comparison of discordant phylogenetic trees https://www.biorxiv.org/content/10.64898/2026.09.18.752558v1
🌳 New findings 🌳
Phylogenetic diversity cannot be used as a proxy for functional diversity in vascular plant communities 🌲🌳🌴🌵🌱🍀🌾🌼 We used the #sPlot database & found a pronounced decoupling between phylogenetic & functional diversity ⬇️
🧪🌐🌏🍁
@natureecoevo.bsky.social
shorturl.at/Bf5IK
Phylogenetic diversity cannot be used as a proxy for functional diversity in vascular plant communities 🌲🌳🌴🌵🌱🍀🌾🌼 We used the #sPlot database & found a pronounced decoupling between phylogenetic & functional diversity ⬇️
🧪🌐🌏🍁
@natureecoevo.bsky.social
shorturl.at/Bf5IK
Global decoupling of functional and phylogenetic diversity in plant communities - Nature Ecology & Evolution
Functional diversity and phylogenetic diversity are expected to be positively correlated. Here the authors show that the covariation between these metrics in vascular plant communities around the worl...
shorturl.at
December 3, 2024 at 8:55 PM
🌳 New findings 🌳
Phylogenetic diversity cannot be used as a proxy for functional diversity in vascular plant communities 🌲🌳🌴🌵🌱🍀🌾🌼 We used the #sPlot database & found a pronounced decoupling between phylogenetic & functional diversity ⬇️
🧪🌐🌏🍁
@natureecoevo.bsky.social
shorturl.at/Bf5IK
Phylogenetic diversity cannot be used as a proxy for functional diversity in vascular plant communities 🌲🌳🌴🌵🌱🍀🌾🌼 We used the #sPlot database & found a pronounced decoupling between phylogenetic & functional diversity ⬇️
🧪🌐🌏🍁
@natureecoevo.bsky.social
shorturl.at/Bf5IK
Phylogenetic turnover of seed plants 🌱 at a global 🌐 and across phylogenetic scales: www.nature.com/articles/s41...
Environmental filtering, not dispersal history, explains global patterns of phylogenetic turnover in seed plants at deep evolutionary timescales - Nature Ecology & Evolution
This modelling study integrates comprehensive regional plant inventories, environmental conditions and palaeogeographical reconstructions to assess the relative roles of environmental filtering and di...
www.nature.com
December 1, 2024 at 12:40 PM
Phylogenetic turnover of seed plants 🌱 at a global 🌐 and across phylogenetic scales: www.nature.com/articles/s41...
Game over, phylogeneticists! New DNA foundation model "Carbon" reconstructs the tree of life. 🙃 huggingface.co/spaces/Huggi...
May 19, 2026 at 11:26 PM
Game over, phylogeneticists! New DNA foundation model "Carbon" reconstructs the tree of life. 🙃 huggingface.co/spaces/Huggi...
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference
www.nature.com/articles/s41...
www.nature.com/articles/s41...
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference - Nature Methods
BEAST X advances Bayesian phylogenetic, phylogeographic and phylodynamic analysis by incorporating a broad range of complex models and leveraging advanced algorithms and techniques to boost statistica...
www.nature.com
July 7, 2025 at 6:25 PM
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The final Discussion Section for GEOL 431 Vertebrate Paleobiology involved recreating the amniote phylogenetic tree
May 13, 2025 at 1:25 PM
The final Discussion Section for GEOL 431 Vertebrate Paleobiology involved recreating the amniote phylogenetic tree
Hey look, it's a casual non-pterodactyloid pterosaur tree I did for pterosaur skulls during my PhD!
June 15, 2026 at 8:38 AM
Hey look, it's a casual non-pterodactyloid pterosaur tree I did for pterosaur skulls during my PhD!
Out late for #FossilFriday, it's our invited @annualreviews.bsky.social paper with @sarahlsheffield.bsky.social and @bigfacecats.bsky.social on why Phylogenetic Paleoecology is useful and how to do it.
doi.org/10.1146/annu...
doi.org/10.1146/annu...
A Practical Guide to Phylogenetic Paleoecology
The burgeoning field of phylogenetic paleoecology combines paleoecological data with hypotheses of phylogenetic relationships to tease apart the roles that ecology and relatedness both play in the evo...
doi.org
November 29, 2025 at 12:31 AM
Out late for #FossilFriday, it's our invited @annualreviews.bsky.social paper with @sarahlsheffield.bsky.social and @bigfacecats.bsky.social on why Phylogenetic Paleoecology is useful and how to do it.
doi.org/10.1146/annu...
doi.org/10.1146/annu...
A new method for trimming alignments in #phylogenomics — PhyIN. It identifies and trims regions with high phylogenetic discord. Able to trim well even on single loci — an advantage for gene tree/species tree studies. #evolbiol #phylogeny 🧪http://doi.org/10.7717/peerj.18504 Some backstory... 🧵
PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites
In phylogenomics, regions of low alignment reliability and high noise are typically trimmed from multiple sequence alignments before they are used in phylogenetic inference. I introduce a new trimming...
doi.org
December 6, 2024 at 12:56 AM
A new method for trimming alignments in #phylogenomics — PhyIN. It identifies and trims regions with high phylogenetic discord. Able to trim well even on single loci — an advantage for gene tree/species tree studies. #evolbiol #phylogeny 🧪http://doi.org/10.7717/peerj.18504 Some backstory... 🧵
Phylogenetic Tree Visualization Using Python
January 9, 2026 at 3:13 AM
Phylogenetic Tree Visualization Using Python
arguing from phylogenetic bracketing, do we think trilobites were delicious? 🤔
October 5, 2024 at 5:23 PM
arguing from phylogenetic bracketing, do we think trilobites were delicious? 🤔
Congratulations to lab member Gabi Alves Ferreira who lead us in this fun project! She modeled how range shifts of neotropical frogs with climate change will change phylogenetic diversity and endemism in the new communities. So great to see this published #ProudPI 💪🐸 www.nature.com/articles/s41...
Climate change is projected to shrink phylogenetic endemism of Neotropical frogs - Nature Communications
Climate change is a major threat to biodiversity. This study predicts that climate change will reshape Neotropical frog diversity, causing losses in phylogenetic diversity and phylogenetic endemism, w...
www.nature.com
April 19, 2025 at 3:57 PM
Congratulations to lab member Gabi Alves Ferreira who lead us in this fun project! She modeled how range shifts of neotropical frogs with climate change will change phylogenetic diversity and endemism in the new communities. So great to see this published #ProudPI 💪🐸 www.nature.com/articles/s41...
The new OrthoFinder paper is out now!
In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets
www.nature.com/articles/s41...
github.com/OrthoFinder/...
In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets
www.nature.com/articles/s41...
github.com/OrthoFinder/...
OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature Methods
The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.
www.nature.com
June 9, 2026 at 12:38 PM
The new OrthoFinder paper is out now!
In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets
www.nature.com/articles/s41...
github.com/OrthoFinder/...
In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets
www.nature.com/articles/s41...
github.com/OrthoFinder/...
I am recruiting Ph.D. students this cycle. Students interested in deep-sea fishes and phylogenetic comparative methods are an especially good fit.
May 18, 2026 at 3:47 PM
I am recruiting Ph.D. students this cycle. Students interested in deep-sea fishes and phylogenetic comparative methods are an especially good fit.
Abstract submitted -- another paper on heterodox phylogenetic hypotheses, fingers crossed!
July 1, 2025 at 4:39 PM
Abstract submitted -- another paper on heterodox phylogenetic hypotheses, fingers crossed!