𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
@basantakhakurel.bsky.social
वसन्त खकुरेल
PhD student at Ludwig Maximilians Universität München.
Phylogenetics | Bayesian statistics | Morphological Evolution | https://basantakhakurel.github.io/
(he/him)
PhD student at Ludwig Maximilians Universität München.
Phylogenetics | Bayesian statistics | Morphological Evolution | https://basantakhakurel.github.io/
(he/him)
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
I updated collegetables.info with latest IPEDS data, also added visualizations on graduation rates and "demographic cliff."
Check also the naive Bayesian #rstats collegetables.info/predict.html page that may help students find good options.
All free, open source, etc.
Check also the naive Bayesian #rstats collegetables.info/predict.html page that may help students find good options.
All free, open source, etc.
November 16, 2025 at 3:54 PM
I updated collegetables.info with latest IPEDS data, also added visualizations on graduation rates and "demographic cliff."
Check also the naive Bayesian #rstats collegetables.info/predict.html page that may help students find good options.
All free, open source, etc.
Check also the naive Bayesian #rstats collegetables.info/predict.html page that may help students find good options.
All free, open source, etc.
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
Agentic Coding For Scientists
A four-part series on using coding agents like Claude Code for scientific programming, covering fundamentals, workflows, best practices, and the human side of AI-assisted development.
matsen.group
November 13, 2025 at 5:08 PM
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
Check out this new paper in Systematic Biology! Aside from the author list including leaders in the field who happen to be some of my favorite scientists, this paper discusses * both * phylogeny inference incorporating continuous characters AND dicynodont evolution. How cool is that? 🧪
Incorporating continuous characters in joint estimation of dicynodont phylogeny
Abstract. Continuous characters have received comparatively little attention in Bayesian phylogenetic estimation. This is predominantly because they cannot
academic.oup.com
November 14, 2025 at 5:29 PM
Check out this new paper in Systematic Biology! Aside from the author list including leaders in the field who happen to be some of my favorite scientists, this paper discusses * both * phylogeny inference incorporating continuous characters AND dicynodont evolution. How cool is that? 🧪
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
Interested in using continuous traits for phylogenetic estimation? We took a hard look at this in a well-studied clade. There’s a lot of promise to these data, but still much work to do to be able to make full use of them
doi.org/10.1093/sysb...
doi.org/10.1093/sysb...
Validate User
doi.org
November 14, 2025 at 6:47 PM
Interested in using continuous traits for phylogenetic estimation? We took a hard look at this in a well-studied clade. There’s a lot of promise to these data, but still much work to do to be able to make full use of them
doi.org/10.1093/sysb...
doi.org/10.1093/sysb...
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
By shifting water to a higher elevation, the giant Three Gorges Dam caused the Earth to spin more slowly. www.wired.com/story/can-a-...
Can a Hydroelectric Dam Really Make the Days Longer?
By shifting water to a higher elevation, the giant Three Gorges Dam caused the Earth to spin more slowly.
www.wired.com
November 14, 2025 at 12:06 PM
By shifting water to a higher elevation, the giant Three Gorges Dam caused the Earth to spin more slowly. www.wired.com/story/can-a-...
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal!
November 14, 2025 at 12:41 PM
Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal!
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
If you're a #teacher interested in a great #openaccess write up on reading #phylogenetic trees, check out www.digitalatlasofancientlife.org/learn/system... created by @jonhendricks.bsky.social and Elizabeth Hermsen.
2.1 Reading Trees
Chapter contents: Systematics — 1. Taxonomy — 2. Phylogenetics —— 2.1 Reading trees ← —— 2.2 Building trees —— 2.3 Character mapping —— 2.4 Phylogenetic trees and classificationParts of a tree A phylo...
www.digitalatlasofancientlife.org
November 11, 2025 at 10:05 PM
If you're a #teacher interested in a great #openaccess write up on reading #phylogenetic trees, check out www.digitalatlasofancientlife.org/learn/system... created by @jonhendricks.bsky.social and Elizabeth Hermsen.
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
PhD position available in evolutionary genomics/bioinformatics (hoehnalab.github.io/job_adverts/...). Topic: analyzing gene expression evolution across several firefly species and linking expression changes to genomic architecture. The position is jointly supervised with @anaevolcatalan.bsky.social
hoehnalab.github.io
November 11, 2025 at 9:00 AM
PhD position available in evolutionary genomics/bioinformatics (hoehnalab.github.io/job_adverts/...). Topic: analyzing gene expression evolution across several firefly species and linking expression changes to genomic architecture. The position is jointly supervised with @anaevolcatalan.bsky.social
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
Glad to have this one out! As some of you might remember, I'd kicked around the idea for some time, but the inestimable @wrightam.bsky.social got it all pulled together properly. It's a first step - we still need to include likelihoods of stasis between first & … www.cambridge.org/core/journal...
Distinguishing punctuated and continuous-time models of character evolution for discrete characters and the implications for macroevolutionary theory | Paleobiology | Cambridge Core
Distinguishing punctuated and continuous-time models of character evolution for discrete characters and the implications for macroevolutionary theory
www.cambridge.org
November 8, 2025 at 6:07 AM
Glad to have this one out! As some of you might remember, I'd kicked around the idea for some time, but the inestimable @wrightam.bsky.social got it all pulled together properly. It's a first step - we still need to include likelihoods of stasis between first & … www.cambridge.org/core/journal...
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
Nice, intelligent review of my book "The Tree of Life" in Nature Ecology and Evolution by @bethanyjallen.bsky.social.
www.nature.com/articles/s41...
www.amazon.co.uk/Tree-Life-So...
Out in USA next Tuesday!
www.amazon.com/Tree-Life-So...
www.nature.com/articles/s41...
www.amazon.co.uk/Tree-Life-So...
Out in USA next Tuesday!
www.amazon.com/Tree-Life-So...
A beginner’s guide to tree thinking - Nature Ecology & Evolution
Nature Ecology & Evolution - A beginner’s guide to tree thinking
www.nature.com
November 5, 2025 at 12:08 PM
Nice, intelligent review of my book "The Tree of Life" in Nature Ecology and Evolution by @bethanyjallen.bsky.social.
www.nature.com/articles/s41...
www.amazon.co.uk/Tree-Life-So...
Out in USA next Tuesday!
www.amazon.com/Tree-Life-So...
www.nature.com/articles/s41...
www.amazon.co.uk/Tree-Life-So...
Out in USA next Tuesday!
www.amazon.com/Tree-Life-So...
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
🚨New paper out in Palaeontology! Check it out if you're interested morphological evolution, fossil phylogenetics, and macroevolution 🧪
"Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data"
"Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data"
Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data
Understanding the evolution and phylogenetic distribution of morphologic traits is fundamental to macroevolutionary research. Despite decades of major advances and key insights from molecular systema...
dx.doi.org
October 27, 2025 at 2:17 PM
🚨New paper out in Palaeontology! Check it out if you're interested morphological evolution, fossil phylogenetics, and macroevolution 🧪
"Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data"
"Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data"
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
The dark truth behind FormatMyPaper.com
Beware giving this site your unpublished data
Users noticed the website had fake testimonials and a domain name registered seemingly overnight.
https://ubadah.substack.com/p/beware-giving-this-site-your-unpublished\
October 24, 2025 at 12:11 AM
The dark truth behind FormatMyPaper.com
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
We call this hypotheses the 'Zarathustran hypothesis', following Nietzsche’s idea that the maintenance of life does not merely follow from conservation, but rather from constant renovation, movement, and expansion. 3/3
October 17, 2025 at 9:12 AM
We call this hypotheses the 'Zarathustran hypothesis', following Nietzsche’s idea that the maintenance of life does not merely follow from conservation, but rather from constant renovation, movement, and expansion. 3/3
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
I’m really happy to see Kat’s first dissertation chapter published! www.cambridge.org/core/journal...
Global evolutionary relationships of Devonian proetide trilobites | Journal of Paleontology | Cambridge Core
Global evolutionary relationships of Devonian proetide trilobites
www.cambridge.org
October 18, 2025 at 5:06 AM
I’m really happy to see Kat’s first dissertation chapter published! www.cambridge.org/core/journal...
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
Excited to share our new paper where we find that the rise, decline and fall of clades is not explained by the usual suspects (diversity-dependence, ecological opportunities) but rather by species' insidious loss of macroevolutionary fitness: www.nature.com/articles/s41... 1/3
Loss of macroevolutionary species fitness explains the rise and fall of clades - Nature Ecology & Evolution
The interplay between speciation and extinction rates shapes clade diversity dynamics. Using a novel phylogenetic model that includes living and fossil lineages, the authors estimate speciation and ex...
www.nature.com
October 17, 2025 at 9:12 AM
Excited to share our new paper where we find that the rise, decline and fall of clades is not explained by the usual suspects (diversity-dependence, ecological opportunities) but rather by species' insidious loss of macroevolutionary fitness: www.nature.com/articles/s41... 1/3
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
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 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
Our paper on perceptions of punctuated equilibrium - including suggestions for how to teach about this essential evolutionary concept - is now available online! doi.org/10.1017/pab....
Taking the temperature of punctuated equilibrium on its semicentennial | Paleobiology | Cambridge Core
Taking the temperature of punctuated equilibrium on its semicentennial
doi.org
September 30, 2025 at 5:11 PM
Our paper on perceptions of punctuated equilibrium - including suggestions for how to teach about this essential evolutionary concept - is now available online! doi.org/10.1017/pab....
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
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!
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
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
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
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
Practical Guide and Review of Fossil Tip-Dating in Phylogenetics https://pubmed.ncbi.nlm.nih.gov/40990492/
September 25, 2025 at 3:44 AM
Practical Guide and Review of Fossil Tip-Dating in Phylogenetics https://pubmed.ncbi.nlm.nih.gov/40990492/
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
Incredibly proud and also very emotional to see this new paper published in @systbiol.bsky.social. The study was lead by Pierre Cockx, who sadly passed away in July.
academic.oup.com/sysbio/advan...
academic.oup.com/sysbio/advan...
September 16, 2025 at 10:57 AM
Incredibly proud and also very emotional to see this new paper published in @systbiol.bsky.social. The study was lead by Pierre Cockx, who sadly passed away in July.
academic.oup.com/sysbio/advan...
academic.oup.com/sysbio/advan...
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
New from #BiologyLetters: Combining fossil taxa with and without morphological data improves dated phylogenetic analyses buff.ly/abJm5Zv | #Evolution #Palaeontology #Taxonomy
August 21, 2025 at 1:02 PM
New from #BiologyLetters: Combining fossil taxa with and without morphological data improves dated phylogenetic analyses buff.ly/abJm5Zv | #Evolution #Palaeontology #Taxonomy
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
I am recruiting a PhD student this application cycle to explore questions on the evolution of morphological variation and phylogenetics. I'm especially seeking folks interested in fossil marine inverts. Please reach out to me if interested! Portal opens Nov. 1 eeb.utoronto.ca/education/gr...
Admissions - Ecology & Evolutionary Biology
Resources For More Information Please contact: [email protected]
eeb.utoronto.ca
September 12, 2025 at 12:38 PM
I am recruiting a PhD student this application cycle to explore questions on the evolution of morphological variation and phylogenetics. I'm especially seeking folks interested in fossil marine inverts. Please reach out to me if interested! Portal opens Nov. 1 eeb.utoronto.ca/education/gr...
Reposted by 𝙱𝙰𝚂𝙰𝙽𝚃𝙰 𝙺𝙷𝙰𝙺𝚄𝚁𝙴𝙻
Excited to share a new paper! "Sorting of ancestral polymorphism and its impact on morphological phylogenetics and macroevolution". Part of some work I've been doing on modelling the evolution of polymorphic traits in fossil echinoderms.
academic.oup.com/evolut/advan...
academic.oup.com/evolut/advan...
Sorting of ancestral polymorphism and its impact on morphological phylogenetics and macroevolution
Abstract. Intraspecific phenotypic variation provides the basic substrate upon which the evolutionary processes that give rise to morphological innovation,
academic.oup.com
September 5, 2025 at 5:43 PM
Excited to share a new paper! "Sorting of ancestral polymorphism and its impact on morphological phylogenetics and macroevolution". Part of some work I've been doing on modelling the evolution of polymorphic traits in fossil echinoderms.
academic.oup.com/evolut/advan...
academic.oup.com/evolut/advan...