Evolutionary biologist, R developer, & occasional heterodox. Tweets mostly about phylogenetics... but sometimes speech, the academy, politics, & COVID.
Joined May 2013
- Tweets 5,863
- Following 1,508
- Followers 10,119
- Likes 6,173
1,956 Photos and videos
Pinned Tweet
27 May 2022
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This is a prototype that should be treated with extreme caution, but here's a discrete-character-dependent multi-θ Ornstein-Uhlenbeck model for #phytools: blog.phytools.org/2026/06/a-….
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Simulating & visualizing a discrete-character-dependent multi-regime OU process on a phylogenetic tree using #phytools: blog.phytools.org/2026/06/vi….
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Ancestral state estimation using the discretized diffusion approximation in #phytools with bounded_bm > ancr: blog.phytools.org/2026/06/an….
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A not-so-old #phytools method that I'd kind of forgotten about... S3 generic plotting of the "fastAnc" object class: blog.phytools.org/2026/06/ge….
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This is an older #phytools plotting method, but still kind of fun - - an ANSI text phylogeny simulator in R: blog.phytools.org/2026/06/an….
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This post to the #phytools blog is not super interesting... it just shows how a discrete approximation can be used to compute the likelihood under OU as well as BM, which DOES have some interesting use-cases (just not any I actually explore in the post): blog.phytools.org/2026/06/co….
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May 12
If anyone's interested, I just posted about accurate estimation of shape parameter α for Γ-distributed variation in the rate of discrete character evolution by edge using #phytools: blog.phytools.org/2026/05/es….
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Apr 22
With various colleagues including @lukejharmon I just published a new pre-print to @biorxivpreprint entitled "Unlocking a flexible set of phylogenetic models for discrete and continuous trait evolution using discretized stochastic diffusion." doi.org/10.64898/2026.04.20.… 1/7
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Apr 22
... and a discrete-character-dependent multi-trend trended Brownian model, among other evolutionary scenarios. 6/7
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Apr 22
I've been blogging (at blog.phytools.org) and speaking about this project for a while, but please check out our new pre-print here & let me know what you think: doi.org/10.64898/2026.04.20.…. Thanks! 7/7
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16 Oct 2025
Can't wait to be able to check out this fun documentary staring my friends & colleagues @lukejharmon & @thesnailhunter_ (Christine Parent) "Snail Hunters (Official Trailer)" youtu.be/0qiAMNMxrJU?si=ugFW… via @YouTube
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2 Oct 2025
The Biology Dept. @UMassBoston is searching for an Asst. Professor in "Microbial Ecology" (but 'microbial' is the operative word -- applicants studying evolution in microbial systems are also encouraged).
For more info or to apply: employmentopportunities.umb.….
Please share/RT.
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29 Sep 2025
Friends, colleagues, & other followers. I'm captaining a team in the Ride for Food '25 to raise money for Pete & Andy's Pantry in Rhode Island & no donation to our efforts is too small. To support us, please visit the team page here: ride.threesquaresne.org/team…. Thank you!!
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25 Sep 2025
The #phytools R package has a new version on CRAN (cran.r-project.org/package=p…) with various new models & updates, including.... 1/9
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25 Sep 2025
New simulator functions for absorbing bounded Brownian motion (sim.absorbing), Brownian motion with reflective bounds (sim.reflective), and multi-trend trended Brownian evolution (sim.multiTrend, blog.phytools.org/2025/07/a-…). 8/9
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25 Sep 2025
For a more compact summary with all updates, check out my blog (blog.phytools.org), where you can also stay tuned for other new #phytools updates & features. 9/9
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