Evolutionary biologist, R developer, & occasional heterodox. Tweets mostly about phylogenetics... but sometimes speech, the academy, politics, & COVID.
Providence, Rhode Island
Joined May 2013
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My department at UMass Boston is searching for an Assistant Professor of Biology in the area of plant ecology &/or evolution. Please contact me with any questions, share widely, and check out the job ad here: employmentopportunities.umb.….
IMO, this is the most significant paper I've written (with various colleagues, incl. @lukejharmon) in at least 10 years, if not my entire career.
After addressing some reviewer feedback, I just posted a new version to @biorxivpreprint.
Check it out: doi.org/10.64898/2026.04.20.….
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
#phytools::fitmultiOU vs. stochastic mapping + OUwie... a small experiment, but a strong case for joint continuous/discrete character modelling: blog.phytools.org/2026/08/a-….
Stochastic character mapping under the threshold model from evolutionary quantitative genetics using #phytools: blog.phytools.org/2026/07/st….
Comparing a discrete character dependent multi-regime OU joint model in #phytools to OUwie: blog.phytools.org/2026/07/co….
Today I was reminded of this post from the #phytools blog archive: "Fitting a Pagel '94 type model to test the hypothesis that the rate of evolution in one discrete character (with any number of levels) depends on the state of another." blog.phytools.org/2023/12/fi…
More on a discrete character dependent multi-optimum OU model in #phytools: blog.phytools.org/2026/07/mo….
Today on my blog -- null model for discrete character dependent multi-θ Ornstein-Uhlenbeck model in #phytools: blog.phytools.org/2026/07/nu…. 1/2
For more on this model, check out my prior post here: xitter.cf/phytools_liam/status/2…. 2/2
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-….
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-….
Simulating & visualizing a discrete-character-dependent multi-regime OU process on a phylogenetic tree using #phytools: blog.phytools.org/2026/06/vi….
Ancestral state estimation using the discretized diffusion approximation in #phytools with bounded_bm > ancr: blog.phytools.org/2026/06/an….
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….
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….
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….
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….
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
... and a discrete-character-dependent multi-trend trended Brownian model, among other evolutionary scenarios. 6/7
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