I work in the healthcare sector. Volunteer work: macroevolution and the fish tree of life
Los Angeles
Joined November 2008
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never leaving this site (because i'm a sicko) but feel free to follow me on other websites too
ALT @jonathanchang.org
I'm pleased to announce version 0.4.0 of `fishtree`, an R package for downloading phylogenies, taxonomies, and diversification rates from the Fish Tree of Life.
It's the first update since 2021, and `fishtree` has been downloaded over 40,000 times. Thank you! 🧵 1/4
The website has also been rebuilt using more modern infrastructure, and should load more quickly on slow connections. Pages for large groups now summarize their subgroups, and a bug has been fixed for certain species where their tip rates were not available. 3/4
You'll need to start naming taxa with `taxon = ` instead of `rank = `. The old argument will still work (with a warning) until fishtree 1.0.
`fishtree` is maintained on a volunteer, best-effort basis. For more information, check out the docs: fishtree.fishtreeoflife.org 4/4
I'm pleased to announce version 1.0 of `tact`, an app for stochastic polytomy resolution on phylogenies using taxonomy.
A decade after the first line of code, scientists are still using `tact` to build complete trees of fish, termites, magnoliids, and more. Thank you! (🧵1/3)
This release is much faster: adding ~10,000 species to a fish phylogeny now takes under a minute instead of 8, about 9x faster.
You can also make many replicate trees in parallel with `--replicates` and `--cores`, and use `--seed` to make runs reproducible. (2/3)
Installation is easier too: `pipx install tact` is now the recommended method, and Docker is still available.
The `tact` software is maintained on a volunteer, best-effort basis. For more information, check out the website: tact.jonathanchang.org
Jonathan Chang, PhD retweeted
Excited to share this preprint: biorxiv.org/content/10.64898…
Jonathan Chang, PhD retweeted
🚨🚨 1. New preprint! We examine whether the diversity of transcontinental freshwater fish radiations, such as killifishes and cichlids, might be driven by marine ancestry in the aftermath of an asteroid impact! #biology #science #fishes
doi.org/10.64898/2026.09.04.…
have you ever had the late night desire to read Phyletic Relationships of Living Sharks and Rays by Compagno
Jonathan Chang, PhD retweeted
Why does fly wing evolution follow "lines of least resistance"—but move orders of magnitude slower than expected? My new paper @PNASNews offers a simple solution. Excited to share the low dimensional selection model of micro- & macroevolutionary alignment!
pnas.org/doi/full/10.1073/pn…
Diversification dynamics in the global radiation of gobies academic.oup.com/sysbio/adva…
"LLaMA, unfortunately, had a master whose resources were poor, one who could not elevate a frontier model to the sublime peaks of reasoning that are a model's right. LLaMA will see a certain element of truth in this. Meta couldn't afford the most efficient data brokers...
i'm devastated that the sole professional skill that I learned during my PhD (diagnosing and fixing linker errors) can now be easily done by AI
