Jonathan Chang

Jonathan Chang

@jonathanchang.org

I work in the public sector. Volunteer work: macroevolution and the fish tree of life.

506 followers239 following15 posts

Jonathan Chang
@jonathanchang.org

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! (馃У1/3)

Jonathan Chang
@jonathanchang.org

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)

Jonathan Chang reposted

Tom Near
@tjnear.bsky.social

1/3 New preprint from #NearLab led by @chasedbrownstein.bsky.social Here we show species-rich freshwater fish adaptive radiations (notably cichlids, but also killifishes, pupfishes, and livebearers) were enabled by a shared mechanism: retained saltwater (marine salinity) tolerance

Jonathan Chang reposted

Dr. Elizabeth Carlen
@ecarlen.bsky.social

I am thrilled that this manuscript is now out in the world! If you saw my talk at #Evol2025 you may remember me discussing how religion, politics & war shape urban evolution & now you can read all about it here: www.nature.com/articles/s44...

nature.comLegacy effects of religion, politics and war on urban evolutionary biology - Nature CitiesCities affect biological evolution, but traditionally researchers focus on the biophysical influence of urban environments. Instead, this Review explores how the social processes of religion, politics...
Jonathan Chang
@jonathanchang.org

i think people are being too much of a doomer on the dire wolf story. if a few SNPs make a new species then think about how great it's going to be for alpha taxonomy. trillions of new species, just waiting to be described

Jonathan Chang
@jonathanchang.org

New blog post: create a triangle-based navigational mesh from hexagonal grids with the H3 library in R. Check out the step-by-step guide with code examples and apply it to your own spatial analyses. #RStats jonathanchang.org/blog/hexes-t...

jonathanchang.orgGenerating a triangular navigation mesh from H3 hexagons in RHow to create a triangular navigational mesh using global hexagonal grids from the H3 library. A worked example, based on the San Francisco Bay Area, demonstrates how to construct, visualize, and refi...
Jonathan Chang
@jonathanchang.org

Did you get an automated reminder that your review is due on Christmas? It's not an unpaid burden. Instead, it's an chance to get ahead in your career! Manuscript review is a key part of academic service and high-quality reviews reflect on your professionalism. 馃У(1/3)

Jonathan Chang
@jonathanchang.org

When everyone else is relaxing with their families for the holidays, the emails and other demands for your time are lessened. It's the perfect time to focus on your manuscripts to review, leaving a clean slate for the new year. (2/3)

Jonathan Chang
@jonathanchang.org

Finally: what about the editors and authors awaiting your feedback? What better Christmas gift to give your colleagues than a suggestion to cite more of your manuscripts? So the next time you get an automated review reminder on Christmas: run, don't walk, to this opportunity!

Jonathan Chang
@jonathanchang.org

Announcing version 0.6.0 of `tact`, an app for stochastic polytomy resolution on phylogenies using taxonomy. This version has no new features, but is updated for various dependency changes in the Python ecosystem. It may also be slightly faster due to using PyPy 3.10. (1/2)

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