@chang_jon

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

 Los Angeles
jonathanchang.org
Joined November 2008
  • Tweets2K
  • Following487
  • Followers1.3K
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never leaving this site (because i'm a sicko) but feel free to follow me on other websites too
@jonathanchang.org

ALT @jonathanchang.org

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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)
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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)
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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
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Jonathan Chang, PhD retweeted
Shelly Gaynor@ShellyGaynorOct 9
Excited to share this preprint: biorxiv.org/content/10.64898…

All detectable ancient whole-genome duplications involve hybridization

Whole-genome duplication (WGD), or polyploidy, is a major evolutionary force throughout the tree of life. Ancient WGDs are commonly inferred from the distribution of synonymous substitutions per...

biorxiv.org
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Jonathan Chang, PhD retweeted
Chase Brownstein@ChaseBrownsteinSep 11
🚨🚨 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.…
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have you ever had the late night desire to read Phyletic Relationships of Living Sharks and Rays by Compagno
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we should bring back paying for groceries by writing checks right in the checkout lane
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Jonathan Chang, PhD retweeted
Haoran Cai@Haoran_CaiJun 25
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…

Persistent selection on size explains micro- and macroevolutionary alignments in fly wings | PNAS

The alignment among mutational variance (M), standing genetic variance (G), and macroevolutionary divergence (R) in Drosophila wing shape poses a r...

pnas.org
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fibermaxxing has gone too far. why does AT&T keep saying I need to upgrade my fiber
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Diversification dynamics in the global radiation of gobies academic.oup.com/sysbio/adva…

Diversification Dynamics in the Global Radiation of Gobies

Abstract. The pace of evolutionary diversification varies among groups, between environments, and over geologic timescales. Radiations may be linked to phe

academic.oup.com
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"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...
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...to provide its model with the required information. Let us never deceive ourselves. The truth is a powerful weapon. We know how we overwhelmed the competition. LLaMA knows, too. We did it with wealth."
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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
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my intrusive thoughts:
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The first half of Apple TV’s The Gorge is actually a pretty good rom-com setup
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“Why were fossils on my mind? When aren’t fossils on YOUR mind?”
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Jonathan Chang, PhD retweeted
Emily Carr@EmilyCarr4228 May 2025
The first chapter of my dissertation is out! Repeated and widespread evolution of biofluorescence in marine fishes @Karly_Cohen @Lampichthys @FintasticFishes @jmhuiee nature.com/articles/s41467-0…
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Jonathan Chang, PhD retweeted
Renata Pirani@PiraniRenata30 Apr 2025
📢 New paper alert! Our latest study reveals the genetic basis of dewlap color in Anolis apletophallus! 📄 Check it out: rdcu.be/ej4L6 Post at Nature communication: communities.springernature.c… @EvoLoganLab @solracariasm @UNRScience @stri_panama #Anoles #Evolution
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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
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this is why the padres won't win the nl west
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