iiinova — where your digital self keeps evolving

David Maddison @bembidion.bsky.social · 10/09/2026

Agreed that for teaching some things MacClade is much simpler. We added the Simplification system in Mesquite (see Simplification tab on the log window) specifically to allow one to make a simpler version for teaching. That won't reduce it to MacClade's simplicity, however.

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David Maddison @bembidion.bsky.social · 10/09/2026

Totally understand. I get confused by it too sometimes. We are trying to decrease the steepness of the learning curve, not only with the program, but by doing more how-to videos.

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David Maddison @bembidion.bsky.social · 10/09/2026

I love MacClade, of course. I am curious though as to whether you have tried Mesquite, which does almost all of the things MacClade did and so much more. Yes, it is much more complex, and at times confusing, but it has been getting better. I can't imagine myself going back to MacClade's limits.

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David Maddison @bembidion.bsky.social · 08/09/2026

I'm also very grateful to Mark Holder ( @mtholder.bsky.social) and Emily McTavish (@snacktavish.bsky.social) for their key roles in waking me up to the possibility it could be resurrected.

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David Maddison @bembidion.bsky.social · 08/09/2026

Thanks also to Maximillian Davensmith (Linux administrator here at Oregon State), who archived the code and data and provided it to Travis’s group.

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David Maddison @bembidion.bsky.social · 08/09/2026

The Tree of Life Web Project is back online! tolweb.org Thanks to Travis Wheeler (@wheelerlab.org), Danny Mandel, and Andrew Lenards, the original programmers for ToLWeb, for retooling the code to work on a modern OS! It is hard for me to believe it lives again.

tolweb.org

Tree of Life Web Project

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David Maddison @bembidion.bsky.social · 09/03/2026

Arden Smith and I are writing a graphic novel about the course, and we published a preview of the novel alongside the scientific paper: ssbbulletin.org/article/id/6...

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David Maddison @bembidion.bsky.social · 09/03/2026

One of my favorite projects ever about species discovery in beetles came to fruition a week and a half ago. The paper that reported the research of my Discovering Insect Species course was published in Bulletin of the Society of Systematic Biologists, at ssbbulletin.org/article/id/5...

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David Maddison @bembidion.bsky.social · 03/11/2025

After almost 30 years, the Tree of Life Web Project has been retired as an actively growing site. It will be unavailable until we can build a static site that contains its final content. More details at subulatepalpomere.com/2025/11/02/t...

subulatepalpomere.com

The Passing of the Tree of Life Web Project

The Tree of Life Web Project began its journey almost 40 years ago, and was formally announced in early 1996. It has served thousands of pages of information about the evolutionary tree of life and…

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Reposted by David Maddison

Wayne Maddison @waynemaddison.bsky.social · 25/10/2025

Mesquite now has a built-in adventure game, which you may be able to find if you say the correct magic word. You can also build your own versions of the game. 🤔

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Reposted by David Maddison

Wayne Maddison @waynemaddison.bsky.social · 25/10/2025

Mesquite 4.02 update released! It fixes a few bugs and adds Codon Alignment and various other improvements. Also, much faster with genomics files with 1000s of loci. www.mesquiteproject.org 🧪 #evolbio @bembidion.bsky.social

Mesquite's two icons, one against a black background, and one against a sun on a sky blue background.

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David Maddison @bembidion.bsky.social · 09/09/2025

I miss its youth too, Ainsley. It still exists (tolweb.org/tree/), but has been dormant for over a decade. I started the project in 1994, with Wayne's (@waynemaddison.bsky.social) help, and then led its growth until I no longer had the resources, and other projects (e.g., EOL) captured the moment.

tolweb.org

Tree of Life Web Project

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Reposted by David Maddison

Oregon State University Botany and Plant Pathology @osubpp.bsky.social · 06/08/2025

The Department of Botany and Plant Pathology at Oregon State University is Hiring! We are searching for a Director of the Oregon State University Herbarium and applications are welcomed at the ranks of assistant, associate, or full professor.

Department of Botany and Plant Pathology at Oregon State University is hiring a Directory of the Herbarium

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David Maddison @bembidion.bsky.social · 10/07/2025

Here's our post for a previous Mesquite video (follow the linked list back in time!). bsky.app/profile/waynemaddison.bsky.social/post/3ltijw3bwms2j

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David Maddison @bembidion.bsky.social · 10/07/2025

A two-minute video showing how to export geographic localities and trees from Mesquite 4 into Google Earth. youtu.be/tdOVmR122ts 🧪 #evolbio

youtu.be

Exporting to Google Earth

YouTube video by Mesquite ProjectTeam

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David Maddison @bembidion.bsky.social · 01/07/2025

A stained-glass piece of mine from a few years ago. #Canada

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David Maddison @bembidion.bsky.social · 28/06/2025

A short video with a Mesquite tip showing how to display chronograms from a BEAST divergence dating analysis. youtu.be/CvxX8GauqLo 🧪 #evolbio @waynemaddison.bsky.social

youtu.be

Displaying Chronograms in Mesquite 4

YouTube video by Mesquite ProjectTeam

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David Maddison @bembidion.bsky.social · 28/06/2025

Celebrating the release of Mesquite 4!

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David Maddison @bembidion.bsky.social · 02/03/2025

A stairwell as musical instrument. The sound is much more striking and visceral in person.

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David Maddison @bembidion.bsky.social · 27/01/2025

It was in that volume of 1802 that Latreille gave the generic name to my beloved beetles of the genus Bembidion. Perhaps this coin went through his hands at some point that year. [The coin’s year is marked as 11, as it was the 11th year of the French Republican Calendar.]

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David Maddison @bembidion.bsky.social · 27/01/2025

And here is a French coin that was minted in September 1802, a couple of months before Pierre André Latreille's third volume of “Histoire naturelle, générale et particulière des crustacés et des insects” was published.

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David Maddison @bembidion.bsky.social · 27/01/2025

And perhaps Charles Darwin had these coins in his pocket when his On the Origin of Species was published.

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David Maddison @bembidion.bsky.social · 27/01/2025

Here are two Swedish coins from 1758, which I recently acquired. I like to think that there is a possibility, however slim, that Carl Linnaeus had one of these in his pocket on the day that the 10th edition of Systema Naturae (the starting point of zoological nomenclature) was published.

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David Maddison @bembidion.bsky.social · 07/12/2024

Hi Darren, I'd love to be added to your starter pack! Thanks, David

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