iiinova — where your digital self keeps evolving

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Peter Wagner (a Real Dr., not a surgeon-barber/body-tech/golfer) @peterjwagner3.bsky.social · 05/10/2026

For a moment, I thought this was an Ophileta fossil....

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Nico Mongiardino Koch @nmkphylo.bsky.social · 01/10/2026

I am looking for graduate students to join my lab in Fall 2027. If your interests lie within the realms of phylogenetics, macroevolution, and/or invertebrate biodiversity please reach out to me!!

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Paul Z. Barrett PhD @nimravenous.bsky.social · 09/09/2026

Happy to announce the publication of our article in Nature Ecology & Evolution on adaptive zone evolution in terrestrial mammal carnivores. Over the next few days, I’ll share the major results—and by extension, take you on a tour of carnivore evolution. (rdcu.be/6okG1hVhvtHa) 1/n

rdcu.be

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 28/08/2026

ah fuck there's a typo--should be brpetrucci not brpetrucc!!! Here's the correct link brpetrucci.github.io/tutorials/sr.... Thank you for sharing! Let me know if I can answer any questions!!

brpetrucci.github.io

Inferring budding phylogenetic trees with the stratigraphic-range fossilized birth-death model

An SRFBD tutorial using BEAST2 and paleobuddy, for my 2026 palaeoverse lecture.

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/08/2026

Please send me a message or e-mail if you have comments or questions about any of these. Would love to help!

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/08/2026

Thank you so much who came to watch my Palaeoverse lecture! Here's a link for anyone that's interested and couldn't catch it live. www.youtube.com/watch?v=JBfi... Also, if you'd like to go through the tutorial I worked through during the lecture: brpetrucc.github.io/tutorials/sr...

youtube.com

Palaeoverse Lecture Series: Bruno do Rosario Petrucci - Budding phylogenetic trees: inference with..

YouTube video by Palaeoverse

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Palaeoverse @palaeoverse.bsky.social · 19/08/2026

🚨Palaeoverse Lecture Series🚨 🗓️27th August 2026, 15:00 UTC🗓️ Join us next Thursday for a talk by @brpetrucci.bsky.social from Iowa State University on “Budding phylogenetic trees: inference with BEAST2 and post-processing with paleobuddy”. Sign up here: palaeoverse.org/training/lec...

A flyer advertising Bruno do Rosario Petrucci's upcoming Palaeoverse Lecture Series talk on the 27th August 15:00 UTC entitled Budding phylogenetic trees: inference with BEAST2 and post-processing with paleobuddy. Bruno is pictured next to a laptop showing a budding phylogeny.

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 29/07/2026

Hope to see you all on August 27th at 15:00UTC (10:00AM Central) for my @palaeoverse.bsky.social lecture! Details on how to register here: palaeoverse.org/events/ I'll be talking about inferring and dealing with budding phylogenetic trees, including a full tutorial!! Hope to see you all there!

palaeoverse.org

Palaeoverse

A community-driven initiative advancing open science in palaeontology through shared tools, training, and resources.

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Tracy Heath @trayc7.bsky.social · 23/06/2026

I’m recruiting a PhD student to join our lab in the fall of 2027. If you’re excited about phylogenetics, comp bio, paleobiology, stats theory, macroevolution, etc. please get in touch! Folks at #Evol2026, you can talk to @brpetrucci.bsky.social & @sigournie.bsky.social to learn more about our lab

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 21/06/2026

#Evol2026 has been a blast!! Hope to see some of you mutuals at my talk this evening. Let’s talk about dogs and fossils and dog fossils 😎

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 17/06/2026

Hope to see y'all at #Evol2026! I'll be talking about my simulation tests of cutting-edge fossilized birth-death models, and what we can learn from the Canidae phylogeny using these models. Come through! It'll be on Sunday (June 21st) at 5:15PM, room 22. Last talk first day 🤙

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 21/05/2026

There's still time to catch our symposium if you run! Come through!!

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Society for the Study of Evolution @sse-evolution.bsky.social · 19/05/2026

Don't miss the virtual Research Synthesis Working Group's symposium at #Evol2026 this week! The symposium is in two sessions across Thursday and Friday. Topic: "Cross disciplinary approaches for understanding budding speciation"

Text: Virtual Evolution 2026, Society for the Study of Evolution, Research Synthesis Working Group Symposium, Cross disciplinary approaches for understanding budding speciation. Session 1: May 21, 6:30 PM EDT, Session 2: May 22, 9:00 AM EDT.

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 19/05/2026

Come watch our symposium this Thursday and Friday at the virtual @evolmtg.bsky.social!! it’ll be a hoot and a half

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Society for the Study of Evolution @sse-evolution.bsky.social · 28/04/2026

Congratulations to our 2026 Huxley Award recipient, Matheus Januario Lopes de Sousa, for the educational resource: “evolved: an open-source R package designed for graduate and advanced undergraduate instruction in evolutionary biology”! Read more: shorturl.at/1ZdFE@mjanua...

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Casey Dunn @caseywdunn.bsky.social · 28/08/2025

I hope to take a PhD student in 2026 to study siphonophores. Please reach out if you are interested in applying this fall. For examples of recent lab projects see www.sciencedirect.com/science/arti... and academic.oup.com/gbe/article/...

sciencedirect.com

Population genomics of a sailing siphonophore reveals genetic structure in the open ocean

The open ocean is a vast, highly connected environment, and the organisms found there have been hypothesized to represent massive, well-mixed populati…

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Joe Spring @joespring.bsky.social · 04/08/2025

Once upon a time, large bone-crushing dogs roamed across our continent. @restingdinoface.bsky.social takes a colorful look back at the lives of the successful carnivores. www.smithsonianmag.com/science-natu...

smithsonianmag.com

What Happened to the Bone-Crushing Dogs That Once Hunted Across North America?

Before going extinct roughly two million years ago, canids known as borophagines took down and consumed much larger prey

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 31/07/2025

Going from reading almost exclusively simulation studies and theory papers to almost exclusively canid systematics/fossil description papers has been an interesting experience! Anyway look at this cool paper about Plio-Pleistocene European foxes! www.sciencedirect.com/science/arti...

sciencedirect.com

Unraveling the fossil record of foxes: An updated review on the Plio-Pleistocene Vulpes spp. from Europe

Fossil foxes, genus Vulpes, are known since the Late Miocene of North America and the Old World but their record is utterly scarce, fragmentary, and r…

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 29/07/2025

They're listening to my private conversations somehow, I'm certain of it. Holy crap I'm excited 🤩

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April Wright @wrightam.bsky.social · 15/07/2025

Updated preprint! Thanks to suggestions from reviewers, we have some new insights on using continuous traits in phylogenetic estimation. And a lot more about dicynodont taxonomy. Seriously, google dicynodonts and tell me you don't want to know what's happening there www.biorxiv.org/content/10.1...

biorxiv.org

Incorporating continuous characters in joint estimation of dicynodont phylogeny

Continuous characters have received comparatively little attention in Bayesian phylogenetic estimation. This is predominantly because they cannot be modeled by a standard phylogenetic Q-matrix approac...

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Reposted by Bruno do Rosario Petrucci

Jasmine 🌌🔭 @astrojaz.bsky.social · 04/07/2025

here are some space fireworks, happy 4th of july 🎆🌌

The brilliant tapestry of young stars flaring to life resemble a glittering fireworks display in this Hubble Space Telescope archival image.

The sparkling centerpiece of this fireworks show is a giant cluster of thousands of stars.

The nebula reveals a landscape of pillars, ridges, and valleys. The pillars, composed of dense gas and thought to be incubators for new stars, are a few light-years tall and point to the central star cluster. Other dense regions surround the pillars, including reddish-brown filaments of gas and dust. The red dots scattered throughout the landscape are a rich population of newly forming stars still wrapped in their gas-and-dust cocoons. The brilliant blue stars seen throughout the image are mostly foreground stars.

The red colors in the nebulosity represent hydrogen; the bluish-green hues are predominantly oxygen.

Caption credit: NASA

$A globular cluster that looks like a very dense, ball-shaped collection of many shining stars in colors of white, yellow-orange, and blue. Some stars appear a bit larger and brighter than others, with the brightest having faint cross-shaped diffraction spikes. The cluster’s stars are scattered mostly uniformly, with their density increasing toward the cluster’s core where they merge into a strong, bright-white glow.$

This image of Cassiopeia A resembles a disk of electric light with red clouds, glowing white streaks, red and orange flames, and an area near the center of the remnant resembling a somewhat circular region of green lightning. X-rays from Chandra are blue and reveal hot gas, mostly from supernova debris from the destroyed star, and include elements like silicon and iron. X-rays are also present as thin arcs in the outer regions of the remnant. Infrared data from Webb is red, green, and blue. Webb highlights infrared emission from dust that is warmed up because it is embedded in the hot gas seen by Chandra, and from much cooler supernova debris. Hubble data shows a multitude of stars that permeate the field of view.

A prominent, eight-pointed star shines in bright white at the center of this image. A clumpy cloud of material surrounds this central star, with more material above and below than on the sides, in some places allowing background stars to peek through. The cloud material is a dark yellow closer to the star, and turns a pinkish purple at its outer edges. Combined together, the central star and its cloud resemble the delicate petals of a cherry blossom. The black background features many smaller white stars scattered throughout.

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 03/07/2025

Having to write an R script to write another script makes me feel like I am in limbo

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Katie Mack @astrokatie.com · 19/06/2025

When a chatbot gets something wrong, it’s not because it made an error. It’s because on that roll of the dice, it happened to string together a group of words that, when read by a human, represents something false. But it was working entirely as designed. It was supposed to make a sentence & it did.

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Katie Mack @astrokatie.com · 19/06/2025

Chatbots — LLMs — do not know facts and are not designed to be able to accurately answer factual questions. They are designed to find and mimic patterns of words, probabilistically. When they’re “right” it’s because correct things are often written down, so those patterns are frequent. That’s all.

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 30/06/2025

It’s great to see researchers exploring the possibilities of learning about current extinction from past extinction patterns. That was my initial idea for my PhD, and I have deviated from that pretty hard since then, but I still hope to get on that wagon later in my career!

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 30/06/2025

Very cool paper! Glad to see Bluesky helping me find new cool science hot off the press 🍞

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Paul D. Taylor @nhmbryozoa.bsky.social · 30/06/2025

#MolluscMonday Ordovician orthoconic nautiloid in a paving stone at Hampton Court Palace. The section intersects the siphuncular tube on the right hand-side just below the living chamber.

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Anthony (Tony) J. Martin @ichnologist.bsky.social · 22/05/2025

Excellent analysis & commentary by @johnhawks.net on 2024 study of 1.5 mya fossil hominin footprints in Kenya showing 2 different species of humans (Homo erectus & Paranthropus boisei) walking in the same direction, & possibly separated by only a few hours. Ichnology FTW! 🧪🐾🪨

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 30/06/2025

For those who followed me without knowing me (thank you and nice to meet you!), it’s very important for you to know that I am unhealthily obsessed with horseshoe crabs. I don’t even study them at all, and they’ve just been my favorite animal since I found out they existed. They’re the coolest!

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

Thank you! Would love to talk more about it any time!!

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

13/13 And that's that! Here's the full talk. I'll record a longer, higher quality version later, and post it here with a more detailed rundown. And of course I'll let you all know when the paper is published! Lots I still want to do for this project. Stay tuned! youtu.be/aS31GnXh3ec

youtu.be

Inferring a complete phylogenetic tree of Canidae under the SRFBD process - Evolution 2025

YouTube video by Bruno do Rosario Petrucci

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

12/13 I'd love to sit here and say "yes, this easier model provides reasonable trees, keep using it!", but SRFBD is the only way to truly accommodate for this data. I think it's worth the implementation challenge, and that it is the future of fossil phylogenetics. And look at this beautiful tree!

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

11/13 We need simulations to be sure of which model is more accurate, but the fact that we can identify specific model violations and connect them to biases in our estimates is concerning. We tried a different workaround than usual for FBD specimen, and unfortunately it doesn't seem to have helped!

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

10/13 This, together with the fact that we are not using all the samples for each of our species, might be related to why we estimate lower fossil sampling rates and higher speciation rates with FBD specimen. This leads to younger estimates of divergence times.

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

9/13 While the first specimen of Epicyon haydeni is correctly placed as a sampled ancestor of the last, the opposite is true for Epicyon saevus. They're tips, and at the same time! Compare that to the same node in our SRFBD tree and you can see the issue.

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

8/13 So the model is telling us Archaeocyon is a canine! Very interesting, and something to look into. We do need to talk about where the FBDS workaround we did (using both the youngest and oldest specimens for a given species) fails. In the MCC tree using both specimens, we see some of this:

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

7/13 A cool example of where they agree: both models estimate a really low posterior probability (<0.005) of the monophyly of Borophaginae. The monophyly of Borophaginae minus Archaeocyon (the first-diverging genus), however, is pretty likely. So is the monophyly of (Archaeocyon, Caninae).

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

6/13 There's no good way to summarize budding trees currently, so to compare the trees I made MCC trees from a modified posterior sample, removing the first specimen of each tree. So this is a tree the way you're used to: one tip per species. You can see they're pretty similar (RF-distance: 0.19)

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

5/13 A limited implementation of SRFBD (allowing for budding speciation only) is implemented in BEAST2 as part of the sRanges package. Check out the package: shorturl.at/nOncC And the preprint: shorturl.at/fzObi I used BEAST2 to do two combined-evidence analyses to compare FBD specimen and SRFBD.

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

4/13 The stratigraphic-range FBD (SRFBD) process corrects these issues by explicitly accounting for taxonomy. Here, the data input are stratigraphic ranges, not individual fossil specimens. Then we can build a phylogenetic tree using all our data, and it even allows for budding speciation!

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

3/13 FBD assumes that each specimen is an independent sampling event, which is violated if you use multiple specimens per species. But if we use just one for a species that has multiple specimens (e.g. most canids), we bias divergence times since we ignore the uncertainty on each specimen

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

2/13 The problem: estimating a complete (i.e. including fossil species) phylogenetic tree of Canidae is challenging with the FBD process, because FBD is a taxonomy-independent model. Like many paleontological datasets, the canid fossil record is structured through a filter of taxonomy.

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 27/06/2025

1/13 Time to talk about dogs and fossilized birth-death models! Here is a quick run-down of my #Evol2025 talk. 🧵

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Bruno do Rosario Petrucci @brpetrucci.bsky.social · 25/06/2025

Thank you so much to all the new and old friends I had the pleasure of speaking to at #Evol2025. Hope I can establish lots of new collaborations and, even more importantly, new connections with these talented folks. See y’all in Cleveland!!

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Nadine, Hunter of Rocks @nadwgab.bsky.social · 11/10/2024

A horseshoe crab and its final footprints preserved in 149.4 million year old limestone from Solnhofen, Germany 😢 On display in the Bürgermeister-Müller-Museum #fossils #FossilFriday #geology ⚒️🧪

A beige limestone slab on display in a glass case. It has an impression of a horseshoe crab and a trail of its footprints.

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