iiinova — where your digital self keeps evolving

Reposted by Chase Brownstein

Tom Near @tjnear.bsky.social · 08/10/2026

2/7 There are 27 living species of sturgeons and every one is imperiled. Taxonomy of genera Acipenser and Huso is paraphyletic in every phylogenetic study for the past 28 years, across molecular and morphological datasets. In 2025, we proposed to fix this, elevating genus Sinotsturio from synonymy

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Reposted by Chase Brownstein

Tom Near @tjnear.bsky.social · 08/10/2026

🧵1/7 New from #NearLab Paraphyletic classification and its consequences for the world’s most endangered fishes🐟 Sturgeons (Acipenseridae) are classified in a way known to be phylogenetically wrong for 28 years. It's time to fix it getting it right matters for conservation, not just taxonomy

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Chase Brownstein @chasedbrownstein.bsky.social · 11/09/2026

🚨🚨 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! Retained salinity tolerance explains their biogeography and diversity!

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Chase Brownstein @chasedbrownstein.bsky.social · 10/09/2026

🎵 When n = 3, then it's testable to me! 🎶

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Reposted by Chase Brownstein

Liam U. Taylor @liamtaylor.bsky.social · 08/09/2026

The world's best mathematicians constantly trying to explain to the world's greediest computer scientists that solving the problem wasn't the actual point is almost, almost, almost funny

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

Thanks to a ton of folks! First and foremost my advisor @tjnear.bsky.social , as well as coauthors Liandong Yang and Alex Dornburg! A huge thanks as well to Yale, the Yale Peabody Museum, and our department for support!

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

12/12 These two complementary investigations demonstrate, and in an immediately observable manner, that our ability to reconstruct the Tree of Life has been heavily influenced by biological factors and deep-time events. Uncertainty is our ally in understanding the past.

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

11/12 ... the common ancestor living gars is estimated to be 5-20 million years old. What this means is that, without fossil evidence, we might not ever reliably figure out how old some clades are.

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

10/12 What's more, when you exclude calibrations from fossils on the ages of living fossil lineages themselves, those ages are 80 million years younger! We have fossil gars from ~100 million years ago in Africa, but when you exclude this evidence...

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

9/12 maybe our models cannot easily accommodate this disparity. To test this, we can ask whether the ages we estimate for fishes change when living fossils are included or excluded. They do! When living fossils are excluded, teleosts and ray-fins are 50-70 MILLION years younger!

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

8/12 We showed these 'living fossils' have exceptionally slow rates of molecular evolution in 2024, but the problem is, their closest relatives, the 35 thousand teleost fishes, have the fastest rates. We use rates of change to estimate absolute age, so...

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

7/12 But what about time? If extrinsic events in time can stop us from understanding evolutionary relationships, can intrinsic biological factors stop us from understanding WHEN clades originated? We go to 'living fossil' fishes for the answer! Enter gars and sturgeon...

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

6/12 The answer is yes! We see an obvious drop in statistical support for relationships ACROSS jawed vertebrates right at the date of the asteroid impact. The uncertainty is telling us something happened! The Chixculub asteroid etched its signature into our DNA.

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

5/12 The thinking goes that this event, by killing 75% of species, opened up opportunity for new species to emerge into restructuring ecosystems. Survivors diversified so fast that we can't figure out how they are related. But is this pattern discernible across jawed verts?

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

4/12 In many different jawed vertebrate clades with uncertain relationships, time-calibrated trees have shown that this uncertainty dates to a very important event: the aftermath of the asteroid impact 66 million years ago.

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

3/12 Yet, despite the ever-growing availability of genomes for jawed vertebrates, we still have no idea how huge proportions of their diversity are related. Take birds for an example. Hundreds of thousands of genes still don't clearly say where a single species-the hoatzin-goes!

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

2/12 Numbering over 60 thousand species, jawed vertebrates have adapted to a smattering of different environments and have been the dominant large animals on land, in sea, and in sky for hundreds of millions of years. They include our own species, Homo sapiens.

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Chase Brownstein @chasedbrownstein.bsky.social · 29/06/2026

1/12 🚨🚨 I am so excited to share chapter 1 of my dissertation, now preprinted here: biorxiv.org/content/10.6... We ask if are their fundamental, shared mechanisms that stop us from inferring the relationship of species and their timescale of divergence #biology #science

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Chase Brownstein @chasedbrownstein.bsky.social · 17/06/2026

Please join me next Tuesday at 3:15 PM (Room 21) at #Evol2026 to learn about the complex history of complex trait loss, extinction, and evolutionary radiation in extreme ecosystems in a clade of thousands of fishes!

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Chase Brownstein @chasedbrownstein.bsky.social · 22/04/2026

10/10 So, just like birds today, the earliest dinosaurs might have been an example of rapid radiation, a classic process in evolution that seems to have contributed to the assembly of much of living biodiversity!

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Chase Brownstein @chasedbrownstein.bsky.social · 22/04/2026

9/10 We might not be able to confidently infer how dinosaurs are related to each other PRECISELY BECAUSE they diversified so rapidly, deep in time, in a world very different from today.

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Chase Brownstein @chasedbrownstein.bsky.social · 22/04/2026

8/10 This rapid radiation pattern has an analogy in living birds, as the lineages alive today famously diversified right after the asteroid impact 66 million years ago AND have really unclear relationships! Photo: Stiller et al. (2024)

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Chase Brownstein @chasedbrownstein.bsky.social · 22/04/2026

7/10 This matches a pattern we see in lineages alive today. It is difficult to infer with certainty how lineages that rapidly diverged from one another a long time ago are related to each other, because only a handful of changes could have accumulated that define each group.

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Chase Brownstein @chasedbrownstein.bsky.social · 22/04/2026

6/10 After dinosaurs first appeared about 240 million years ago, it seems like their skeletons were changing rapidly over time as different groups appeared!

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Chase Brownstein @chasedbrownstein.bsky.social · 22/04/2026

5/10 We looked at a bunch of different datasets used to reconstruct dinosaur relationships, and we find that, when placed in time, they suggest the successive divergences among the major dinosaur lineages were characterized by rapid skeletal evolution! An "early burst"!

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Chase Brownstein @chasedbrownstein.bsky.social · 22/04/2026

4/10 Chris and I suspected there might be more to this than just methodological limits, so we checked something: how fast did new features in the skeletons of the first dinosaurs evolve?

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Chase Brownstein @chasedbrownstein.bsky.social · 22/04/2026

3/10 In recent years, the classic bird-hipped lizard-hipped dichotomy that all dinosaur-lovers know has been challenged. We can't figure out how the ornithischians (most herbivores), the sauropodomorphs (long-necks), and the theropods (meat eaters & kin) are related! Photo: PBS

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Chase Brownstein @chasedbrownstein.bsky.social · 22/04/2026

2/10 Dinosaurs were the dominant land vertebrates for 140 million years before the asteroid impact, and nowadays dominate the skies as birds. But what about their origins? Photo: @yalepeabody

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Chase Brownstein @chasedbrownstein.bsky.social · 22/04/2026

1/10 🚨🚨🚨 New paper on dinosaur evolution! Chris Griffin and I look at why we can't seem to figure out how the major groups are related! It might be a hint about how dinosaurs came to be! Photo: Anchisaurus @yalepeabodymuseum royalsocietypublishing.org/rspb/article...

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Chase Brownstein @chasedbrownstein.bsky.social · 13/03/2026

Glad to see our work @tjnear.bsky.social being covered in Nature! I look forward to both preprints being published, and I want to add that it appears genomes AGREE with morphology, and REFUTE the mtDNA-based hypothesis that was controversial when it first appeared! www.nature.com/articles/d41...

nature.com

No such thing as a shark? Genomes shake up ocean predator’s family tree

Sharks might not be a natural biological group, with most species potentially closer kin to rays than to an oddball group of sharks.

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Chase Brownstein @chasedbrownstein.bsky.social · 11/03/2026

40-44 (GOP combined) in MTG's seat. Republicans are COOKED in November god DAYUM

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Chase Brownstein @chasedbrownstein.bsky.social · 15/02/2026

10/10 Thanks to Yale University & the Peabody Museum for support as always, and to our lab and department for helpful discussions!

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Chase Brownstein @chasedbrownstein.bsky.social · 15/02/2026

9/10 These results highlight how, even in a period when genomes and phylogenies are becoming available for all orders of biodiversity, major questions remain about the relationships of some of the most iconic and threatened animal lineages!

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Chase Brownstein @chasedbrownstein.bsky.social · 15/02/2026

8/10 Based on the results of these phylogenomic analyses, we suggest that sharks and rays ancestrally underwent a single major genome size increase as long ago as the Permian. Sharks have had massive genomes for nearly 300 million years!

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Chase Brownstein @chasedbrownstein.bsky.social · 15/02/2026

7/10 By using genomic data to calibrate this phylogeny in time, we also demonstrate that sharks and rays participated in the Mesozoic Marine Revolution, a major period of diversification in the oceans that lasted from between 200 and 100 million years ago.

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Chase Brownstein @chasedbrownstein.bsky.social · 15/02/2026

6/10 Regardless of whether sharks form a clade exclusive of rays, we still can reach consensus around key aspects of their evolutionary history, such as the origins of live birth and pelagic specialization!

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Chase Brownstein @chasedbrownstein.bsky.social · 15/02/2026

5/10 We highlight the monophyly of sharks as a major remaining issue in vertebrate and animal phylogenetics. This issue is also of conservation importance, since it would impact the estimated evolutionary distinctiveness of many species! (Photo: Stein et al., 2018 Nature EE)

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Chase Brownstein @chasedbrownstein.bsky.social · 15/02/2026

4/10 This controversy hinges on the position of the Hexanchiformes, which include the sixgill and frilled sharks! These bizarre species share some aspects of their anatomy with sharks that existed before the dinosaurs!

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Chase Brownstein @chasedbrownstein.bsky.social · 15/02/2026

3/10 We discovered that sing different types of commonly used genome-wide markers, such as UCEs and BUSCO genes, produce fundamentally different hypotheses about shark and ray evolution! Depending on the type used, sharks are NOT necessarily their own clade!

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Chase Brownstein @chasedbrownstein.bsky.social · 15/02/2026

2/10 As it happens, the relationships of sharks, skates, rays, and chimaeras, which compose the cartilaginous vertebrates, are historically contentious. I wanted to see what we could do with genome sequences, and Tom and I went to work!

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Chase Brownstein @chasedbrownstein.bsky.social · 15/02/2026

1/10 ⏰⏰ New stuff from me & @tjnear.bsky.social ! We show that sharks themselves might not be a natural group ... it depends on what spots in the genome you analyze! Preprint here: www.biorxiv.org/content/10.6...

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Chase Brownstein @chasedbrownstein.bsky.social · 09/08/2025

16/16 Finally, thanks to @lifesciencestudios.bsky.social for the watercolors! I want to say finally that this type of interdisciplinary work is not possible at all without federal funding. Please #standupforscience

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Chase Brownstein @chasedbrownstein.bsky.social · 09/08/2025

15/16 Thanks, as always, to my coauthors, including co-first author Maxime Policarpo, my advisor @tjnear.bsky.social and Richard Harrington, Eva Hoffman, Maya Stokes, and Didier Casane! Thanks as well to the Yale Peabody Museum, Yale EEB and TPG TPG for support!

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Chase Brownstein @chasedbrownstein.bsky.social · 09/08/2025

14/16 The ages of the cave-related vision gene loss logically postdate the caves, so the ages we get are the minimum ages of the subterranean ecosystems! This suggests that some of these cave systems are up to 15 million years old! These systems have been here since the Miocene!

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Chase Brownstein @chasedbrownstein.bsky.social · 09/08/2025

13/16 But we can go further! What about the caves themselves? The ages of eastern North America's iconic karst caves, such as Mammoth Cave, are actually really hard to date using conventional methods. Cavefishes fill the gap! (Photo: NPS)

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Chase Brownstein @chasedbrownstein.bsky.social · 09/08/2025

12/16 Well, most anyways. Some, like species in the genera Amblyopsis and Typhlichthys, actually have pseudogene ages that predate their divergence from other species in each genus! Thus, these genomic markers of cave adaptation came before-these fishes speciated underground!

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