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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

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 · Aug 9

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 · Aug 9

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 · Aug 9

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 · Aug 9

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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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

11/16 As it turns out, the ages we get from examining this pseudogene clock are younger than the divergence times of cavefish lineages from one another! So, they experienced cave-associated degenerative evolution AFTER diverging from other fishes, and thus independently!

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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

10/16 To get to the bottom of this, we used a trick. By estimating generation times since a gene was pseudogenized, and then multiplying that by years per generation, we can estimate how many millions of years ago a cavefish, well, became a cavefish!

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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

9/16 The problem is that, for single species diverging from a surface-dwelling ancestor, cave colonization and adaptation could have happened anywhere along the branch on the tree leading to the living cave dweller. This is because its closest surface relatives might be extinct!

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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

8/16 We noticed that the number of pseudogenes might be associated with the age of cave lineages themselves. For example, Troglichthys rosae, the first obligate cave-dweller to diverge, pseudogenized 25 vision and light related genes ancestrally!

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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

7/16 What's more, no loss of function mutations appear ancestral to lineages including multiple obligate cave-dwelling amblyopsid genera, nor are none present in Forbesichthys! This indicates independent cave colonization and subsequent gene function loss. But there's more!

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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

6/16 Different sets of vision-related genes, including several involved in human disease, lost functionality in different lineages of obligate cave-dwelling amblyopsids! Not only that, but the loss of function mutations themselves are not identical among lineages!

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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

5/16 Although the similarities of obligate cave-dwelling amblyopsids are not just skin deep (they have all elongated their skulls and bodies, deossified their circumorbital series, and reduced or lost pelvic fins), comparisons of their genomes show these fishes are convergent!

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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

4/16 A clue is that eyed, pigmented species in Forbesichthys are deeply nested within blind, obligate cave dwelling amblyopsids, suggesting multiple origins. By using genomes, personal examination of key fossils, and CT scans, we built the most comprehensive tree yet to do so!

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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

3/16 Most amblyopsids have degenerated their eyes and lost external pigment to become obligate cave-dwellers. Yet, the different ways in which the eyes of different species have degenerated has led to a 125-year debate about how many times these fishes invaded caves! (Photo: NPS)

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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

2/16 Amblyopsids are one of North America's most obscure and most interesting vertebrate lineages. Endemic to eastern North America, they are part of a species-poor lineage that also includes pirate and trout perches and originated 80 million years ago!

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Chase Brownstein @chasedbrownstein.bsky.social · Aug 9

1/16 🚨🚨 New paper!! I am thrilled to share our study that uses fossils, genomes, and a bit of geology to investigate how many times cavefishes evolved, and how they can help us figure out the ages of caves themselves! Link: academic.oup.com/mbe/advance-...

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Chase Brownstein @chasedbrownstein.bsky.social · Jun 21

Checking genbank for an obscure clade

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Chase Brownstein @chasedbrownstein.bsky.social · Jun 20

Pulling up to #Evol2025

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Reposted by Chase Brownstein

Life Science Studios - Scientific Illustration @lifesciencestudios.bsky.social · Jun 3

Anytime a fish has stripes or spots, they all have to be painted on at the end, after I’ve nearly completed the painting. It always makes me nervous!

This is Percina caprodes, the common logperch.

#teamfish #sciart

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Reposted by Chase Brownstein

Carl T. Bergstrom @carlbergstrom.com · Jun 3

RFK Jr. May Have Just Ruined Our Best Weapon Against Bird Flu

He just made two bad decisions on vaccines, and he made them in the worst way possible.

www.thebulwark.com

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Reposted by Chase Brownstein

Jacquelyn Gill @jacquelyngill.bsky.social · May 22

A large proportion of these canceled awards are focused on broadening the participation of underrepresented groups in STEM, which NSF was mandated to do by Congress. At what point does Congress plan to act to restore the balance of power?

Dr. Diaz Eaton up to Good Trouble @mathprofcarrie.bsky.social · May 22

NSF just released a public list of terminated awards. It’s linked on the bottom of the FAQ page at: nsf.gov/updates-on-priorities#termination-list

Updates on NSF Priorities

nsf.gov

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Reposted by Chase Brownstein

Matt Lesser @mattlesser.bsky.social · May 19

Connecticut has long been a cash cow for the federal government. But now the federal administration is threatening to withhold funds we are legally entitled to - in defiance of court orders.

If they do, we should return the favor and stop collecting money for the feds.

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Chase Brownstein @chasedbrownstein.bsky.social · May 16

Awesome new paper from @prosanta.bsky.social, Melanie Stiassny, et al!
academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syaf032/8129685?login=true

Phylogenomic and Population Genomic Analyses of Ultraconserved Elements Reveal Deep Coalescence and Introgression Shaped Diversification Patterns in Lamprologine Cichlids of the Congo River

Abstract. Understanding the drivers of diversification is a central goal in evolutionary biology but can be challenging when lineages radiate quickly and/o

academic.oup.com

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Reposted by Chase Brownstein

Steve Brusatte @stevebrusatte.bsky.social · May 13

Immigration policy in my two countries, 2025:

🇺🇸No longer give me your tired, your poor, your huddled masses yearning to breathe free, only white people who didn’t like that apartheid ended

🇬🇧Stay away all of you squalid strangers

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Reposted by Chase Brownstein

Carl T. Bergstrom @carlbergstrom.com · May 12

Even the Trojans weren't stupid enough to get IN the horse.

Carl T. Bergstrom @carlbergstrom.com · May 11

nothing to worry about here at all

Air Force One with "FREE CANDY" sprayed on the side.

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