Chase Brownstein
@chasedbrownstein.bsky.social
Graduate Student, Yale E&EB
YC '23
Call me the ancient mariner cus I'm about to Bust a Rime
https://chasebrownstein.weebly.com
https://scholar.google.com/citations?user=hGy-fr8AAAAJ&hl=en&authuser=1
he/him
YC '23
Call me the ancient mariner cus I'm about to Bust a Rime
https://chasebrownstein.weebly.com
https://scholar.google.com/citations?user=hGy-fr8AAAAJ&hl=en&authuser=1
he/him
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)
August 9, 2025 at 12:56 AM
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)
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!
August 9, 2025 at 12:56 AM
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!
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!
August 9, 2025 at 12:56 AM
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!
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!
August 9, 2025 at 12:56 AM
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!
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!
August 9, 2025 at 12:56 AM
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!
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!
August 9, 2025 at 12:56 AM
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!
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!
August 9, 2025 at 12:56 AM
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!
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!
August 9, 2025 at 12:56 AM
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!
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!
August 9, 2025 at 12:56 AM
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!
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!
August 9, 2025 at 12:56 AM
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!
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)
August 9, 2025 at 12:56 AM
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)
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!
August 9, 2025 at 12:56 AM
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!
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-...
August 9, 2025 at 12:56 AM
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-...
Checking genbank for an obscure clade
June 21, 2025 at 4:56 AM
Checking genbank for an obscure clade
6/10 As in previous analyses of sturgeon relatives, the monophyly of the clade we recognize as Huso is weakly supported. We also reject monophyly of the shovelnose sturgeon clade Scaphirhynchinae.
April 25, 2025 at 5:54 PM
6/10 As in previous analyses of sturgeon relatives, the monophyly of the clade we recognize as Huso is weakly supported. We also reject monophyly of the shovelnose sturgeon clade Scaphirhynchinae.
5/10 So, Acipenser now includes Atlantic and Gulf Sturgeon, whereas Sinosturio includes White Sturgeon, Chinese Sturgeon, and relatives. We also expand the genus Huso to include European and western Asian species. This clade includes some of the largest freshwater fishes.
April 25, 2025 at 5:54 PM
5/10 So, Acipenser now includes Atlantic and Gulf Sturgeon, whereas Sinosturio includes White Sturgeon, Chinese Sturgeon, and relatives. We also expand the genus Huso to include European and western Asian species. This clade includes some of the largest freshwater fishes.
4/10 In order to provide a revised taxonomy of sturgeons, we used a rank-free phylogenetic approach to delimit genera. We restrict Acipenser to the first lineage to diverge among Acipenseridae, and resurrect the genus Sinosturio for a clade containing Asian and western NA species
April 25, 2025 at 5:54 PM
4/10 In order to provide a revised taxonomy of sturgeons, we used a rank-free phylogenetic approach to delimit genera. We restrict Acipenser to the first lineage to diverge among Acipenseridae, and resurrect the genus Sinosturio for a clade containing Asian and western NA species
3/10 For a while, the taxonomy of sturgeons has been in question, as molecular and morphological phylogenies consistently resolve the most species-rich genus, Acipenser, as paraphyletic. Figure: Shen et al. (2020) Genomics
April 25, 2025 at 5:54 PM
3/10 For a while, the taxonomy of sturgeons has been in question, as molecular and morphological phylogenies consistently resolve the most species-rich genus, Acipenser, as paraphyletic. Figure: Shen et al. (2020) Genomics
2/10 Sturgeons are one of several lineages that are classically considered to be living fossils! Like gars and bowfins, they have exceptionally slow rates of molecular evolution. Figure: Brownstein et al. (2024) Evolution.
(academic.oup.com/evolut/artic...)
(academic.oup.com/evolut/artic...)
April 25, 2025 at 5:54 PM
2/10 Sturgeons are one of several lineages that are classically considered to be living fossils! Like gars and bowfins, they have exceptionally slow rates of molecular evolution. Figure: Brownstein et al. (2024) Evolution.
(academic.oup.com/evolut/artic...)
(academic.oup.com/evolut/artic...)
1/10 🚨🚨 New paper with @tjnear.bsky.social! Here, we revise the systematics of sturgeons using a phylogenetic approach! We confirm an Early Cretaceous origin for the sturgeon total clade and resurrect several genera for living species!
April 25, 2025 at 5:54 PM
1/10 🚨🚨 New paper with @tjnear.bsky.social! Here, we revise the systematics of sturgeons using a phylogenetic approach! We confirm an Early Cretaceous origin for the sturgeon total clade and resurrect several genera for living species!
New paper with Michael Caldwell, Mike Lee, Tiago Simoes, Dalton Meyer, and Simon Scarpetta! In it, we respond to claims that †Cryptovaranoides is a squamate, and show that they are indefensible. t.co/MLjFcy5ivx
April 23, 2025 at 5:14 PM
New paper with Michael Caldwell, Mike Lee, Tiago Simoes, Dalton Meyer, and Simon Scarpetta! In it, we respond to claims that †Cryptovaranoides is a squamate, and show that they are indefensible. t.co/MLjFcy5ivx
10. They presented manipulated versions of the figures used in our lab’s 2025 paper that included outdated map data showing species distributions, but framed these manipulations (left) as being from the original paper (right).
April 18, 2025 at 9:27 PM
10. They presented manipulated versions of the figures used in our lab’s 2025 paper that included outdated map data showing species distributions, but framed these manipulations (left) as being from the original paper (right).
8. repeatedly attacked the scientific conduct of my colleagues’ manuscript. Our lab was accused of manipulating data by failing to provide vouchers (all data is public), using the wrong ‘dendrogram’ analysis (they referred to the maximum likelihood tree as a parsimony analysis)....
April 18, 2025 at 9:27 PM
8. repeatedly attacked the scientific conduct of my colleagues’ manuscript. Our lab was accused of manipulating data by failing to provide vouchers (all data is public), using the wrong ‘dendrogram’ analysis (they referred to the maximum likelihood tree as a parsimony analysis)....
3. and also showed that Snail Darter is deeply nested within Stargazing Darter phylogenetically. Fst (a measure of gene flow) for Snail vs. Stargazing Darter across SNPs is 0.078, even below the 0.10+ average value among different populations of people.
April 18, 2025 at 9:27 PM
3. and also showed that Snail Darter is deeply nested within Stargazing Darter phylogenetically. Fst (a measure of gene flow) for Snail vs. Stargazing Darter across SNPs is 0.078, even below the 0.10+ average value among different populations of people.