Fish biodiversity, genomics. @INHSIllinois Asst Research Scientist. Also aquarium fish hobbyist and plant parent. Profile pic: With a tamandua knifefish. He/him
Joined July 2009
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Compsaraia samueli, the pelican knifefish. The males grow extremely long jaws in the breeding season used to fight one another. Pictured are a male and a putative female, which does not possess the extended jaws.
Images © Milton Tan
Milton Tan retweeted
We can't brute force compute all possible moves in Go, a static game with a simple 19 x 19 grid, yet somehow people think we're going to simulate a dynamic system of trillions of cells each containing trillions of molecules.
If you had an exponential amount of compute you could solve simulate biology exactly and wouldn't need to run any experiments.
Some of you will think "of course, but that's an unrealistic assumption" and others will think "no, you need experiments even with that much compute. That's just How It's Done".
You would of course need evaluations once you have a solution, but you don't in principle need experiments to find it: Experiments are a way to save compute, dating from a time when it was much more expensive.
And I think the presentation is exponential but real systems aren't irreducibly exponential. AlphaFold worked, after all.
Milton Tan retweeted
Long time ago in the hill streams of Western Ghats collecting loaches for my former PhD kiddo @AryaSidharthan
#WesternGhats #freshwaterfish
Milton Tan retweeted
🧬 We have been using 𝗔𝗜-𝗮𝗰𝗰𝗲𝗹𝗲𝗿𝗮𝘁𝗲𝗱 𝗮𝗹𝗴𝗼𝗿𝗶𝘁𝗵𝗺 𝗱𝗲𝘀𝗶𝗴𝗻 to rethink foundational methods in molecular evolution from first principles.
🚀 Our new preprint introduces 𝗥𝗵𝗶𝘇𝗔𝗲𝗼𝗻—a new paradigm for recombination analysis that replaces discrete tree searches and combinatorial triplet tests with 𝗰𝗼𝗻𝘁𝗶𝗻𝘂𝗼𝘂𝘀 𝘁𝗿𝗮𝗷𝗲𝗰𝘁𝗼𝗿𝘆 𝗺𝗲𝗰𝗵𝗮𝗻𝗶𝗰𝘀 in linear O(NKL) time.
📄 Preprint: biorxiv.org/content/10.64898…
📖 Blog & 60-sec slides: spond.github.io/CV.js/blog/2…
🌐 Browser app: veg.github.io/rhizaeon-code/
💻 Code: github.com/veg/rhizaeon-code
⚙️ 𝗛𝗼𝘄 𝘁𝗵𝗲 𝘀𝘁𝗮𝗰𝗸 𝘄𝗼𝗿𝗸𝘀:
🧭 𝗠𝗲𝘁𝗿𝗶𝗰 𝗠𝗮𝗽 & 𝗥𝗼𝗼𝘁 𝗦𝗶𝗻𝗸: K reference genomes form a fixed metric map with an unpolarized root sink at the origin. Branch-specific rate bursts flow into the sink, holding false positives at 0.58%–1.01% across 333,334 clonal genomes in a 1,000,000-alignment sweep.
🎯 𝗔𝘁𝘁𝗲𝗻𝘁𝗶𝗼𝗻 𝗠𝗮𝗽𝘀 & 𝗚𝗵𝗼𝘀𝘁 𝗔𝘅𝗶𝘀: Each sequence is tracked along the chromosome via soft attention weights over the landmarks, plus an orthogonal projection that captures unsampled ("ghost") donor lineages.
⚡ 𝗙𝗼𝗿𝗰𝗲 𝗗𝗶𝗽𝗼𝗹𝗲𝘀: Crossovers shift attention from one donor to another, creating an equal-and-opposite force dipole across the breakpoint that we test against a Brownian-bridge null.
🌊 𝗗𝘆𝗮𝗱𝗶𝗰 𝗪𝗮𝘃𝗲𝗹𝗲𝘁 𝗣𝗼𝗹𝗶𝘀𝗵𝗶𝗻𝗴: Multi-scale wavelet filters, 5-state Viterbi decoding, likelihood polishing, and iterative tract scrubbing resolve nested transfers from 80 bp gene conversions to 30 kb cassettes while merging shared clade transfers into a single ancestral event (98.8% exact).
🦀 Written in Rust and Python and compiled to WebAssembly for zero-install browser runs, RhizAeon maps:
🦠 83 whole sarbecovirus genomes (31 kb) in 2.6 seconds
🧫 240 S. pneumoniae chromosomes (2.22 Mb) in 36.1 seconds
🛡️ 379 primate HLA Class I alleles in 1.1 seconds
🤝 With Danielle Callan, @stvnwvr Hannah Verdonk, @JD_zehr @SpyrosLytras, @nekrut, @tpaisie, and @DarrenM98230782 .
Milton Tan retweeted
New contributor Dean Connelly shares his experiences so far with keeping, and breeding, the newly described jewel gourami (Nanosphronemus gemma) in the November issue of Practical Fishkeeping.
Milton Tan retweeted
I'm pleased to announce version 1.0 of `tact`, an app for stochastic polytomy resolution on phylogenies using taxonomy.
A decade after the first line of code, scientists are still using `tact` to build complete trees of fish, termites, magnoliids, and more. Thank you! (🧵1/3)
Milton Tan retweeted
Svante Pääbo and colleagues used AlphaGenome as a time machine to reconstruct the evolution of human gene regulation. An impressive new bioRxiv preprint! 🧬⏩
Fifty years ago, scientists proposed that the differences between humans and chimpanzees might be driven less by changes in genes themselves and more by changes in how those genes are regulated.
The authors revisited this hypothesis using deep learning and identified more than 71,000 genomic regions predicted to have gained regulatory activity along the human lineage. But the most interesting finding is how these changes happened!
In 71% of cases, evolution repurposed existing regulatory elements rather than creating new ones. A single mutation could introduce a tissue-specific transcription factor binding site, activating an existing element in another tissue.
To investigate this, the researchers used AlphaGenome to predict the regulatory effects of 17 million nucleotide substitutions, linking them to gene expression differences between humans and other great apes.
Interestingly, the vast majority of these regions fell outside known Human Accelerated Regions, genomic regions that evolved unusually rapidly along the human lineage. This suggests that the rate of sequence evolution does not necessarily reflect its functional impact.
Comparisons with Neanderthal and Denisovan genomes revealed that 99.6% of the regulatory gains fixed in modern humans and successfully dated arose before our evolutionary split from these archaic lineages.
There are also fascinating examples involving individual genes. One is SLC47A1, which encodes a transporter involved in eliminating drugs and toxins. The researchers identified five regulatory gains associated with increased expression in the human liver. Reverting these changes to their ancestral states in silico reduced predicted gene expression by 60%.
Of course, many of these predictions still require experimental validation. But the broader idea is remarkable: ancient DNA has allowed us to discover which mutations occurred in the past. Now, deep learning is beginning to reveal how those mutations may have changed the way genes worked.
biorxiv.org/content/10.64898…
#aDNA #evolution #regulation #AlphaGenome
Milton Tan retweeted
New paper out 🎉
Multiple drivers of genomic novelty across ruminants
sciencedirect.com/science/ar…
Milton Tan retweeted
Rapid turnover of sex chromosomes is associated with speciation in Neotropical armored catfish Harttia (Siluriformes, Loricariidae)
researchgate.net/publication…
Milton Tan retweeted
📖Published📖
Check out our new research article 👉 Distinguishing pairwise species spatial associations from multi-species distribution patterns
Read the whole article here 👇
buff.ly/dHXxpXE
Milton Tan retweeted
#NewSpeciesAlert - 𝐵𝑢𝑛𝑜𝑐𝑒𝑝ℎ𝑎𝑙𝑢𝑠 𝑔𝑎𝑟𝑐𝑖𝑎𝑖, a new species of banjo catfish (Aspredinidae), is described from the Tocantins-Araguaia River basin, Brazil.
🔒 mapress.com/zt/article/view/…
𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵 𝗧𝗶𝘁𝗹𝗲
Description of new species of 𝐵𝑢𝑛𝑜𝑐𝑒𝑝ℎ𝑎𝑙𝑢𝑠 Kner 1855 (Siluriformes: Aspredinidae) from the Tocantins-Araguaia River basin, using an integrative approach
𝗖𝗶𝘁𝗮𝘁𝗶𝗼𝗻
Crispim, J.L., Frisoni, W.J.M., Costa, N.S., Sabaj, M.H. & Oliveira, C. (2026) Description of new species of 𝐵𝑢𝑛𝑜𝑐𝑒𝑝ℎ𝑎𝑙𝑢𝑠 Kner 1855 (Siluriformes: Aspredinidae) from the Tocantins-Araguaia River basin, using an integrative approach. Zootaxa, 5894 (1), 65–83. doi.org/10.11646/zootaxa.589…
𝗔𝗯𝘀𝘁𝗿𝗮𝗰𝘁
𝐵𝑢𝑛𝑜𝑐𝑒𝑝ℎ𝑎𝑙𝑢𝑠 currently comprises 14 valid species and is the most species-rich genus within the banjo catfish family (Aspredinidae), occurring widely across major trans- and cis-Andean drainages of South America. Despite this broad distribution, no species has yet been described from the Tocantins-Araguaia basin, a region recognized for its high level of endemism.
Here, we describe a new species of 𝐵𝑢𝑛𝑜𝑐𝑒𝑝ℎ𝑎𝑙𝑢𝑠 from the Tocantins–Araguaia basin using an integrative taxonomic approach, applied for the first time in the genus. We also discuss the molecular and morphological diversity within a lineage previously represented by a single valid species, 𝐵𝑢𝑛𝑜𝑐𝑒𝑝ℎ𝑎𝑙𝑢𝑠 𝑎𝑙𝑒𝑢𝑟𝑜𝑝𝑠𝑖𝑠. Species delimitation analyses based on the cytochrome c oxidase subunit I (COI) marker recovered additional distinct Molecular Operational Taxonomic Units (MOTUs), suggesting the presence of further undescribed species within 𝐵𝑢𝑛𝑜𝑐𝑒𝑝ℎ𝑎𝑙𝑢𝑠.
𝗘𝘁𝘆𝗺𝗼𝗹𝗼𝗴𝘆
The specific epithet “𝑔𝑎𝑟𝑐𝑖𝑎𝑖” honours the Peruvian ichthyologist Dr James Raúl Garcia Ayala, of the Laboratório de Biologia e Genética de Peixes (LBP-UNESP), who helped collect part of the type series, in recognition of his research on Neotropical fishes, especially the taxonomy of the subfamily Stethaprioninae.
𝗣𝗵𝗼𝘁𝗼 𝗖𝗿𝗲𝗱𝗶𝘁
Holotype of 𝐵𝑢𝑛𝑜𝑐𝑒𝑝ℎ𝑎𝑙𝑢𝑠 𝑔𝑎𝑟𝑐𝑖𝑎𝑖 (LBP 37103, 92.2 mm SL) in dorsal (top), lateral (middle) and ventral (bottom) views. Scale bar = 10 mm. Photographed by J. L. Crispim.
© 2026 the Author(s). Published in the journal Zootaxa.
#NewSpecies #Ichthyology #Taxonomy #Biodiversity #AquariumHobby #Fishkeeping #Aquarist #TropicalFish #FishTank #Bunocephalus #Catfishes #BanjoCatfish #Siluriformes #Aspredinidae #Brazil #rioTocantins #rioAraguaia
ALT Holotype of 𝐵𝑢𝑛𝑜𝑐𝑒𝑝ℎ𝑎𝑙𝑢𝑠 𝑔𝑎𝑟𝑐𝑖𝑎𝑖 (LBP 37103, 92.2 mm SL) in dorsal (top), lateral (middle) and ventral (bottom) views. Scale bar = 10 mm. Photographed by J. L. Crispim.
Milton Tan retweeted
New in @PNASNews:
In two large experiments (~18k obs from ~14.8k people), we find that brief conversations with AI can get people to take real political action - incl. signing real petitions and giving money to charity.
Surprisingly, the persuasion strategy that worked best for changing people's attitudes - packing convos with info - was the least effective at changing behavior!
🧵
Milton Tan retweeted
Museum Resource 🐟 Fishes in the Fresh Waters of Florida
Explore our state's freshwater fish species, including collection records & photos.
Shown: African Jewelfish (Hemichromis letourneuxi), non-indigenous to Florida's freshwaters
🔗 Info & browse:
floridamuseum.ufl.edu/discov…
ALT Two side-profile views of a fish species. The top fish has a red head and underbelly, a yellowish-brown body with light spots, a dark spot on its flank, and red-tipped dorsal and caudal fins. The bottom fish has a darker brown body with iridescent blue spots and markings, a similar dark flank spot, and translucent fins with reddish-blue highlights.
Milton Tan retweeted
Just out: some fish 🐟 lost their green opsins but evolved a functional alternative from duplicated red (LWS) opsins — much like the evolution of red-green vision in primates! 🔴🟢 Different lineages, similar evolutionary solutions! Go red opsins! Go gobies! Thks co-authors🤗
Milton Tan retweeted
We are searching for a new colleague in our Department of Biology at University of Oregon!
This is a super special opportunity-- an endowed chair position in Genetics/Genomics. Come join us!
I'm happy to answer any questions folks might have
careers.pageuppeople.com/726…
Milton Tan retweeted
Cities alter the latitudinal diversity gradient of birds in North America
link.springer.com/article/10…
Milton Tan retweeted
Nantis indefessus, a freshwater fish endemic to the upper Bermejo and Juramento river basins in northwestern Argentina. A distinctive representative of the native fish fauna of the Andean portion of the La Plata basin.
#Characiformes #CONICET #ArgentineFish #Biodiversity
Milton Tan retweeted
Oligosarcus bolivianus, a freshwater fish endemic to the Andean portion of the La Plata River basin, inhabiting the upper Bermejo and Pilcomayo river systems. A remarkable representative of the unique mountain fish fauna of northwestern Argentina and southern Bolivia.
Milton Tan retweeted
A female Urkumayu gladysae, an armored catfish endemic to Argentina’s Calchaquí River. Living at ~2,400 m, it is among the highest-altitude Callichthyidae. Adapted to cold Andean waters, it shares its habitat with introduced rainbow trout.
#Corydoradinae #AndeanFish
Milton Tan retweeted
📖 Published 📖
Theia: An end-to-end edge-AI mobile framework for high-throughput field phenotyping and on-device geometric morphometrics 🖥️ 📊 🌻
👉️ buff.ly/oC3rIiT
Milton Tan retweeted
Researchers delve into the evolutionary distribution of axillary and pectoral spine glands in Corydoradinae catfishes, showing the presence of axillary glands across all genera in the subfamily, though the venom gland associated with the pectoral spine is restricted to a clade comprising 𝑂𝑠𝑡𝑒𝑜𝑔𝑎𝑠𝑡𝑒𝑟, 𝐵𝑟𝑜𝑐ℎ𝑖𝑠, and 𝐻𝑜𝑝𝑙𝑖𝑠𝑜𝑚𝑎.
🔓 scielo.br/j/ni/a/S5R5LLscXVT…
"This pattern is congruent with phylogenetic relationships and implies that mimicry rings may involve Müllerian, quasi-Batesian, and Batesian components depending on their species composition and the degree of defense exhibited by the species present."
"The presence of venom-associated pectoral spine glands only in the clade comprising 𝐵𝑟𝑜𝑐ℎ𝑖𝑠, 𝐻𝑜𝑝𝑙𝑖𝑠𝑜𝑚𝑎, and 𝑂𝑠𝑡𝑒𝑜𝑔𝑎𝑠𝑡𝑒𝑟 supports a single origin of these glands in the Corydoradinae. Further, our histological analyses indicate that these glands are absent in 𝐶𝑜𝑟𝑦𝑑𝑜𝑟𝑎𝑠, 𝐴𝑠𝑝𝑖𝑑𝑜𝑟𝑎𝑠, 𝑆𝑐𝑙𝑒𝑟𝑜𝑚𝑦𝑠𝑡𝑎𝑥, and 𝐺𝑎𝑠𝑡𝑟𝑜𝑑𝑒𝑟𝑚𝑢𝑠. Interestingly, several species from both venom-bearing and non-venom-bearing lineages have been reported to participate in mimicry rings, often forming mixed-species shoals and exhibiting highly convergent color patterns. Alexandrou et al. (2011) identified 52 Corydoradinae species forming 24 putative Müllerian mimicry rings, with more than 90% of these rings composed of species from different genera that, nonetheless, share strikingly similar coloration. Classical Müllerian mimicry requires that all participating species are defended, contribute to predator deterrence, and share the costs associated with predator learning a common warning signal (Ruxton et al., 2018). Our results partially support this interpretation, as all examined Corydoradinae possess at least some combination of mechanical and glandular defenses. However, the additional presence of venom-associated pectoral spine glands in only some genera suggests that defensive effectiveness may not be equivalent among lineages."
𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵 𝗧𝗶𝘁𝗹𝗲
Morphological diversification of defensive glands in Corydoradinae catfishes indicates a mixed Müllerian-Batesian mimicry system
𝗖𝗶𝘁𝗮𝘁𝗶𝗼𝗻
Jiménez-Vergara, C. R., Thomaz, A. T., Garzón-Restrepo, A. J., Malabarba, L. R., & Monroy, M. (2026). Morphological diversification of defensive glands in Corydoradinae catfishes indicates a mixed Müllerian-Batesian mimicry system. Neotropical Ichthyology, 24(3), e260051. doi.org/10.1590/1982-0224-20…
𝗔𝗯𝘀𝘁𝗿𝗮𝗰𝘁
Axillary and pectoral-fin spine glands play a central role in the defensive biology of Siluriformes by releasing toxic secretions; however, their distribution, structural diversity, and evolutionary significance within Corydoradinae remain poorly understood.
Here, we present the first comparative histological analysis of these glands across seven genera of Corydoradinae. Axillary glands were present in all examined genera and exhibited a conserved lobular organization consistent with a holocrine secretion type as described previously in other Siluriformes.
In contrast, venom-associated pectoral spine glands were restricted to a clade comprising 𝐻𝑜𝑝𝑙𝑖𝑠𝑜𝑚𝑎, 𝐵𝑟𝑜𝑐ℎ𝑖𝑠, and 𝑂𝑠𝑡𝑒𝑜𝑔𝑎𝑠𝑡𝑒𝑟. In these genera, gland position and cellular morphology closely match venom glands described in other siluriform lineages, supporting a lineage-specific derived condition. Conversely, 𝐶𝑜𝑟𝑦𝑑𝑜𝑟𝑎𝑠, 𝐴𝑠𝑝𝑖𝑑𝑜𝑟𝑎𝑠, 𝑆𝑐𝑙𝑒𝑟𝑜𝑚𝑦𝑠𝑡𝑎𝑥, and 𝐺𝑎𝑠𝑡𝑟𝑜𝑑𝑒𝑟𝑚𝑢𝑠 lacked true venom-associated pectoral spine glands and instead displayed abundant epidermal granular cells and club cells, consistent with the retention of a non-venomous ancestral state.
This pattern is congruent with phylogenetic relationships and implies that mimicry rings may involve Müllerian, quasi-Batesian, and Batesian components depending on their species composition and the degree of defense exhibited by the species present.
𝗣𝗵𝗼𝘁𝗼 𝗖𝗿𝗲𝗱𝗶𝘁
Mimicry ring involving 𝐶𝑜𝑟𝑦𝑑𝑜𝑟𝑎𝑠 𝑠𝑖𝑚𝑢𝑙𝑎𝑡𝑢𝑠 and the venomous 𝐻𝑜𝑝𝑙𝑖𝑠𝑜𝑚𝑎 𝑚𝑒𝑡𝑎𝑒 co-occurring in the Meta River basin. Although both possess axillary glands of similar morphology, they differ in the presence of venom spine glands.
© 2026 the Author(s). Published in the journal ZooKeys. An open access article, distributed under the terms of the Creative Commons Attribution 4.0 International (CC-BY-4.0) licence. creativecommons.org/licenses…
#Corydoradinae #Corydoras #Aspidoras #Scleromystax #Gastrodermus #Brochis #Hoplisoma #Osteogaster #Ichthyology #Biodiversity #AquariumHobby #Fishkeeping #Aquarist #TropicalFish #FishTank #Mimicry #Venom #ToxicSecretions #Müllerian #VenomGlands #PectoralSpine
ALT Mimicry ring involving 𝐶𝑜𝑟𝑦𝑑𝑜𝑟𝑎𝑠 𝑠𝑖𝑚𝑢𝑙𝑎𝑡𝑢𝑠 and the venomous 𝐻𝑜𝑝𝑙𝑖𝑠𝑜𝑚𝑎 𝑚𝑒𝑡𝑎𝑒 co-occurring in the Meta River basin. Although both possess axillary glands of similar morphology, they differ in the presence of venom spine glands.