Xtremo-Devo Lab @ WMU

#OTD 10 years ago we published the spotted #gar genome. 600+ citations later, we are proud of its impact on vertebrate genomics. @jpostlethwait.bsky.social

Check out the new assemblies generated with @vertebrategenomes.bsky.social
www.ncbi.nlm.nih.gov/datasets/gen...

#EndlessFishMostBeautiful

Black lung fish 🤔

Please repost and share! We look forward to seeing you there!

"Medaka: A novel model for analyzing genome-environment interactions"
by Kiyoshi Naruse & colleagues

"Endemic to habitats spanning from 4 to 40°C and varying salinities, [medaka] combines broad ecological adaptability with experimental tractability."

Read more:
authors.elsevier.com/sd/article/S...

The little fish that could. Today sees the publication of a long awaited paper from my group. This has been.

Super cool work on medaka by @ewanbirney.bsky.social and colleagues www.cell.com/cell-genomic...

Includes an excellent summary from Ewan via linkedin... and I maintain that 'humans aren't special' 😊 www.linkedin.com/pulse/little...

And it's out indeed! Huge congrats to @josanesousa.bsky.social, @gabrielalima19.bsky.social, @perezlouise.bsky.social & Hannah Schof! A true tour-de-force that highlights how emerging model systems can shed new light on long-standing macro-evolutionary questions. Go #axolotl, #polypterus #zebrafish!

Figure depicting the four classes of important questions that frequently arise when using research organisms to study biomedical questions and translating findings to humans. a, How to predict disease–gene or function–gene relationships across species? Diagram depicts genes in each species associating with specific functions, diseases and phenotypes. b, How to identify functionally equivalent molecular components across species? Diagram depicts finding the most equivalent gene, pathway or expression module or phenotype between species. c, How to infer perturbed molecular profiles across species? Diagram depicts gene expression in each species as a result of taking a particular perturbation like a drug. d, How to map equivalent cell types and cell states across species? Diagram depicts alignment of cell types across species. This Perspective comprehensively lays out the landscape of recent and state-of-the-art data-driven strategies, including those that leverage artificial intelligence and machine learning (ML), for answering these questions.

Our Perspective article on Computational Strategies for Cross-Species Knowledge Transfer is now published in @natmethods.nature.com!

This was a collab b/w @krishnanlab.bsky.social & @fishevodevogeno.bsky.social, led by the amazing Hao Yuan @yhbioinfo.bsky.social. 🧵

www.nature.com/articles/s41...

How do four-eyed fish see above & underwater? 🌤️🌊 Our new preprint reveals how Anableps rewired its retina for dual vision- evolution at work 👁️👁️ Kudos to @perezlouise.bsky.social @josanesousa.bsky.social @keylapruett.bsky.social + team!
🔗 tinyurl.com/3a8r9xy5

MBE | Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes A graphic visualizing the finding by Bogan et al. that antifreeze protein (AFP) genes increased in copy number among shallow-water, polar species of Zoarcoidei fishes. Top left: Pholis gunnellus photographed by Chris Isaacs (CC-BY-NC). Top right: Cebidichthys violaceus photographed by Alex Heyman (CC0 1.0). Bottom left: Lycenchelys sp. photographed by Julien Savoie (CC BY 4.0). Bottom right: Lycodes sp. photographed by Julien Savoie (CC BY 4.0).

@snbogan.bsky.social @notothentoma.bsky.social @scotthotaling.bsky.social @paulbfrandsen.bsky.social et al. explore the evolution of type III antifreeze proteins in deep sea zoarcoid fishes.

🔗 doi.org/10.1093/molbev/msaf219

#evobio #molbio

Parallel shifts in differential gene expression reveal convergent miniaturization in fishes | PNAS Body size variation in vertebrates is a complex polygenic trait, tightly correlated with numerous aspects of a species’ biology, ecology, and physi...

Why are some species smaller than a paperclip while others grow longer than a school bus? How is body size evolution governed in animals? Out now in @pnas.org we tackle these longstanding questions through a genetic lens using my favorite group of fishes as our model!! www.pnas.org/doi/10.1073/...

New preprint up with collaborators Jianguo Lu, @mpodobnik.bsky.social, Uwe Irion, Braedan McCluskey, John Postlethwait and others. New Danio genomes, evolution and pigment pattern variation. Long time in the making www.biorxiv.org/content/10.1...

Zebrafish embryo undergoing gastrulation. Credit to Dr. Gopi Shah at EMBL. #ZebrafishZunday 🧪

👻 G-g-ghost? Nope, s-s-snailfish! 🤍

Meet the mesmerizing new addition to our Into the Deep/En lo Profundo exhibit, rough snailfish! These ethereal charmers live in the benthic zone, a scientific term for the seafloor.

Congrats @liujuan.bsky.social, our very own @zzhou32.bsky.social and all co-authors! Fintastic work!

Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs Phenotypic variation among individuals plays a key role in evolution, since variation provides the material on which natural selection can act. One important link between genetic and phenotypic variat...

Update of our preprint on Inter-individual gene expression variability in fishes! We improved statistical analyses of continuous variables, and especially added machine learning on promoters which confirms cis-regulation of organ-specific expression variability.
www.biorxiv.org/content/10.1...

You're fin-tastic! 🐟🐠🌟🤩

Our fish community present #PASEDB2025!
@nakamuralab.bsky.social @phernandez.bsky.social @patyschneider22.bsky.social @ischneider.bsky.social @xtremo-devo-lab.bsky.social @fishevodevogeno.bsky.social @homeobox.bsky.social and more!

Help us to tag them

Our dear friend @ischneider.bsky.social receiving the Young Investigator Award from @evodevopanam.bsky.social! So incredibly deserved!
#PASEDB2025

To infishity and beyond! Great work, Igor!

EvoDevotees, if you are at #PASEDB2025 and interested in either of these job opportunities for Fish Facility Manager or Presidential Postdoc at Michigan State U, let’s grab a coffee and chat

#EndlessFishMostBeautiful

@evodevopanam.bsky.social

#PanAmEvodevo2025 is about to start! Starting countdown, engines on! @fishevodevogeno.bsky.social @xtremo-devo-lab.bsky.social @patyschneider22.bsky.social

Our latest issue is now live! On the cover is a species of Asian noodlefish characterized by their transparency due to the absence of red blood cells, slender bodies and scaleless skins, and a poorly ossified skeleton. www.cell.com/current-biol...

Schematics depicting the dorsal and ventral sides of fins and limbs

We take for granted that our hands have two sides and can articulate in an endless number of ways. But what about a fish’s fin? Can a fish know something “like the back of its fin,” or have its future told with a fin palm reading? Check out this bluetorial to find out 👇🧪🧬🐟 doi.org/10.1101/2025...

The Braasch Lab @fishevodevogeno.bsky.social will soon post a position to replace manager of our *Ancient Fish Facility* at Michigan State. Looking for aquaculturist excited for unusual 🐟 species (gar, bowfin, paddlefish, polypterus) + zebrafish. Pls send candidates our way (DM or braasch@msu.edu)!

At #PASEDB we embrace all organisms. Each one has its own evolutionary trajectory that makes life so diverse 🌈🦄

Artwork: Ximena Gutierrez Ramos and Katie Reding

DaniocellDesktop logo, depicting a fish on a laptop screen.

If you love Daniocell, but wish it could generate analyses specific to YOUR genes & cell types of interest, check out DaniocellDesktop - a new point-and-click app for Mac and Windows that enables reanalysis of the Daniocell data without programming: daniocell.nichd.nih.gov/desktop/ (1/4)

You have so-fish-ticated taste 🐟
Fish satellite symposia speaker talks at #PASEDB

Invited speaker: Andrew Thompson

Organizers: @nakamuralab.bsky.social @patyschneider22.bsky.social & Joaquín Letelier

Register: evodevo.wildapricot.org/event-6007396

deep-sea adaptations have evolved independently in several groups. Eye shape: A prominent morphological example is the evolution of an elongated tubular, barrel eye to maximize photon capture in several deep-sea groups. Groups, where tubular eyes are common, are marked by a black square and a tubular eye scheme; groups with one/ few cases of tubular eyes but where the majority of species have a camera-type eye are marked with black dots (i.e. anglerfishes and dragonfishes). Retina: Rod-only retinas are a common feature of many adult deep-sea fishes. In other cases, they possess the typical duplex retina with cones (green cells) and rod cells (grey cells). Multibank: In some species, the rod cells are organized in multiple layers, forming a multibank retina, while other deep-sea fishes have the typical vertebrate single layer. Cone/rod id: Some deep-sea fishes have photoreceptor cells with an uncertain id that is intermediate between rods and cones due to a mismatch of the opsin and phototransduction cascade genes (e.g. in Scopelarchidae and Evermanellidae; Aulopiformes), or thanks to the presence of transmuted cells (i.e. rod-like cones in Maurolicus spp.; Sternoptychidae; Stomiiformes). Rhodopsins: Like other vertebrates, most lineages only have one rhodopsin (rh1) gene. Two rhodopsins are found in pearleyes (Scopelarchidae; Aulopiformes), and hatchetfishes (Sternoptychidae, Stomiiformes), and more than three rhodopsin genes are found in lanternfishes (Myctophiformes), spinyfins (Diretmidae), and tube-eye (Stylephoriformes). Photos (from top to bottom): Threadfin dragonfish, Echiostoma barbatum (Stomiiformes; photo Zuzana Musilova); pearleye, Benthalbella sp. (Aulopiformes; photo Zuzana Konvičková); and silver spinyfin, Diretmus argenteus (Trachichthyiformes; photo Vít Kaufman). Based on data from Collin and Partridge (1996), De Busserolles et al. (2017), De Busserolles et al. (2020), Lupše et al. (2021) and Musilova, Cortesi, et al. (2

An (omics) perspective on the evolution of vision in deep-sea
fishes reveals exceptional adaptations to life in the extreme

Musilova & Cortesi 2025 Functional Ecology

besjournals.onlinelibrary.wiley.com/doi/pdfdirec...

#ichthyology #teamfish neat review of genetics of deep-sea vision in fishes

Photograph of a grey and green fish, with a green box inside which is a green play button.

🐟 Thanks to everyone who joined our Killifish Webinar!

We chatted with four expert voices about the brilliant killifish conservation work they have been doing in the Mediterranean Basin #freshwater

ICYMI it's now available to watch again on YouTube 👇
buff.ly/R4wxOcY

Sturgeon surprise! 🧜‍♀️

Gotta tag some #library people! @jacquelinethompson.bsky.social

Backflippin’ feeding action!

#Paddlefishing
#Polyodon
#EndlessPaddlefishMostBeautiful

Le fin!