🚨 Why can’t mammals regenerate limbs like frog tadpoles or salamanders?
In our new paper in @science.org , we show that species-specific oxygen sensing acts as a gatekeeper for initiating limb regeneration 🐭🐸
🔗 www.science.org/doi/10.1126/... #EvoDevo
Lizard head on the journal cover
Our work as Editor's choice in @evolletters.bsky.social !✨️
Developmental biases & micro- to macroevution in the lizard skull 🦎
academic.oup.com/evlett/advan...
Phenotypic correlations across environments suggest beneficial mutations impact relatively few latent phenotypes underlying fitness. Top: A library of 4,000 barcoded, evolved yeast strains was competed simultaneously against their ancestor across a panel of environments (multiple “base” media with individual small perturbations like extra glucose or EtOH). Middle: The reaction norm of fitness (δX) of evolved yeast strains (a to f) is plotted across a panel of perturbations (Pi). Each line connects the phenotypes from a single mutant representing its pleiotropic consequence across environments. The phenotypic profile of mutants clustered into discrete patterns (here termed ‘fitnotypes’). For simplicity, two such clusters are shown representing single fitnotypes (red = mutants a, b, c; blue = d, e, f). For example, F1 includes mutants who only demonstrated a benefit in P3. Note mutant phenotypes can also form linear combinations of fitnotypes (purple). When these mutants are tested across the same perturbations but in a new base environment, the outcome could range, at its extremes, from (bottom left) being maintained as the exact same groups that fell into the original fitnotypes, or (bottom right) these groups could split, clustering into entirely new sets (purple = b, d, e, f; green = a, c). Data from Ghosh and colleagues indicate that evolved strains fall in between, representing a blend of the bottom left and bottom right panels. There remain just three or four fitnotypes per environment, but these still overlap partially with the original fitnotypes.
How predictable are the collateral effects of adaptation? This Primer explores a @plosbiology.org study suggesting that growth across environments is fairly predictable because selected mutations only affect a few latent fitness-impacting phenotypes 🧪 Paper: plos.io/4dLy2Ez Primer: plos.io/4lYdUBh
Two models for the nature of pleiotropy in adaptation. Left: Schematic of the environmental structure in this study. Environments can be mapped onto a multidimensional environment space characterized by chemical and physical compositions. The large green circle represents an environment where adaptive mutants evolved, and the large pink circle is a distant environment. Around each base, a set of identical environmental perturbations (arrows) is applied, generating clusters of similar environments around distinct base environments. Top right: Schematic of fitnotype map for adaptive mutants near their home base environment. By measuring fitness in each of the green environments, one can infer how many fitnotypes matter for this set of mutants in their home environment. Here, only four of the possible 8 fitnotypes matter. Bottom right: When the mutants are moved to the distant base environment, and their fitness is measured in all pink environments (base and perturbations), there are two possibilities. Either more fitnotypes become important and the space appears higher-dimensional (left, pleiotropic expansion), or the set of fitnotypes that matters remains low-dimensional, but shifts (right, pleiotropic shift).
Predicting the effect of a #mutation on #fitness is hard. @oliviamghosh.bsky.social @petrovadmitri.bsky.social &co use fitness effects of adaptive yeast mutants to show that underlying genotype-phenotype-fitness maps are low-dimensional but context-dependent @plosbiology.org 🧪 plos.io/4dLy2Ez
Repeated cloning cannot be sustained indefinitely in mammals, according to a 20-year study in mice published in Nature Communications. The results suggest that sexual reproduction is necessary to eliminate large-scale genetic mutations that can accumulate in mammalian clones. 🧬 🧪
You're invited to complete a short anonymous survey about device failures in bird biologger deployments! 📡 🦆
Responses accepted within the next 8 weeks. 📆
Survey link is in our bio 🔗
If you have questions please email failedbiologgingdevices@gmail.com 📧
New paper + new species: Tokara Leaf Warbler (𝘗𝘩𝘺𝘭𝘭𝘰𝘴𝘤𝘰𝘱𝘶𝘴 𝘵𝘰𝘬𝘢𝘳𝘢𝘦𝘯𝘴𝘪𝘴). Genome-wide nuclear + mtDNA, backed by song differences, show it’s distinct from Ijima’s Leaf Warbler despite near-identical morphology. We recommend protection/Vulnerable status and monitoring. buff.ly/VpQBCro
Leipzig U and the MPI for Evolutionary Anthropology (MPI-EVA) have an open faculty position (W2) in evolutionary population genetics! This position is tenured and comes with generous core funding. We are eager to welcome a new colleague! Deadline March 11.
www.uni-leipzig.de/en/newsdetai...
Excited to see our FML Research Group Leader
@luisapallares.bsky.social
in the latest Max Planck Research! 🎉
The article follows her journey from Colombia to Germany and her work on how genes and environment shape complex traits using fruit flies.
Read the full story: www.mpg.de/26180374/W00...
@jomcinerney.bsky.social proposes that genomes do not encode fixed functions but rather “probability distributions” over functional and phenotypic outcomes, and introduces “genomic perplexity” as a measure of gene-context incompatibility.
🔗 doi.org/10.1093/molbev/msag041
#evobio #molbio
New teaching neurosis drops.
Student: It's funny. When I listen to the lecture recording the microphone picks up you heart beating, and so I can hear when you get nervous.
<sees look on my face>
Oh don't worry, it's not very noticeable.
2nd Student: Oh yeah, I've totally noticed that too!
I used Claude Opus 4.5/4.6 (and a bit of Codex GPT-5.3) to port edgeR to Python. See edgePython github.com/pachterlab/e...
This allowed me to develop a single-cell DE method that extends NEBULA with edgeR Empirical Bayes. All in one week. Details in doi.org/10.64898/202...
1. Kevin Gross and I have a new paper out today PLOS Biology.
We used economic models based around screening games and the market for unpaid labor to highlight a meltdown cycle threatening peer review.
Have you ever wondered 🤔... Does phenotypic variance respond to environmental perturbation? Does it have a genetic basis? Are mean and variance regulating loci exposed to different selection pressures? These and more questions are explored in our new preprint 🔥
www.biorxiv.org/content/10.6...
Our BehaveAI paper has just come out!
Easy & effective tracking & behavioural classification, even with tiny (2px), fast moving, camouflaged objects.
Paper: doi.org/10.1371/jour...
Download: github.com/troscianko/B...
@uniexecec.bsky.social @kevinjgaston.bsky.social @jimamclgalloway.bsky.social
Proud to present: Suitcase Science, a new outreach format containing 6 assignments to take on a journey to schools in the region, to teach kids about terns, how to study them, their fascinating behaviour and some of the things that threaten them. Wanna book us? Drop me a line. :-)
"Nothing could be less inviting than the first appearance. A broken field of black basaltic lava, thrown into the most rugged waves, and crossed by great fissures, is everywhere covered by stunted, sun-burnt brushwood, which shows little signs of life. The dry and parched surface, being heated by the noon-day sun, gave to the air a close and sultry feeling, like that from a stove: we fancied even that the bushes smelt unpleasantly. Although I diligently tried to collect as many plants as possible, I succeeded in getting very few; and such wretched-looking little weeds would have better become an arctic than an equatorial Flora."
In celebration of #DarwinDay, here are his decidedly mixed first impressions after landing on the Galápagos (17 Sept 1835; from 'the Voyage' Chap X):
"Nothing could be less inviting..."
Zhang et al. compared the genomes of six hibernating mammals, identifying an ancient amino acid substitution in POMT2 exhibiting signals of both convergent and positive selection. Functional studies demonstrated a role in hypoxia adaptation.
🔗 doi.org/10.1093/molbev/msag001
#evobio #molbio
elifesciences.org/articles/105...
Postdoc Yannick Günzel, who studies how clonal raider ants interact with their larvae, went to a comedy show in NYC. Now he’s famous… 🤪
youtube.com/shorts/ZETUy...
Throat coloration in common wall lizards (Podarcis muralis). From top to bottom: White morph with the characteristic green and black coloration of the nigriventris syndrome; White morph with the ancestral brown phenotype; yellow and orange morphs from populations where individuals show varying expression of the nigriventris characters.
Two new Science studies on lizard coloration reveal how a delicate interplay of genetics, environment, and social dynamics can either preserve or erase polymorphic diversity in species.
📄: https://scim.ag/4srYKHi
📄: https://scim.ag/4qCcsWn
It is out, it is out! Our study on neural crest cells and micro to macroevolution in lizard skull 🦎
Final version of paper with @smishra677.bsky.social now published in a wonderful issue of GENETICS!
academic.oup.com/genetics/art...
In a new GBE Review, @david-peede.bsky.social et al. overview the SMC model and extensions, discuss examples of discoveries made with the help of SMC-based inference, and comment on the assumptions, benefits, and drawbacks of various methods.
🔗 doi.org/10.1093/gbe/...
#genome #evolution #compbio
What looked like a hearing organ on a tiny stinkbug’s leg turned out to be something far stranger: a fungal nursery that mother bugs use to coat their newly laid eggs in protective symbiotic hyphae, shielding their offspring from parasitic wasps, a Science study finds. https://scim.ag/3MXQ4bt
🧬 Just out in Bioinformatics Advances: “tskit arg visualizer: Interactive plotting of ancestral recombination graphs.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf302
Authors include: @kitchensjn.bsky.social, @yanwong.bsky.social
