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Профиль

Todd Oakley

Профиль Vively

I am an evolutionary and marine biologist interested in how new structures and functions originate during evolution. Eyes, vision; photophores, bioluminescence. Macroevolution. Phylogenetics. Molecular Evolution. Integrative and Comparative Biology.

link.growkudos.com/1eecw54o9vk

Jellyfish and relatives repeatedly evolved the same genetic changes across 600 million yearsWe compared thousands of genes across 86 species of jellyfish and their relatives to ask how often natural selection appears to have produced the same changes in proteins in different lineages. These repeated changes were surprisingly widespread. They were somewhat less common in more distantly related species, but remained more frequent than expected by chance even in lineages that separated more than 600 million years ago. Yet pairs of species that had independently evolved the same conspicuous traits—eyes, loss of the jellyfish stage, or upright colonies—did not share more repeated protein changes than other pairs. Instead, the changes were concentrated in genes involved in metabolism, immunity, and processing foreign chemicals. These results suggest that evolution often repeats at the molecular level, but this repetition reflects complex interactions between organisms and their environments rather than being tightly linked to the same obvious traits.link.growkudos.com
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Happy to share that this paper led by @caberger.bsky.social with @stoilovamarina.bsky.social @rebeccavarney.bsky.social @pcart.bsky.social Sam Abrams and Maria Pia is published -- Unexpectedly predictable molecular evolution with diverse ecologies 🧪 🧬 🌊 #Molevol #EvoBio www.pnas.org/doi/10.1073/...

PNASProceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...www.pnas.orgTodd Oakley

We started by studying gene reuse in eyes over deep time -- but were astonished to find adaptive molecular convergence to be rampant and not directly related to important traits, including eyes. Led by PD Cory Berger www.biorxiv.org/content/10.6...

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🧵 Here is a time-lapse video of bioluminescent ostracods that we used as data in a just-posted preprint. What's going on?

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The formatted paper is now out in MBE - describing OPTICS software to predict color sensitivy based on opsin sequence alone: academic.oup.com/mbe/article/...

Validate Useracademic.oup.comTodd Oakley

🧵 New paper! We’re excited to release OPTICS: software that immediately predicts color sensitivity from any opsin protein sequence. In other words: give OPTICS any opsin sequence, and it predicts the wavelength of light the pigment is most sensitive to 🌈👁️ academic.oup.com/mbe/advance-...

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🧵 New paper! We’re excited to release OPTICS: software that immediately predicts color sensitivity from any opsin protein sequence. In other words: give OPTICS any opsin sequence, and it predicts the wavelength of light the pigment is most sensitive to 🌈👁️ academic.oup.com/mbe/advance-...

Accessible and Robust Machine Learning Approaches to Improve the Opsin Genotype-Phenotype MapAbstract. Predicting phenotypes from genetic variation is a central challenge in biology. Here, machine learning (ML) offers great promise, but its use isacademic.oup.com
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We started by studying gene reuse in eyes over deep time -- but were astonished to find adaptive molecular convergence to be rampant and not directly related to important traits, including eyes. Led by PD Cory Berger www.biorxiv.org/content/10.6...

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Symbiotic entrenchment through ecological Catch-22: Cell www.cell.com/cell/fulltex...

Symbiotic entrenchment through ecological Catch-22A symbiotic rove beetle develops a stealth phenotype by silencing production of its hydrocarbon pheromones, enabling it to infiltrate ant colonies, steal ant pheromones, and achieve social acceptance ...www.cell.com
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