Todd Oakley

youtu.beThe hidden language of proteins: understanding the evolution of color vision using AIYouTube video by Society for Integrative & Comparative Biology

We’re developing a database of opsins—light-sensitive protein. One reason is to simulate the evolution of color sensitivity. Seth Frazer and I joined student journalist Momin Ahmed Khaki to discuss our work in this SICB interview: youtu.be/MIEy79nv5N8

sicb.orgThe hidden language of proteins: understanding the evolution of color vision using AI - SICBA popular 2013 webcomic by The Oatmeal sparked a widespread online fascination with the idea that mantis shrimp can see mysterious “shrimp colors” beyond human imagination. Although the story is more ...

We presented this work at SICB 2026, where student journalist Momin Ahmed Khaki covered how we’re exploring the ways ancient starting points shape the evolution of light sensitivity. Read his story: sicb.org/sicb-news/th...

nytimes.comNational Science Foundation Diverted $1.4 Billion in Science Funds Mandated by Congress (Gift Article)The move, affecting about one-fifth of the National Science Foundation’s primary research budget, is the latest sign of how the White House is asserting more control over grants.

Interested in the tools or data? OPTICS predicts opsin peak light sensitivity from amino acid sequences: academic.oup.com/mbe/article/... Explore, search, and download opsin genotype–phenotype data from our VisPhys database: visphys.eemb.ucsb.edu

Todd Oakley reposted

David Ho

@davidho.bsky.social

I don’t think everyone realizes how bad things are for US science: For the fiscal year that just ended, the Trump regime withheld $1.4 billion from the National Science Foundation’s research budget, which is about 1/5 of its primary research budget.

Todd Oakley reposted

bioRxiv Evolutionary Biology

@biorxiv-evobio.bsky.social

Evolutionary contingency facilitates scent divergence in an emergent orchid population https://www.biorxiv.org/content/10.64898/2026.09.26.753903v1

Todd Oakley reposted

Andrew Straw

@andrewstraw.bsky.social

4 Sept

We are hiring! Come join us in the Straw Lab at the @biologyunifreiburg.bsky.social . Seeking a scientist to work on the neural and computational mechanisms of visual navigation in honey bees. uni-freiburg.de/en/job/00005...

Todd Oakley reposted

Sean Carroll

@seanmcarroll.bsky.social

17 Aug

Applications for this year's Guggenheim Fellowships @guggfellows.bsky.social are now open! Mid-career awards to individuals across the arts, humanities, natural sciences, social sciences, and interdisciplinary areas. Deadline Sept. 15. www.gf.org/program/how-...

gf.orgApplication Guidelines — Guggenheim Fellowship — Guggenheim Fellowships: Supporting Artists, Scholars, & ScientistsFind detailed information on the application process for the Guggenheim Fellowship and learn how to submit your application for a grant.

Todd Oakley reposted

Lauren Sumner-Rooney

@laurensr.bsky.social

10 Aug

Two weeks left to apply for our postdoc position on vision in trilobites! Come and explore the exciting world of reconstructing vision in the fossil record, using some of the most iconic extinct animals to grace our oceans! Please reach out + RT! (*Deadline in fact 23.59 BST on the 26th August!*)

Lauren Sumner-Rooney@laurensr.bsky.social

📢 JOB ALERT! 📢 I am recruiting a 30-month postdoc to work on modelling the vision of trilobites @hfspo.bsky.social ! If you like 3D data, fossils, and functional morphology, this is the one for you! 📆Deadline 27. Aug Pls contact me with any Qs and share widely! www.bristol.ac.uk/jobs/find/de...

bristol.ac.ukDetails | Working at Bristol | University of Bristol

@sarahmackattack.bsky.social

10 Aug

Here is a great article written about some of our ongoing work on the evolution of vision that we presented at a conference earlier this year: sicb.org/sicb-news/th... #evolution 🧪

Todd Oakley reposted

Sarah McAnulty, Ph.D.

30 July

Hey Philadelphia!! Do you want this mural on your building?? Here’s what we’re looking for: You must own the building. Must be in Philly The flatter the surface the better! The more people that will see it the better. We want to install in September Email me if that's you SkypeAScientist@gmail.com

link.growkudos.com/1eecw54o9vk

31 July

link.growkudos.comJellyfish 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.

Todd Oakley reposted

Marc Robinson-Rechavi

@marcrr.bsky.social

eebmentormatch.comEEB Mentor MatchVisit the post for more.

New preprints! 1/3 Spider venom glands are modified salivary glands which have recruited appendage and myogenic programs from other the developmental programs of other organs. Led by Giulia Zancolli, with @yehumoran.bsky.social doi.org/10.64898/202...

Todd Oakley reposted

Casey terHorst

@ecoevolab.bsky.social

28 July

EEB Mentor Match is now open! But apps due soon (8/17). Mentees: get help applying for grad school or fellowships in ecology & evolution. Mentors: senior grads, post-docs, or faculty in these fields willing to give advice Org by Diversity Cmte of @asn-amnat.bsky.social Pls share! eebmentormatch.com

Todd Oakley reposted

Hoyaboya

@hoyaboya1.bsky.social

Berger et al. (2026-07, Proceedings of the National Academy of Sciences) Adaptive molecular convergence is pervasive across deep time and largely decoupled from phenotypic convergence doi.org/10.1073/pnas...

Todd Oakley reposted

Hoyaboya

@hoyaboya1.bsky.social

McDermott et al. (2026-07, Proceedings of the Royal Society B: Biological Sciences) 「動物における対称性の進化に対する形態系統学的アプローチ」 A morphological phylogenetic approach to the evolution of symmetry in animals doi.org/10.1098/rspb... うおおおおおおお！！！！！

Todd Oakley reposted

phy_papers

@phypapers.bsky.social

Adaptive molecular convergence is pervasive across deep time and largely decoupled from phenotypic convergence https://pubmed.ncbi.nlm.nih.gov/42520128/

pnas.orgPNASProceedings 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...

28 July

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/...

Todd Oakley@ostratodd.bsky.social

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...

Todd Oakley reposted

Joe Brennan

@biologyjoe87.bsky.social

UC Davis Ecology & Evolution Grad Preview Program is accepting applications until July 20th! It's a fully virtual program where you are paired with a grad student mentor and learn about what grad school entails, how to apply, and what student life is like! Please share widely!

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

We also noticed that day time metablic rate seemed lower than night time. We'd also noticed during our years of field work that ostracods seem to "sleep" during the day

biorxiv.orgDiel metabolic variation and the energetic demands of courtship in bioluminescent Photeros ostracodsThe energetic demands of courtship are central to sexual selection, but their magnitude and temporal variation remain poorly quantified in many signalling systems. We used closed-chamber respirometry ...

This is a small study, but hopefully sets the stage for future work in this area, especially by establishing a protocol :) 🧪 Here is the preprint link, for anyone interested: www.biorxiv.org/content/10.6...

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

Adriana and Dan know fiber optic respirometry and we wanted to try it with sea fireflies. So a UCSB glassblower made custom vessels where we could measure oxygen depletion in a closed container where ostracods could also signal. In that original video, the blue streaks are signals in cylinders

We also used smaller vessels that did not permit courtship signaling. We were able to quantify the metabolic demands associated with courtship compared to swimming along (medium vessels) and low activity demands (small vessels).

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

I was talking about this with co-author Dan Speiser at a SICB conference and he and his lab have been measuring oxygen consumption. So we dreamed of doing this one day with signaling sea fireflies

So we planned to make it happen. We started discussing with co-authors Adriana Halvonik-Sanchez and @nikohensley.bsky.social and @cheyennemckinley.bsky.social about how it might work. The respirometry expertise of Adriana and Dan along with ostracod expertise of Niko and Cheyenne was key

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

Male representatives of Luxorina ostracods produce bioluminescent courtship displays. People often ask if this is costly

The closest published work on that question found that luxorines (sea fireflies) could produce a lot of signals before exhausting their stores. Yet I often wondered about the impact of the swimming they must do. These little guys swim and stop rapidly to make the signals

Todd Oakley reposted

Atal Pande

@atal-pande.bsky.social

cell.comHunting ecology predicts eye arrangements in the modular visual system of spidersPande et al. show that visually hunting spiders have convergently evolved forward-facing eyes. The positions and orientations of the eyes show the greatest morphological disparity and fastest evolutio...

Really excited to share that my first PhD chapter is now out in @currentbiology.bsky.social! 🕷️👀 We show that visually hunting spiders have repeatedly evolved forward-facing eyes, highlighting the remarkable evolutionary flexibility of their modular visual system. doi.org/10.1016/j.cu...

Todd Oakley reposted

Niko Hensley, PhD.

@nikohensley.bsky.social

28 June

Replying to @biorxiv-behav.bsky.social

In quick succession, a fun behavior project with data collected by co-authors before I even knew what an ostracod was! Also happy for another paper with JG Morin, who discovered these ostracods in 1979. Good to have a citation for how these lil shrimp with big lights actually defend themselves

academic.oup.comValidate User

26 June

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/...

Todd Oakley@ostratodd.bsky.social

🧵 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-...

academic.oup.comAccessible 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 is

Todd Oakley reposted

Molecular Biology and Evolution

@molbioevol.bsky.social

22 June

Seth Frazer & @ostratodd.bsky.social advance ML modeling of the opsin genotype–phenotype map, introducing the Opsin Phenotype Tool for Inference of Color Sensitivity platform, and present the Mine-N-Match (MNM) pipeline. 🔗 doi.org/10.1093/molbev/msag138 #evobio #molbio

Todd Oakley reposted

Dr. Elizabeth Santos

@lizmillermacroevo.bsky.social

18 May

I am recruiting Ph.D. students this cycle. Students interested in deep-sea fishes and phylogenetic comparative methods are an especially good fit.

Todd Oakley reposted

Laura Alencar 🇧🇷🐍🦎

@alencarlrv.bsky.social

11 June

Interested in #macroevolution, #macroecology, and mountain biodiversity? I'm recruiting a #postdoc for an NSF-funded project at Yale, in collaboration with Martha Muñoz (Yale) and Maya Stokes (Florida State University). I'll be at #Evol2026 and happy to chat! Link below

OPTICS is out now, and we’re excited to see what people do with it. Stay tuned for more developments — and please get in touch if you have ideas, questions, cool opsins, or organisms with mysterious visual worlds! 🌈👁️✨

🧬 🧪 i am not so good with the icons

Colleagues around the world are already using these approaches to predict opsin phenotypes in krill, fishes, and other amazing organisms. It is opening the door to asking how visual systems evolve across environments and across the tree of life. 🌊🐟🦐

We are also using simulations of opsin evolution to ask how things like epistasis shape phenotypic diversity. In other words: how do molecular changes interact with each other to affect how visual systems evolve?

galaxy-dev.cnsi.ucsb.edu:8080galaxy-dev.cnsi.ucsb.edu:8080

For quick predictions from one or a few opsin genes, we also have a simple Galaxy interface: galaxy-dev.cnsi.ucsb.edu:8080

Why are we excited? Because this gives us a practical genotype–phenotype map for opsins. We can now make informed predictions about visual sensitivity very quickly and easily, even when physiology is hard to measure directly.

visphys.eemb.ucsb.eduVPOD Explorer

First author Seth Frazer has also built a very nice interface for exploring VPOD here: visphys.eemb.ucsb.edu It makes the database much easier to search, visualize, and use. If you know of data we missed, you can upload it there, and we will verify and add it to the next version

github.comGitHub - VisualPhysiologyDB/optics: An open-source tool that predicts the Opsin Phenotype (λmax) from unaligned opsin amino-acid sequences.An open-source tool that predicts the Opsin Phenotype (λmax) from unaligned opsin amino-acid sequences. - VisualPhysiologyDB/optics

Now we are releasing the Opsin Phenotype Tool for Inference of Color Sensitivity OPTICS 🎉 The most flexible way to use it is in Python, and Seth Frazer has done a terrific job with the documentation. github.com/VisualPhysio...

The story actually began with a failed grant proposal 😅 Even though the proposal was never funded, it forced us to think hard about what the field needed: better organized data, better tools, and more accessible ways to predict functions from gene sequences

academic.oup.comDiscovering genotype–phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)AbstractBackground. Predicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlig

We started building the Visual Physiology Opsin Database, bringing together opsins and measured visual pigment sensitivities, giving us training data for machine learning. Published with collaborators from GW who built deepBreaks, the engine that powers OPTICS academic.oup.com/gigascience/...