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Todd Oakley

@ostratodd.bsky.social
2K followers 1.8K following 237 posts

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.

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Reposted by Todd Oakley
David Ho @davidho.bsky.social · 03/10/2026
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.
nytimes.com
National 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.
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 02/10/2026
Evolutionary contingency facilitates scent divergence in an emergent orchid population www.biorxiv.org/content/10.64898/20…
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Andrew Straw @andrewstraw.bsky.social · 04/09/2026
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...
Bee trajectories in agricultural landscape and two photon microscope for in-vivo calcium activity imaging.
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Sean Carroll @seanmcarroll.bsky.social · 17/08/2026
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.org
Application Guidelines — Guggenheim Fellowship — Guggenheim Fellowships: Supporting Artists, Scholars, & Scientists
Find detailed information on the application process for the Guggenheim Fellowship and learn how to submit your application for a grant.
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Reposted by Todd Oakley
Lauren Sumner-Rooney @laurensr.bsky.social · 10/08/2026
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!*)
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Todd Oakley @ostratodd.bsky.social · 10/08/2026
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 🧪
sicb.org
The hidden language of proteins: understanding the evolution of color vision using AI - SICB
A 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 ...
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Reposted by Todd Oakley
Sarah McAnulty, Ph.D. @sarahmackattack.bsky.social · 30/07/2026
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
words say "Do you want this mural on your building?" with a bunch of lightning bugs and native plants on a mural that is labeled as being 10 by 10 ft
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Todd Oakley @ostratodd.bsky.social · 31/07/2026
link.growkudos.com/1eecw54o9vk
link.growkudos.com
Jellyfish and relatives repeatedly evolved the same genetic changes across 600 million years
We 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.
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Reposted by Todd Oakley
Marc Robinson-Rechavi @marcrr.bsky.social · 29/07/2026
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...
Schematic view of the embryonic expression pattern of the genes Sage, Sum1 and Dll in a spider embryo, showing Sage only in venom gland primordia, Sum1 in chelicerae and other appendages, and Dll at the distal end of appendages
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Casey terHorst @ecoevolab.bsky.social · 28/07/2026
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
eebmentormatch.com
EEB Mentor Match
Visit the post for more.
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Reposted by Todd Oakley
Hoyaboya @hoyaboya1.bsky.social · 29/07/2026
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...
Cory A. Berger et al., CC BY 4.0, https://doi.org/10.1073/pnas.2616248123
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Hoyaboya @hoyaboya1.bsky.social · 29/07/2026
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!!!!!
James W. McDermott et al., CC BY 4.0, https://doi.org/10.1098/rspb.2026.1111
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Reposted by Todd Oakley
phy_papers @phypapers.bsky.social · 29/07/2026
Adaptive molecular convergence is pervasive across deep time and largely decoupled from phenotypic convergence pubmed.ncbi.nlm.nih.gov/42520128
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Todd Oakley @ostratodd.bsky.social · 28/07/2026
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/...
pnas.org
PNAS
Proceedings 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...
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Reposted by Todd Oakley
Joe Brennan @biologyjoe87.bsky.social · 03/07/2026
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!
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Todd Oakley @ostratodd.bsky.social · 03/07/2026
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...
biorxiv.org
Diel metabolic variation and the energetic demands of courtship in bioluminescent Photeros ostracods
The 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 ...
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Todd Oakley @ostratodd.bsky.social · 03/07/2026
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
Slope graph where almost all paired comparisons are higher in night than day for metabolic rate
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Todd Oakley @ostratodd.bsky.social · 03/07/2026
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).
Bar chart showing large vessels with highest metabolic rate, medium vessels with intermediate rate, and small vessels with lowest metabolic rate. Small vessels had lower activity during the day than at night
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Todd Oakley @ostratodd.bsky.social · 03/07/2026
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
A graduated cylinder with a screw capped top fused to it
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Todd Oakley @ostratodd.bsky.social · 03/07/2026
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
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Todd Oakley @ostratodd.bsky.social · 03/07/2026
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
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Todd Oakley @ostratodd.bsky.social · 03/07/2026
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
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Todd Oakley @ostratodd.bsky.social · 03/07/2026
Male representatives of Luxorina ostracods produce bioluminescent courtship displays. People often ask if this is costly
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Todd Oakley @ostratodd.bsky.social · 03/07/2026
🧵 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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Reposted by Todd Oakley
Atal Pande @atal-pande.bsky.social · 03/07/2026
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...
cell.com
Hunting ecology predicts eye arrangements in the modular visual system of spiders
Pande 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...
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Niko Hensley, PhD. @nikohensley.bsky.social · 28/06/2026
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
static.klipy.com
Bioluminescence Giant Squid
ALT: Bioluminescence Giant Squid
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Reposted by Todd Oakley
Anna Klompen, PhD @gelatinoussting.bsky.social · 29/06/2026
First postdoc paper and first Nematostella project! By using the dynamic expression pattern of minicollagens, we describe the transcriptional profile during biogenesis for two major stinging cell types: nematocytes and spirocytes www.biorxiv.org/content/10.6... #StunningStella
biorxiv.org
Minicollagen expression dynamics reveal a transcriptional program for cnidogenesis in the sea anemone Nematostella vectensis
Cnidae are explosive harpoon-like organelles localized within stinging cells, or cnidocytes, of the phylum Cnidaria (jellyfish, hydroids, sea anemones, and corals). These unique Golgi-derived vesicula...
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Todd Oakley @ostratodd.bsky.social · 26/06/2026
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/...
academic.oup.com
Validate User
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Reposted by Todd Oakley
Molecular Biology and Evolution @molbioevol.bsky.social · 22/06/2026
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
MBE | Accessible and robust machine learning approaches to improve the opsin genotype-phenotype map
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Reposted by Todd Oakley
Dr. Elizabeth Santos @lizmillermacroevo.bsky.social · 18/05/2026
I am recruiting Ph.D. students this cycle. Students interested in deep-sea fishes and phylogenetic comparative methods are an especially good fit.
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Laura Alencar 🇧🇷🐍🦎 @alencarlrv.bsky.social · 11/06/2026
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
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
🧬 🧪 i am not so good with the icons
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
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! 🌈👁️✨
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
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?
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
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. 🌊🐟🦐
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
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.
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
For quick predictions from one or a few opsin genes, we also have a simple Galaxy interface: galaxy-dev.cnsi.ucsb.edu:8080
galaxy-dev.cnsi.ucsb.edu
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
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...
github.com
GitHub - 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
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
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
visphys.eemb.ucsb.edu
VPOD Explorer
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
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/...
academic.oup.com
Discovering 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
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
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
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
We are on a long road toward a big goal: predicting phenotype from genotype For vision, one key phenotype we are starting with is spectral sensitivity - the color of light a visual pigment “sees” best
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
🧵 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.com
Accessible and Robust Machine Learning Approaches to Improve the Opsin Genotype-Phenotype Map
Abstract. Predicting phenotypes from genetic variation is a central challenge in biology. Here, machine learning (ML) offers great promise, but its use is
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 04/06/2026
#SMBE2026 S02: Powers and pitfalls of artificial intelligence for molecular evolution and phylogenetics 🗓️ Mon Jun 29, 10:20am 🔗 smbe2026.org/programme
SMBE2026 | S02 Powers and pitfalls of artificial intelligence for molecular evolution and phylogenetics
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Molecular Biology and Evolution @molbioevol.bsky.social · 05/06/2026
Muñoz-Mérida & Muñoz-Pajares introduce the concept of the pan-functionome — the full set of protein functions encoded by the proteome of individuals belonging to a taxonomic group — and explore its evolutionary implications. 🔗 doi.org/10.1093/molbev/msag121 #evobio #molbio
MBE | Beyond genomes: functional signatures reveal evolutionary patterns across the tree of life
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John Wares @johnwares.bsky.social · 02/06/2026
I’m obliged to pass on our study of light spectrum 🌈 variation in fireflies onlinelibrary.wiley.com/doi/full/10.... by former PhD student Margot Popecki 😊
onlinelibrary.wiley.com
The Role of Pigments in Light Color Variation of the Firefly Photinus pyralis
We tested the novel hypothesis that genes encoding enzymes and transporters in pigment pathways (“pigment genes”) produce pigments in the firefly light organ that filter bioluminescent light, tuning ...
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Todd Oakley @ostratodd.bsky.social · 11/05/2026
... and seems to have evolved multiple times: www.science.org/doi/full/10....
science.org
A morphological basis for path-dependent evolution of visual systems
Multiple convergent origins of visual systems show that macroevolution of complex traits can be rapid and contingent upon preexisting traits.
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Todd Oakley @ostratodd.bsky.social · 11/05/2026
Some with lenses made from aragonite like the shell: www.cell.com/current-biol...
cell.com
A Chiton Uses Aragonite Lenses to Form Images
Hundreds of ocelli are embedded in the dorsal shell plates of certain chitons [1]. These ocelli each contain a pigment layer, retina, and lens [2], but it is unknown whether they provide chitons with ...
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Todd Oakley @ostratodd.bsky.social · 09/05/2026
It was a great day! Thanks for the hospitality!!
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Ivan Ferreira @ptychodera.bsky.social · 09/05/2026
We @lowelab.bsky.social had a blast hosting @ostratodd.bsky.social at the Hopkins Marine Station! A fantastic day talking all things bioluminescence, ostracods, chitons, repeatability, contigency, phylogeny, courtship, mentoring, surfing, baseball, brewing and all The first of many visits I hope!
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