iiinova — where your digital self keeps evolving

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

🧵 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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Todd Oakley @ostratodd.bsky.social · 25/04/2026

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...

Box jellyfish Tripedalia cystophora. Photo by David Liitschwager taken in the lab of Todd Oakley at UCSB

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Todd Oakley @ostratodd.bsky.social · 12/10/2025

We have sea pansies (Renilla) for our inverts class and we got some photos of the bioluminescence

Green dots on black background in a donut shape

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Todd Oakley @ostratodd.bsky.social · 19/04/2025

Huge blooms and beaching of Valella valella lately in SB!

An individual Valella valella on a rock on a Santa Barbara beach

Thousands of Valella valella on the beach high tide line in Santa Barbara

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Todd Oakley @ostratodd.bsky.social · 31/12/2024

I like to ask the class, ‘what is wrong with this phylogeny?’ I always get answers like, humans should be most evolved, etc. But of course this tree is correct

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Todd Oakley @ostratodd.bsky.social · 18/12/2024

I got to spend some time this weekend with family among the giant trees :)

Person standing in a hollow fallen sequoia

Two cousins in front of a giant redwood tree

Me standing in front of a giant redwood tree (needed 0.5x lens making me look tall and thin)

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Todd Oakley @ostratodd.bsky.social · 09/12/2024

I hadn’t been to the physical library for a while. It was hoppin’ this week with students studying for finals. Smelled like knowledge

Title pages of two classic books on bioluminescence

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Todd Oakley @ostratodd.bsky.social · 05/12/2024

Also proud of the persistence here of co-authors and I. From proposal to pub -> ~10 years, 3 postdocs, 1 lab tech, 14 months in review. Not to mention ~7 MY it took Chiton to evolve eye spots and ~260 MY it took to evolve all the chiton visual systems www.science.org/doi/full/10....

Phylogeny of chitons shows two different types of eyes each evolved twice

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Todd Oakley @ostratodd.bsky.social · 05/12/2024

Clades with bioluminescent courtship - a sexually selected trait - have more species than their closest relatives without it. Led by @emily-ellis.bsky.social (If I am forced to pick just one. The result is just so clean) doi.org/10.1016/j.cu...

In 10 of 10 comparisons, clades with luminous courtship have more species than the most closely related clade without

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Todd Oakley @ostratodd.bsky.social · 30/11/2024

Seems like a tall ‘tale’ but it happens all the time. Photo from very recently.

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Todd Oakley @ostratodd.bsky.social · 30/11/2024

Among secretory innovations, bioluminescence is particularly important because it evolved convergently many times to influence predator–prey interactions, while often producing courtship signals (pictured) linked to increased rates of speciation.

Long exposure of courtship displays of luxorine ostracods with a coral in the foreground. Blue wisps spiral above the sea floor.

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Todd Oakley @ostratodd.bsky.social · 30/11/2024

Bioluminescence evolved in ostracod crustaceans some 200 Million Years ago, first used to ward off predation, later as a courtship signal. How did this eco-system-altering trait originate? The final version of a paper led by Lisa Mesrop, just released, addresses this question. 🧪🦑 #evolution #evodevo

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Todd Oakley @ostratodd.bsky.social · 29/11/2024

I watched the first episode of Our Oceans yesterday on The Pacific. In an opening montage, I spotted some ostracod bioluminescence. Hoping they are featured in the Atlantic

Looks like a cardinal fish that tried to eat a se firefly and is now glowing electric blue

A lionfish surrounded by delicate bioluminescent pulses from the blue courtship signals of sea fireflies

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Todd Oakley @ostratodd.bsky.social · 23/11/2024

Surf was UP today at ucsb. Rain coming tomorrow

UCSB’s campus point at sunset with surfers riding waves

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Todd Oakley @ostratodd.bsky.social · 18/11/2024

Tide pooling with invert zoology class today

Low tide at ucsb with students on Rocky tidepools

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Todd Oakley @ostratodd.bsky.social · 14/11/2024

I’m working on a graphic to better understand lunar cycle for our lab’s work at UCSB on lunar rhythms in crustaceans

Figure showing how the full moon rises at sunset and rises 50 minutes later each night, with less illumination each night until the new moon. After new moon, it’s in the sky at sunset and sets 50 minutes later each night, growing in illumination until full again.

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Todd Oakley @ostratodd.bsky.social · 11/11/2024

Found something like this on Catalina Island a few years back

Crystal shell on black lab bench surface

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Todd Oakley @ostratodd.bsky.social · 11/11/2024

Ostracodologist here 👋 I mainly study the bioluminescent ones (sea fireflies)

Long exposure photo of bioluminescent courtship signals of sea fireflies by Kyle McBurnie. Magical blue wisps hang in the black ocean over corals

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Todd Oakley @ostratodd.bsky.social · 09/11/2024

Congratulations to Lisa Mesrop for publishing in MBE. She finds an ostracod bioluminescent system uses old and new genes. Many of the conserved genes may be involved in secretory processes or toxin production, perhaps for anti-predation. A link to the paper is here: academic.oup.com/mbe/article/...

In the dark, a cardinalfish, is lit up when it bites a bioluminescent ostracod. The fish spits out the ostracod with a floating ring of bioluminscence, as the ostracod zips down to the bottom of view leaving a bright trail of blue

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Todd Oakley @ostratodd.bsky.social · 28/10/2024

Seth is also developing a tool called Opsin Phenotyping Tool for Inferring Color Sensitivity (OPTICS), where you just plug in an opsin sequence and predict its lambda max. If you want to try it, get in touch. In this figure from OPTICS, I predicted lambda max of a box jellyfish opsin

Histogram showing mean about 492 nm with wide scatter from 460-525 nm as predictions of Tripedalia lambda max

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Todd Oakley @ostratodd.bsky.social · 28/10/2024

Especially for vertebrates, where there is A LOT of data, we can very accurately predict phenotypes from sequences alone. We even looked at cases of epistasis, and I was surprised how well the predictions can do

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Todd Oakley @ostratodd.bsky.social · 28/10/2024

A histogram of all the opsins and their lambda-max phenotypes is Figure 1:

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Todd Oakley @ostratodd.bsky.social · 03/05/2024

Fighting with a copy editor to include Oxford commas in our manuscript, but the journal policy is to not use them :(

Text "With the Oxford comma: We invited strippers, JFK, and Stalin" shows a cartoon of JFK, Stalin, and two women in lingerie. Below text "Without the Oxford comma: We invited strippers, JFK and Stalin" shows JFK and Stalin in the same lingerie because without the extra comma, the phrase might imply they are strippers.

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Todd Oakley @ostratodd.bsky.social · 15/03/2024

Our findings underscore the critical and fundamental importance historical events (that sometimes may seem inconsequential) in shaping future evolutionary pathways. This work was a true team effort that I am proud to have been a part of!

George McFly finally stands up to Biff in Back to the Future, the movies own Critical Junction

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Todd Oakley @ostratodd.bsky.social · 15/03/2024

We thought if Path Dependent evolution is at play, we'd see a morphospace gap. Rebecca tallied slit number and aesthtete number (a proxy for how many nerves run through the shell).

Morphospace graph of chiton shell slits and aesthetes showing morphospace gap

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Todd Oakley @ostratodd.bsky.social · 15/03/2024

The moment of realization that chitons evolved visual systems four distinct times in two different ways was one of those "a ha" moments, made possible and confirmed when @rebeccavarney.bsky.social meticulously put all the molecular data together

Chiton phylogeny showing 4 origins of 2 eye types

Doc Brown and Marty McFly in a "Great Scott" moment

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Todd Oakley @ostratodd.bsky.social · 15/03/2024

Morris Aguilar and Joie Cannon developed methods for target DNA capture in chitons, with probes designed from Dan's transcriptomes, enabling us to sequence specific parts of genomes using DNA from Doug's worldwide collection.

Chiton on a rock with USVI beach blurred in the background. Photo by Doug Eernisse

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Todd Oakley @ostratodd.bsky.social · 15/03/2024

As a co-anchor author of this fun project, I had the privilege of working with an incredible team to study visual systems in chitons, which evolved not once but four times! Chiton visual systems either use thousands of eye spots (G), or hundreds of eyes with aragonite lenses (F)

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Todd Oakley @ostratodd.bsky.social · 15/03/2024

Unlike the movies, we don't have a time machine. Still, we can study evolutionary predictability and Time’s Arrow vs Time’s Cycle – using comparative methods, especially when there are convergent evolutionary events that act like replicate histories – almost like a time machine.

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Todd Oakley @ostratodd.bsky.social · 15/02/2024

Not only that, but we can go the other way. We can find amino acid sites that have a strong correlation with changes in lambda-max. In the opsin world, these are called spectral tuning sites because they alter the color sensitivity of the opsin, and therefore the animal

Bar charts showing position 181 and 261 show very different l-max values depending on the amino acid at that position

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Todd Oakley @ostratodd.bsky.social · 15/02/2024

If we use ML can we predict the lambda-max? Yes! Often we can! There is high correlation between predicted and actual, and no obvious systematic errors.

Scatter plot of known and predicted l-max values shows R^2 of 0.968

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Todd Oakley @ostratodd.bsky.social · 15/02/2024

This was not easy, as much of the old data are not computationally readable, and often buried in supplements, or needed to be inferred by careful reading and reconstruction of the mutations. Here is a histogram of all the data, over 800 sequences!

Histogram of sequences counted by wavelength of l-max

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Todd Oakley @ostratodd.bsky.social · 11/02/2024

Big minus tide today at UCSB. We tried to find staurozoa, but didn’t find any. Yet.

Coal Oil Point tide pools on a clear day

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Todd Oakley @ostratodd.bsky.social · 14/12/2023

Bioluminescence in ostracods, fireflies, and sea pansies is distinct: different functions, genes, & substrates. EXCEPT Each system metabolizes each luminous substrate using the same gene family - sulfotransferases! (next draft now live) by: @emilylau.bsky.social www.biorxiv.org/content/10.1...

A female ostracod of species Photeros annecohenae is a smooth oval with bristly antennae visible on one end and a large charismatic compound eye visible. An ethereal blue light streams downward from the animal, its bioluminescent mucus. Photo by E. Lowndes

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Todd Oakley @ostratodd.bsky.social · 13/12/2023

Here was Kerry and I Manawa hunting this past August. We only found half a valve this time :(

View from the Manawa collecting site - ocean, beach, pelagic bird

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Todd Oakley @ostratodd.bsky.social · 14/10/2023

Projecting the current partial solar eclipse on the wall of my patio

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Todd Oakley @ostratodd.bsky.social · 29/09/2023

Diversity in Diving at UCSB: giving.ucsb.edu/Funds/Give?i...

Help students dive deeper
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For many students, getting certified in SCUBA diving can be daunting — physically, mentally, and financially. Significant barriers exist to gaining all the training, equipment, and certifications required to conduct research underwater, especially for underrepresented students who may have no previous exposure to the ocean or SCUBA as a research tool. Diversity in Diving launched last year in recognition that some of the brightest emerging environmental scientists face barriers to
becoming scientifically certified SCUBA divers

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Todd Oakley @ostratodd.bsky.social · 26/09/2023

The ostracods are, I agree, quite charismatic

A group of cyprinida ostracods under a dissecting microscope

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Todd Oakley @ostratodd.bsky.social · 23/09/2023

Very easy to use! Looks right for me

Oakley research word cloud. Eyes evolution opsin

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Todd Oakley @ostratodd.bsky.social · 15/09/2023

Last month I checked an item off my bucket list and saw #bioluminescent fungus gnats in NZ. I also learned of a Gould essay about them and how the adult stage of life is sometimes more of an afterthought: www.online-keys.net/sciaroidea/1...

Green dots are glow worms on a dark background in a NZ cave

Mucus lines of bioluminescent fungus gnats aka ‘glow worms’

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