Todd Oakley

I’m in Cincinnati right now with a student trying to learn how to knock down genes in ostracods with RNAi 😎

Ancient Secretory Pathways Contributed to the Evolutionary Origin of an Ecologically Impactful Bioluminescence System - PubMed Evolutionary innovations in chemical secretion-such as the production of secondary metabolites, pheromones, and toxins-profoundly impact ecological interactions across a broad diversity of life. These secretory innovations may involve a "legacy-plus-innovation" mode of evolution, whereby new biochem …

Cool! We’ve been thinking about chemical properties of secreted bioluminescence lately: pubmed.ncbi.nlm.nih.gov/39418132/#:~...

Symbiotic entrenchment through ecological Catch-22 A 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 ...

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

Neil H. Shubin has been elected as the next NAS President! A leading evolutionary biologist and science communicator, Shubin will succeed Marcia McNutt on July 1. The Academy also named Cherry Murray as International Secretary and elected new councilors. Read more: www.nasonline.org/news/2026_pr...

📣 Welcome to DPCB!
We’re SICB’s Division of Phylogenetics & Comparative Biology — the home for tree-thinking, evolutionary relationships, and comparative approaches across organisms.
#DPCB #SICB2026 #Phylogenetics

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#DPCB #Phylogenetics #TreeThinking

Evolution of the Tri-PDZ Domain in PSD95 (DLG-4 Gene) Abstract. Some genes encoding proteins within the co-evolved pre- and postsynaptic compartments are present in genomes long preceding the origination of th

Nilkant et al. construct the phylogeny of the tri-PDZ domains in DLG4 (one of the most abundant synaptic proteins) to its deep ancestral origin in Filozoa, which includes animals and their nearest unicellular relatives.

🔗 doi.org/10.1093/molbev/msaf309

#evobio #molbio

BREAKING: In AAUP et al v. Trump (wall-to-wall union lawsuit challenging the administration’s unlawful use of TItle VI to reshape the University of California system), the faculty and staff of the UC system WON!!!

We were granted our preliminary injunction! @aaup.org

Insertion of an invading retrovirus regulates a novel color trait in swordtail fish For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...

I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A

Saving science by the sea As funding for science tightens across the United States, attention has turned to pressures faced by universities and biomedical research institutions. An often overlooked part of the nation’s science...

"Saving Science by the Sea" – a piece on the importance of marine laboratories in advancing biomedical science, including the beginning of the Meselson-Stahl collaboration that ultimately elucidated the process of DNA replication:

www.science.org/doi/10.1126/...

A scientific figure showing speciation and explaining the concept of species delimitation, and including a quote by the paper's first author.

Check out the recent publication in Annual Reviews of Ecology, Evolution, and Systematics where the authors explore genomic species delimitation in depth. You'll see a number of #sciart figures I created to help explain some of the concepts!

www.annualreviews.org/content/jour...

Parallel shifts in differential gene expression reveal convergent miniaturization in fishes | PNAS Body size variation in vertebrates is a complex polygenic trait, tightly correlated with numerous aspects of a species’ biology, ecology, and physi...

Why are some species smaller than a paperclip while others grow longer than a school bus? How is body size evolution governed in animals? Out now in @pnas.org we tackle these longstanding questions through a genetic lens using my favorite group of fishes as our model!! www.pnas.org/doi/10.1073/...

Adaptive Disruption of Carotenoid Metabolism in Cavefish via Loss of Beta-carotene oxygenase 2a (Bco2a) https://www.biorxiv.org/content/10.1101/2025.10.06.680734v1

A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).

A paper in Nature Ecology & Evolution presents a time-calibrated phylogeny of Fungi. This timescale suggests an older age of crown Fungi, as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems. #phylo 🧪

Green dots on black background in a donut shape

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

Great to see Sergi's blog post about the recent study on the macroevolutionary dynamics of arcade games.
doi.org/10.1017/ehs....
🧪 ⚒️ #Complexity #EvoBio

a black and white dog is sitting on a couch with its tongue sticking out . ALT: a black and white dog is sitting on a couch with its tongue sticking out .

👁️The retina — strikingly conserved across vertebrates, but an oddity among bilaterians!

So how did it evolve?

With @mikebok.bsky.social, @neurofishh.bsky.social and @denilsson.bsky.social, we argue that retinal complexity may 𝑝𝑟𝑒𝑑𝑎𝑡𝑒 𝑡ℎ𝑒 𝑒𝑦𝑒 𝑖𝑡𝑠𝑒𝑙𝑓.

www.biorxiv.org/content/10.1...
1/n

Shedding Light on Patterns of Unconventional Expression of Opsin Genes in Hydra vulgaris Synopsis. Opsins are G-protein-coupled receptors often expressed in neuronal photoreceptor cells and used for light detection in most animals, including cn

First, first-author paper alert!

“Shedding Light on Patterns of Unconventional Expression of Opsin Genes in Hydra vulgaris” is out and open access in @sicbjournals.bsky.social

academic.oup.com/icb/advance-...

Keep reading for some highlights in the thread below!

🦑🧪

Fun fact - the photo of me in this article was taken in Mendel’s Garden (in Brno, Czechia)!

It was great meeting @masahitotsuboi.bsky.social at #eseb2025 and learning about his fantastic research. Check his paper showing the interaction between micro and macro evolution! 🔥

Katherine Esau on Plant Anatomy, Electron Microscopy, and Why Foundational Science Matters: The Botanist Who Wrote the Book on Plant Life Katherine Esau, Ukrainian immigrant who revolutionised plant biology, discusses her journey from sugar beet fields to pioneering electron microscopy. The definitive plant anatomist explains how her…

Katherine Esau on Plant Anatomy, Electron Microscopy, and Why Foundational Science Matters: The Botanist Who Wrote the Book on Plant Life
voxmeditantis.com/2025/08/19/k...

#WomenInSTEM #STEM #Botany #Phloem #Microscopy

Writing is sculpting -- get the slab of rock down first -- all the ideas. Then start to carve the story from the slab. Then the rough sanding and the fine sanding -- and one day you will get to the polish. Progress comes from processing the words, feedback of others, and the labor of co-authors.

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.

Applications are now open for the Guggenheim Fellowship:
www.gf.org/program/how-...

Plot of global benthic δ18O data for 0 – 5.3 Ma (Lisiecki & Raymo, 2005) with geomagnetic polarity subchrons displayed on the top x-axis and planktic foraminiferal primary biozones plotted on the bottom x-axis using the deeptime package.

A mammal phylogeny (Garland et al., 1992) plotted in the fan layout using the ggtree and deeptime packages. The greyscale concentric circles in the background indicate geological stages, whereas the linear colored timescale indicates geological epochs.

Early tetrapod occurrence data (Jones et al., 2023) plotted as a taxonomic/biostratigraphic range plot using the geom_points_range() function from the deeptime package.

A stratigraphic column of Cretaceous lithostratigraphic units from the San Juan Basin, USA. The deeptime package has been used to add pattern fill which indicate the primary lithologies of the units as reported by the Macrostrat API (Peters et al., 2018) via the rmacrostrat R package (Jones et al., 2024).

📢 deeptime: an R package that facilitates highly customizable and reproducible visualizations of data over geological time intervals

🔗 doi.org/10.1080/2096...

Fully #openaccess in @bigearthdata1.bsky.social with insight about deeptime📦 development and code examples!

#rstats #geology #paleontology

a fish is swimming in a tank with the number 21 on the side Alt: a fish is swimming in a tank when it tries to eat an ostracod. The ostracod spits bioluminescence and the fish expels a luminous cloud rapidly against the side of the tank

Just for fun, one of the famous videos of a fish spitting out a glowing ostracod after the latter's anti-predator display

This review was a challenge for me, as it is quite broad and a bit outside my core expertise. But I learned a lot. I feel like I never really achieved a true synthesis in the time I had, but I have started down that path and will keep thinking!

In terms of differences - bright light visual information systems often diversify quickly in color space, but bioluminescent systems diversify quickly in spatial and temporal aspects (although bioluminescence tends to track environmental light)

One hypothesis is that bioluminescent systems first originated for predator-prey dynamics, and were later co-opted as sexual signals. This is an area ripe for meta-analysis

In terms of similarity - both have probably led to aesthetic radiations, the diversification of traits and species driven by sexual selection. Another similarity is that that sensory capabilities predate the radiation of signals