Todd Oakley
@ostratodd.bsky.social
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.
Reposted by Todd Oakley
"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/...
www.science.org/doi/10.1126/...
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...
www.science.org
November 10, 2025 at 1:17 AM
"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/...
www.science.org/doi/10.1126/...
Reposted by Todd Oakley
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...
www.annualreviews.org/content/jour...
October 29, 2025 at 1:00 PM
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...
www.annualreviews.org/content/jour...
Reposted by Todd Oakley
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/...
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...
www.pnas.org
October 22, 2025 at 9:33 PM
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/...
Reposted by Todd Oakley
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
October 7, 2025 at 2:32 AM
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
Reposted by Todd Oakley
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 🧪
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).
go.nature.com
October 11, 2025 at 1:01 AM
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 🧪
We have sea pansies (Renilla) for our inverts class and we got some photos of the bioluminescence
October 12, 2025 at 4:09 PM
We have sea pansies (Renilla) for our inverts class and we got some photos of the bioluminescence
Reposted by Todd Oakley
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
doi.org/10.1017/ehs....
🧪 ⚒️ #Complexity #EvoBio
October 9, 2025 at 7:54 PM
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
doi.org/10.1017/ehs....
🧪 ⚒️ #Complexity #EvoBio
Reposted by Todd Oakley
👁️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
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
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 .
media.tenor.com
September 12, 2025 at 12:58 PM
👁️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
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
Reposted by Todd Oakley
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!
🦑🧪
“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!
🦑🧪
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
academic.oup.com
August 27, 2025 at 6:41 PM
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!
🦑🧪
“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)!
Congratulations to @jgi.doe.gov's 2025 Functional Genomics awardees:
@ostratodd.bsky.social @philmuslab.bsky.social @aaronrashotte.bsky.social @taylorlabgroup.bsky.social Hao Chen, Matthew Cope-Arguello, Olufemi Isimikalu, Paul Scesa, K. Scott, S. Wakao, B. Woolston
jgi.doe.gov/user-science...
@ostratodd.bsky.social @philmuslab.bsky.social @aaronrashotte.bsky.social @taylorlabgroup.bsky.social Hao Chen, Matthew Cope-Arguello, Olufemi Isimikalu, Paul Scesa, K. Scott, S. Wakao, B. Woolston
jgi.doe.gov/user-science...
JGI announces 2025 Functional Genomics awardees | Joint Genome Institute
This year's project goals range from engineering drought-tolerant woody bioenergy crops through transcriptional network mapping, developing microbial systems to convert renewable feedstocks into advan...
jgi.doe.gov
August 26, 2025 at 4:04 AM
Fun fact - the photo of me in this article was taken in Mendel’s Garden (in Brno, Czechia)!
Reposted by Todd Oakley
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! 🔥
Using a dataset of wing variation in Drosophila flies, the authors demonstrate that micro- and macroevolution align across levels and they propose multi-directional causal paths to explain the pattern, contributing to the development of a unified theory of evolution. www.nature.com/articles/s42...
Conserved wing shape variation across biological scales unveils dialectical relationships between micro- and macroevolution - Communications Biology
Using a dataset of wing variation in Drosophila flies, the authors demonstrate that micro- and macroevolution align across levels. The authors propose multi-directional causal paths to explain the pat...
www.nature.com
August 24, 2025 at 1:06 PM
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! 🔥
Reposted by Todd Oakley
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
voxmeditantis.com/2025/08/19/k...
#WomenInSTEM #STEM #Botany #Phloem #Microscopy
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…
voxmeditantis.com
August 19, 2025 at 8:47 PM
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
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.
August 12, 2025 at 11:36 PM
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.
Applications are now open for the Guggenheim Fellowship:
www.gf.org/program/how-...
www.gf.org/program/how-...
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.
www.gf.org
August 6, 2025 at 5:59 PM
Applications are now open for the Guggenheim Fellowship:
www.gf.org/program/how-...
www.gf.org/program/how-...
Reposted by Todd Oakley
📢 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
🔗 doi.org/10.1080/2096...
Fully #openaccess in @bigearthdata1.bsky.social with insight about deeptime📦 development and code examples!
#rstats #geology #paleontology
August 6, 2025 at 1:06 PM
📢 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
🔗 doi.org/10.1080/2096...
Fully #openaccess in @bigearthdata1.bsky.social with insight about deeptime📦 development and code examples!
#rstats #geology #paleontology
Visual information in the dark: Bioluminescence and perceptual design through evolution - Oakley - Functional Ecology - Wiley Online Library besjournals.onlinelibrary.wiley.com/doi/10.1111/...
Visual information in the dark: Bioluminescence and perceptual design through evolution
Read the free Plain Language Summary for this article on the Journal blog.
besjournals.onlinelibrary.wiley.com
July 20, 2025 at 2:47 PM
Visual information in the dark: Bioluminescence and perceptual design through evolution - Oakley - Functional Ecology - Wiley Online Library besjournals.onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Todd Oakley
📢 NEW GENOME ALERT
In #G3journal, @aidemm.bsky.social and colleagues sequenced and assembled the genome of Bougainvillia—a jellyfish, not the plant!—with 28 eyes and identified 20 cnidarian opsins in the species.
Read more: buff.ly/MSyC8Aa
In #G3journal, @aidemm.bsky.social and colleagues sequenced and assembled the genome of Bougainvillia—a jellyfish, not the plant!—with 28 eyes and identified 20 cnidarian opsins in the species.
Read more: buff.ly/MSyC8Aa
July 18, 2025 at 8:01 PM
📢 NEW GENOME ALERT
In #G3journal, @aidemm.bsky.social and colleagues sequenced and assembled the genome of Bougainvillia—a jellyfish, not the plant!—with 28 eyes and identified 20 cnidarian opsins in the species.
Read more: buff.ly/MSyC8Aa
In #G3journal, @aidemm.bsky.social and colleagues sequenced and assembled the genome of Bougainvillia—a jellyfish, not the plant!—with 28 eyes and identified 20 cnidarian opsins in the species.
Read more: buff.ly/MSyC8Aa
Reposted by Todd Oakley
OrthoFinder just dropped a major update
It’s faster, more accurate, and ready for thousands of genomes
Let’s break it down (1/10)
github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...
It’s faster, more accurate, and ready for thousands of genomes
Let’s break it down (1/10)
github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...
July 16, 2025 at 5:51 PM
OrthoFinder just dropped a major update
It’s faster, more accurate, and ready for thousands of genomes
Let’s break it down (1/10)
github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...
It’s faster, more accurate, and ready for thousands of genomes
Let’s break it down (1/10)
github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...
Reposted by Todd Oakley
🧪 BREAKING (good news): Senate subcommittee says NO! to Trump's proposed slashes to NASA & NSF funding.
Today, the subcommittee said to keep NASA + NSF funding at $33.9 billion, the same as in FY24.
See 7:15 below. Full Senate appropriations committee meets tomorrow about it.
🧵 1/3
Today, the subcommittee said to keep NASA + NSF funding at $33.9 billion, the same as in FY24.
See 7:15 below. Full Senate appropriations committee meets tomorrow about it.
🧵 1/3
Subcommittee Markup of the Commerce, Justice, Science, and Related Agencies Appropriations Act | United States Senate Committee on Appropriations
United States Senate Committee on Appropriations
www.appropriations.senate.gov
July 10, 2025 at 12:23 AM
🧪 BREAKING (good news): Senate subcommittee says NO! to Trump's proposed slashes to NASA & NSF funding.
Today, the subcommittee said to keep NASA + NSF funding at $33.9 billion, the same as in FY24.
See 7:15 below. Full Senate appropriations committee meets tomorrow about it.
🧵 1/3
Today, the subcommittee said to keep NASA + NSF funding at $33.9 billion, the same as in FY24.
See 7:15 below. Full Senate appropriations committee meets tomorrow about it.
🧵 1/3
Reposted by Todd Oakley
What theoretical and methodological challenges emerge when investigating #behavior across the tree of life? 📢 Final reminder: CfA for an interdisciplinary workshop (September 26-27) at KU Leuven! Come join us, and please help us share! hiw.kuleuven.be/clps/events/... #philsci #HPbio #evosky #ecology
July 9, 2025 at 12:46 PM
What theoretical and methodological challenges emerge when investigating #behavior across the tree of life? 📢 Final reminder: CfA for an interdisciplinary workshop (September 26-27) at KU Leuven! Come join us, and please help us share! hiw.kuleuven.be/clps/events/... #philsci #HPbio #evosky #ecology
Reposted by Todd Oakley
Please RT!
I'm hiring a postdoc to work in my new lab at UCSB (!) on an NSF-funded project investigating the phenotypic consequences of WGD for photosynthesis and respiration.
Check out the full posting here:
recruit.ap.ucsb.edu/JPF02986
And more info about the lab here:
sharbroughlab.com
I'm hiring a postdoc to work in my new lab at UCSB (!) on an NSF-funded project investigating the phenotypic consequences of WGD for photosynthesis and respiration.
Check out the full posting here:
recruit.ap.ucsb.edu/JPF02986
And more info about the lab here:
sharbroughlab.com
July 8, 2025 at 4:44 PM
Please RT!
I'm hiring a postdoc to work in my new lab at UCSB (!) on an NSF-funded project investigating the phenotypic consequences of WGD for photosynthesis and respiration.
Check out the full posting here:
recruit.ap.ucsb.edu/JPF02986
And more info about the lab here:
sharbroughlab.com
I'm hiring a postdoc to work in my new lab at UCSB (!) on an NSF-funded project investigating the phenotypic consequences of WGD for photosynthesis and respiration.
Check out the full posting here:
recruit.ap.ucsb.edu/JPF02986
And more info about the lab here:
sharbroughlab.com
Reposted by Todd Oakley
Interested in (studying) biological #clocks?
Here is a brilliant and concise introduction to the field, focussing on #ciradian clocks, and stressing the #adaptive nature of clocks.
And it's #OpenAccess !
#chronobiology 🧪 @doabooks.bsky.social
doi.org/10.21827/686...
Here is a brilliant and concise introduction to the field, focussing on #ciradian clocks, and stressing the #adaptive nature of clocks.
And it's #OpenAccess !
#chronobiology 🧪 @doabooks.bsky.social
doi.org/10.21827/686...
On the Essential Principles and Practice of Circadian Biology: A Road Map – Simple Book Publishing
Circadian Biology is about the adaptation of life to our rotating world, to the Earth’s 24-hour rhythm of day and night. Not surprisingly, the field has attracted considerable popular and scientific ...
doi.org
July 5, 2025 at 7:54 AM
Interested in (studying) biological #clocks?
Here is a brilliant and concise introduction to the field, focussing on #ciradian clocks, and stressing the #adaptive nature of clocks.
And it's #OpenAccess !
#chronobiology 🧪 @doabooks.bsky.social
doi.org/10.21827/686...
Here is a brilliant and concise introduction to the field, focussing on #ciradian clocks, and stressing the #adaptive nature of clocks.
And it's #OpenAccess !
#chronobiology 🧪 @doabooks.bsky.social
doi.org/10.21827/686...
Reposted by Todd Oakley
Excited to share our new work on the 3D architecture of the ctenophore aboral organ!
We explored its remarkable cellular diversity and integration with the syncytial nerve net, uncovering connectivity and insights into the evolution of sensory complexes.
www.biorxiv.org/content/10.1...
We explored its remarkable cellular diversity and integration with the syncytial nerve net, uncovering connectivity and insights into the evolution of sensory complexes.
www.biorxiv.org/content/10.1...
June 28, 2025 at 1:03 PM
Excited to share our new work on the 3D architecture of the ctenophore aboral organ!
We explored its remarkable cellular diversity and integration with the syncytial nerve net, uncovering connectivity and insights into the evolution of sensory complexes.
www.biorxiv.org/content/10.1...
We explored its remarkable cellular diversity and integration with the syncytial nerve net, uncovering connectivity and insights into the evolution of sensory complexes.
www.biorxiv.org/content/10.1...
Reposted by Todd Oakley
Did you know that a study of lizard venom led to the development of Wegovy and Ozempic? American Scientist explains how even the most obscure research can lead to life-changing results.
“Why Are We Funding This?”
Long-standing myths about “silly science” have contributed to the reckless slashing of government-supported research.
www.americanscientist.org
June 24, 2025 at 5:00 PM
Did you know that a study of lizard venom led to the development of Wegovy and Ozempic? American Scientist explains how even the most obscure research can lead to life-changing results.
Reposted by Todd Oakley
Glad to see this paper finally out! An episodic burst of massive genomic rearrangements and the origin of non-marine annelids
@natecoevo.nature.com @ibe-barcelona.bsky.social @csic.es @erc.europa.eu www.nature.com/articles/s41...
@natecoevo.nature.com @ibe-barcelona.bsky.social @csic.es @erc.europa.eu www.nature.com/articles/s41...
An episodic burst of massive genomic rearrangements and the origin of non-marine annelids - Nature Ecology & Evolution
An analysis of annelid genomes reveals massive reshuffling of chromosomes in the ancestral lineage leading to clitellates, a clade composed of non-marine annelids, with potential implications for the ...
www.nature.com
June 18, 2025 at 12:33 PM
Glad to see this paper finally out! An episodic burst of massive genomic rearrangements and the origin of non-marine annelids
@natecoevo.nature.com @ibe-barcelona.bsky.social @csic.es @erc.europa.eu www.nature.com/articles/s41...
@natecoevo.nature.com @ibe-barcelona.bsky.social @csic.es @erc.europa.eu www.nature.com/articles/s41...