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Reposted by Todd Oakley

Georgios Kafetzis @gkafetzis.bsky.social · 26d

👁️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

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

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Reposted by Todd Oakley

Marina Stoilova @stoilovamarina.bsky.social · Aug 27

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

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

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Todd Oakley @ostratodd.bsky.social · Aug 26

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

Axel Visel @axelvisel.bsky.social · Aug 19

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...

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

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Reposted by Todd Oakley

Roberto Toro @r3rt0.bsky.social · Aug 24

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! 🔥

Communications Biology @commsbio.nature.com · Jul 10

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

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Reposted by Todd Oakley

Bob Lynn @boblynn.bsky.social · Aug 19

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

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

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Todd Oakley @ostratodd.bsky.social · Aug 12

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.

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Todd Oakley @ostratodd.bsky.social · Aug 6

Applications are now open for the Guggenheim Fellowship:
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

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Reposted by Todd Oakley

Will Gearty @willgearty.bsky.social · Aug 6

📢 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

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).

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Todd Oakley @ostratodd.bsky.social · Jul 20

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

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

media.tenor.com

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Todd Oakley @ostratodd.bsky.social · Jul 20

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!

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Todd Oakley @ostratodd.bsky.social · Jul 20

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)

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Todd Oakley @ostratodd.bsky.social · Jul 20

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

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Todd Oakley @ostratodd.bsky.social · Jul 20

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

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Todd Oakley @ostratodd.bsky.social · Jul 20

I try to compare and contrast how evolution has molded dark (bioluminescent) and bright (especially color) visual information systems

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Todd Oakley @ostratodd.bsky.social · Jul 20

I am happy to share a new review article, as part of a future special issue on vision in challenging environments, led by @fishevo.bsky.social and @drfishvis.bsky.social

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Todd Oakley @ostratodd.bsky.social · Jul 20

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

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Reposted by Todd Oakley

Genetics Society of America @genetics-gsa.bsky.social · Jul 18

📢 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

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Reposted by Todd Oakley

Laurie Belcher @lauriebelch.bsky.social · Jul 16

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...

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Reposted by Todd Oakley

Dr. David Miller 🏳️‍🌈 @davidimiller.bsky.social · Jul 10

🧪 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.

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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

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Reposted by Todd Oakley

Alejandro Fábregas-Tejeda @alejandrofabregastejeda.com · Jul 9

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

Poster for the Interdisciplinary Workshop “Behavior Across the Tree of Life: Theoretical and Methodological”, taking place on September 26–27, 2025 at the Institute of Philosophy, KU Leuven. The event is organized by Gianmaria Dani, Alejandro Fábregas-Tejeda, and Grant Ramsey. The poster features circular images of diverse biological organisms (lichens, bacteria, ants, carnivorous plants) surrounding a central announcement.

Call for Applications:

Deadline: July 14th, 2025

Notification: July 18th, 2025

Open to philosophers and scientists interested in comparative behavioral biology and its theoretical and methodological foundations.

Abstracts of up to 500 words (excluding references), including affiliation and contact info, should be sent to:

gianmaria.dani@kuleuven.be

alejandro.fabregastejeda@kuleuven.be

Invited Speakers:

Kristin Aleklett (Lund University)

Silvia Guerra (University of Padua)

Tobias Starzak (Ruhr University Bochum)

Kirsty Y. Wan (University of Exeter)

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Reposted by Todd Oakley

Joel Sharbrough @jsharbro.bsky.social · Jul 8

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

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Reposted by Todd Oakley

Kaiser Lab @clocksevolution.bsky.social · Jul 5

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...

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

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Reposted by Todd Oakley

Anna Ferraioli @annaferraioli.bsky.social · Jun 28

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...

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Reposted by Todd Oakley

AAU @aau.edu · Jun 24

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

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Reposted by Todd Oakley

Rosa Fernández @rosafernandez.bsky.social · Jun 18

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...

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

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