OSCR

Sensory receptor expansion and neural accommodation in butterfly color vision

Code ↔ Paper

The paper beside its authors' code: matches between them have not been computed for this paper yet.

Paper

Loaded from Europe PMC by your browser; OSCR does not store it: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

Markdown · 11 lines · 2.1 KB · CC-BY-4.0

  1. # Code for Manuscript: Sensory receptor expansion and neural accommodation in butterfly color vision
  2. **Ke Gao**, Julia Ainsworth, Antoine Donati, Yunchong Zhao, Michelle F. Ragsac, Cara Genduso, Zoie Andre, Andrew Tomlinson, Michael W. Perry
  3. > bioRxiv Link: [https://www.biorxiv.org/content/10.1101/2025.10.30.685642v1](https://www.biorxiv.org/content/10.1101/2025.10.30.685642v1)
  4. ## Abstract
  5. The evolution of complex brains required the incorporation of new neurons into existing circuits, yet the genetic and developmental mechanisms enabling their integration remain poorly understood. Butterflies expanded their color vision by adding a second R7 photoreceptor per ommatidium, a rare departure from the conserved insect eye ground plan. Because each R7 makes an independent stochastic fate choice, this duplication increased the number of ommatidial types from two to three. We identified the genetic basis of this expansion and demonstrated how the brain accommodates the new input. R7 duplication was achieved by converting R3/4 cells to an R1/6 fate, triggering the R7 recruitment program on both sides of the ommatidium. By manipulating transcription factor expression in Drosophila, we engineered a "butterfly-fly" that recapitulates this ancient R7 duplication and three-type stochastic mosaic. In the fly brain, two R7 subtypes connect to specific types of Dm8 neurons, which are born in excess and undergo apoptosis if they fail to find synaptic partners. In our butterfly-fly model, these surplus Dm8s are immediately rescued and form subtype-appropriate connections. These findings suggest that population-level variation maintains a reservoir of potentially interacting neurons, providing a developmental substrate that allows the brain to immediately accommodate newly evolved neurons.
  6. ## Experimental Design
  7. Pupal retinas from V. cardui (painted lady butterfly) were dissected then flash frozen in liquid nitrogen and stored at -80°C before being sequenced with the 10x Genomics Multiome Kit for single-cell library preparation with a target recovery of 6000 cells. Retinas were split into two biological replicates, each with a target sequencing depth of ~300 million reads.

README.md, under CC-BY-4.0 · at the source

Overview

  1. Department of Cell & Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
  2. Halicioğlu Data Science Institute, University of California San Diego, La Jolla, CA 92093, USA
  3. Department of Biology, New York University, New York, NY 10003, USA
  4. Department of Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
  5. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
Journal: Science advances, volume 12, issue 41, article eaei7570
Dates: received 11 May 2026; accepted 1 September 2026; published online 7 October 2026; in print October 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI · PMCID PMC13644764
Status: code verified (how the code is found and verified)
Categories: other (organism), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Smoothing, state filtering, decompositions, Evoked potentials
Journal subjects: Biomedicine and Life Sciences, Developmental Biology
Citations: not cited yet (Europe PMC); 53 references in the paper

Abstract

The evolution of complex brains required the incorporation of newly evolved neurons into existing circuits, yet the genetic and developmental mechanisms enabling their integration remain poorly understood. Butterflies expanded their color vision by adding a second R7 photoreceptor per ommatidium, a rare departure from the conserved insect eye ground plan. Because each R7 makes an independent stochastic fate choice, this duplication increased the number of ommatidial types from two to three. We identified the genetic basis of this expansion and demonstrated how the brain accommodates the new input. R7 duplication was achieved by converting R3/4 cells to an R1/6 fate, triggering the R7 recruitment program on both sides of the ommatidium. By manipulating transcription factor expression in Drosophila, we engineered a “butterfly-fly” that recapitulates this ancient R7 duplication and three-type stochastic mosaic. In the fly brain, two R7 subtypes connect to specific types of Dm8 neurons, which are born in excess and undergo apoptosis if they fail to find synaptic partners. In our butterfly-fly model, these surplus Dm8s are immediately rescued and form subtype-appropriate connections. These findings suggest that population-level variation maintains a reservoir of potentially interacting neurons, providing a developmental substrate that allows the brain to immediately accommodate newly evolved neurons.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above.

Zenodo 21811741

License: CC-BY-4.0
State: the link answers, verified on 9 October 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data, code, and materials availability:”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 9 October 2026: the link answers (HTTP 200)
  • 9 October 2026: the link answers (HTTP 200)
1 file

kekebird888/scrnaseq-butterfly

License: none: the authors keep all their rights
State: the link answers, verified on 9 October 2026
Evidence: files inventoried
Commit: 34fce4e222c2ac060f99e0fde4c4f2e72f9004ed, 15 July 2026
Size: 2 files, 0 scripts
Software Heritage: not archived
Found in: “Data, code, and materials availability:”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 9 October 2026: the link answers
  • 9 October 2026: the link answers
1 file

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 0 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data, code, and materials availability

All data and code needed to evaluate and reproduce the results in the paper are present in the paper and/or the Supplementary Materials. Raw and processed snRNAseq data generated in this study have been deposited in the NCBI GEO under accession no. GSE338277 (https://ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE338277). Reads were aligned to the V. cardui genome assembly ilVanCard2.1 (NCBI accession no. GCF_905220365.1; https://ncbi.nlm.nih.gov/datasets/genome/GCF_905220365.1/). R scripts used to process, analyze, and visualize the snRNAseq data have been archived on Zenodo at https://doi.org/10.5281/zenodo.21811741 and are also available on GitHub (https://github.com/kekebird888/scrnaseq-butterfly). This study generated new antibodies (VcBar, VcRo, VcLz, VcChaoptin, and VcDIP-γ); the sequence information required to produce these antibodies is provided in the Supplementary Materials (table S3). To obtain the antibodies, please contact M.W.P. at , while supplies last.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 9 October 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 4 funders, 53 references.

Cite

This paper

Gao, K., Ainsworth, J., Donati, A., Zhao, Y., Ragsac, M. F., Genduso, C., Andre, Z., Tomlinson, A., & Perry, M. W. (2026). Sensory receptor expansion and neural accommodation in butterfly color vision. Science advances, 12(41), eaei7570.

BibTeX

@article{gao2026sensory,
author = {Gao, Ke and Ainsworth, Julia and Donati, Antoine and Zhao, Yunchong and Ragsac, Michelle Franc and Genduso, Cara and Andre, Zoie and Tomlinson, Andrew and Perry, Michael W.},
title = {{Sensory receptor expansion and neural accommodation in butterfly color vision}},
journal = {Science advances},
year = {2026},
month = oct,
volume = {12},
number = {41},
pages = {eaei7570},
publisher = {American Association for the Advancement of Science},
issn = {2375-2548},
pmcid = {PMC13644764}
}

RIS

TY - JOUR
AU - Gao, Ke
AU - Ainsworth, Julia
AU - Donati, Antoine
AU - Zhao, Yunchong
AU - Ragsac, Michelle Franc
AU - Genduso, Cara
AU - Andre, Zoie
AU - Tomlinson, Andrew
AU - Perry, Michael W.
TI - Sensory receptor expansion and neural accommodation in butterfly color vision
T2 - Science advances
J2 - Sci Adv
PY - 2026
DA - 2026/10/09
VL - 12
IS - 41
SP - eaei7570
SN - 2375-2548
PB - American Association for the Advancement of Science
LA - en
ER -

CSL-JSON

{
"id": "pmcid:PMC13644764",
"type": "article-journal",
"title": "Sensory receptor expansion and neural accommodation in butterfly color vision",
"container-title": "Science advances",
"author": [
{
"family": "Gao",
"given": "Ke"
},
{
"family": "Ainsworth",
"given": "Julia"
},
{
"family": "Donati",
"given": "Antoine"
},
{
"family": "Zhao",
"given": "Yunchong"
},
{
"family": "Ragsac",
"given": "Michelle Franc"
},
{
"family": "Genduso",
"given": "Cara"
},
{
"family": "Andre",
"given": "Zoie"
},
{
"family": "Tomlinson",
"given": "Andrew"
},
{
"family": "Perry",
"given": "Michael W."
}
],
"container-title-short": "Sci Adv",
"volume": "12",
"issue": "41",
"page": "eaei7570",
"PMCID": "PMC13644764",
"ISSN": "2375-2548",
"publisher": "American Association for the Advancement of Science",
"language": "en",
"issued": {
"date-parts": [
[
2026,
10,
9
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1002/bies.70122 [code]
Imprecision in Vision: Lessons From Neural Circuits in the Fly.
Journal: BioEssays : news and reviews in molecular, cellular and developmental biology
In common: cellular / molecular, 7 references
[2] doi:10.1038/s41467-024-45971-z [code]
Heterogeneity of synaptic connectivity in the fly visual system.
Journal: Nature communications
In common: cellular / molecular, 6 references
[3] doi:10.1038/s41586-025-08746-0 [code]
Connectome-driven neural inventory of a complete visual system.
Journal: Nature
In common: 5 references
[4] doi:10.1038/s41586-024-07981-1 [code]
Neuronal parts list and wiring diagram for a visual system.
Journal: Nature
In common: 5 references
[5] doi:10.1038/s41586-025-09037-4 [code]
Molecular gradients shape synaptic specificity of a visuomotor transformation.
Journal: Nature
In common: cellular / molecular, 4 references
[6] doi:10.1016/j.crmeth.2023.100477
A conditional strategy for cell-type-specific labeling of endogenous excitatory synapses in <i>Drosophila</i>.
Journal: Cell reports methods
In common: cellular / molecular, 4 references
[7] doi:10.1038/s41593-024-01640-4 [code]
Hue selectivity from recurrent circuitry in Drosophila.
Journal: Nature neuroscience
In common: 4 references
[8] doi:10.1038/s41586-025-09276-5 [code]
Eye structure shapes neuron function in Drosophila motion vision.
Journal: Nature
In common: 4 references
[9] doi:10.1371/journal.pbio.3002989 [code]
Genetic, developmental, and neural changes underlying the evolution of butterfly mate preference.
Journal: PLoS biology
In common: other, 3 references
[10] doi:10.7554/elife.80660
A searchable image resource of <i>Drosophila</i> GAL4 driver expression patterns with single neuron resolution.
Journal: eLife
In common: cellular / molecular, 4 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Add the badge to the code's README

OSCR: the badge of this paper

If you are an author or a maintainer of this paper's code, you can add this badge. It says what OSCR knows of the paper (its code, its validated tracing map) and links the code to this page. Paste one of these snippets under the README's title. Keep the two marks around it, so that the badge can be replaced in place and is never added twice. OSCR changes nothing in your repository.

Markdown
<!-- oscr-badge:start -->
[![OSCR](https://openscicode.org/badge/repo/zenodo:21811741.svg)](https://openscicode.org/badge/repo/zenodo:21811741)
<!-- oscr-badge:end -->
reStructuredText
.. oscr-badge:start

.. image:: https://openscicode.org/badge/repo/zenodo:21811741.svg
   :target: https://openscicode.org/badge/repo/zenodo:21811741
   :alt: OSCR

.. oscr-badge:end
HTML
<!-- oscr-badge:start -->
<a href="https://openscicode.org/badge/repo/zenodo:21811741"><img src="https://openscicode.org/badge/repo/zenodo:21811741.svg" alt="OSCR"></a>
<!-- oscr-badge:end -->

On GitHub, open the README, choose Edit (the pencil), paste the snippet under the title, then "Commit changes".

If you choose to, you can have the badge kept up to date for you, with oscr badge --write from the command line or with the GitHub Action in your repository's workflows. Every other form and option (a card, AsciiDoc, LaTeX, shields.io) is on the badge page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: code errors and mismatches between the code and the paper about this paper and its code, from readers and its authors, beside the paper and its tracing map.

Report a mismatch between the code and the paper · Report a code error (signed in)

Reproductions: reports from readers who ran the authors' code and did not get the paper's result, what they ran, with which environment, commit and data.

Report a reproduction failure (signed in)

Versions of its code: the releases of its code tied to a version of this paper (the preprint, the accepted manuscript, the version of record…), each with the tracing map versioned with it.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.