{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:17:33Z","timestamp":1785417453021,"version":"3.56.0"},"posted":{"date-parts":[[2026,5,14]]},"group-title":"Evolutionary Biology","reference-count":88,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T00:00:00Z","timestamp":1778716800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"award":["R24 OD030214"],"award-info":[{"award-number":["R24 OD030214"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,5,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Understanding how naturally occurring genetic variation shapes human health and disease is critical for improving diagnosis and treatment strategies. The Mexican cavefish,\n                  <jats:italic>Astyanax mexicanus<\/jats:italic>\n                  , represents a powerful system for evolutionary medicine, enabling investigation of naturally evolved mechanisms of resilience to disease-related traits including diabetes, obesity, insomnia, and eye loss. Larval\n                  <jats:italic>A. mexicanus<\/jats:italic>\n                  , like zebrafish, are transparent, allowing whole-brain imaging, circuit mapping, and the generation of computationally derived atlases that precisely quantify neuroanatomical differences between surface and cave populations. Developing a molecular map of brain cell types provides a foundation for identifying evolved differences in neural circuits and physiology. Here, we present a single-cell atlas of the larval cavefish brain that reveals widespread divergence in the abundance and molecular signatures of neurons and glia. Our cell type map validates known neuroanatomical differences, including a reduction of the optic tectum and expansion of the pineal gland in cavefish. We uncover substantial changes in multiple glial cell classes that are linked to neural regulation of behavior, including microglia. Analysis of differential gene expression between surface and cavefish microglia revealed enhanced genes associated with synaptic pruning and clearance of neural debris, suggesting cavefish increased microglia activity to shape brain development. We also analyzed cell types that did not classify as canonical neurons or glia and identified notable divergence in transcriptomes and cell composition, including reduced meningeal fibroblasts in cavefish and substantial transcriptional changes related to phototransduction in non-visual photoreceptors within the pineal gland. Together, these findings provide a comprehensive atlas of cell type-specific gene expression differences between\n                  <jats:italic>A. mexicanus<\/jats:italic>\n                  surface and cavefish, establishing a platform for dissecting the molecular and cellular basis of evolved disease resilience in cavefish\n                <\/jats:p>","DOI":"10.64898\/2026.05.12.723532","type":"posted-content","created":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T05:00:24Z","timestamp":1778821224000},"source":"Crossref","is-referenced-by-count":0,"title":["A comparative brain atlas in the Mexican cavefish identifies widespread changes in cellular composition and gene expression"],"prefix":"10.64898","author":[{"given":"Kathryn","family":"Gallman","sequence":"first","affiliation":[{"name":"Department of Biology, Texas A&M University, College Station, TX 77840"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward","family":"Ricemeyer","sequence":"additional","affiliation":[{"name":"Bond Life Science Center, University of Missouri, Columbia, MO 65211"},{"name":"Chair for Animal Systems Genomics, Faculty of Veterinary Medicine, Ludwig-Maximillans-Universit\u00e4t, Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aakriti","family":"Rastogi","sequence":"additional","affiliation":[{"name":"Department of Biology, Texas A&M University, College Station, TX 77840"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"X","family":"Maggs","sequence":"additional","affiliation":[{"name":"Bond Life Science Center, University of Missouri, Columbia, MO 65211"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emilio","family":"M\u00e9ndez Scolari","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Rice University, Houston, TX 77005"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik R.","family":"Duboue","sequence":"additional","affiliation":[{"name":"Harriet Wilkes Honors College, Florida Atlantic University, Jupiter, FL"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Rohner","sequence":"additional","affiliation":[{"name":"Institute of Integrative Cell Biology and Physiology, University of M\u00fcnster, 48143 M\u00fcnster, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harini","family":"Iyer","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Rice University, Houston, TX 77005"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wes","family":"Warren","sequence":"additional","affiliation":[{"name":"Division of Animal Sciences, Department of Surgery, Bond Life Sciences Center, Institute of Data Science and Informatics, University of Missouri, Columbia, MO 65211"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex C.","family":"Keene","sequence":"additional","affiliation":[{"name":"Department of Biology, Texas A&M University, College Station, TX 77840"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026051904250968000_2026.05.12.723532v1.1","doi-asserted-by":"publisher","DOI":"10.1080\/01677063.2016.1177049"},{"key":"2026051904250968000_2026.05.12.723532v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41573-021-00210-8"},{"key":"2026051904250968000_2026.05.12.723532v1.3","doi-asserted-by":"publisher","DOI":"10.1124\/pr.110.003293"},{"key":"2026051904250968000_2026.05.12.723532v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/nrg751"},{"key":"2026051904250968000_2026.05.12.723532v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbadis.2014.01.015"},{"key":"2026051904250968000_2026.05.12.723532v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2013.01.009"},{"key":"2026051904250968000_2026.05.12.723532v1.7","doi-asserted-by":"publisher","DOI":"10.1002\/jez.b.22589"},{"key":"2026051904250968000_2026.05.12.723532v1.8","doi-asserted-by":"publisher","DOI":"10.1242\/dmm.012245"},{"key":"2026051904250968000_2026.05.12.723532v1.9","unstructured":"Ad Konings . 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