An adult brain atlas reveals broad neuroanatomical changes in independently evolved populations of Mexican cavefish

Cody Loomis, View ORCID ProfileRobert Peuß, James Jaggard, Yongfu Wang, Sean McKinney, Stephen Raftopoulos, Austin Raftopoulos, Daniel Whu, Matthew Green, Suzanne E. McGaugh, Nicolas Rohner, Alex C. Keene, Erik R. Duboue

A shift in environmental conditions impacts the evolution of complex developmental and behavioral traits. The Mexican cavefish, Astyanax mexicanus, is a powerful model for examining the evolution of development, physiology, and behavior because multiple cavefish populations can be compared to an extant and ancestral-like surface population of the same species. Many behaviors have diverged in cave populations of A. mexicanus, and previous studies have shown that cavefish have a loss of sleep, reduced stress, an absence of social behaviors, and hyperphagia. Despite these findings, surprisingly little is known about the changes in neuroanatomy that underlie these behavioral phenotypes. Here, we use serial sectioning to generate a brain atlas of surface fish and three independent cavefish populations. Volumetric reconstruction of serial-sectioned brains confirms convergent evolution on reduced optic tectum volume in all cavefish populations tested. In addition, we quantified volumes of specific neuroanatomical loci within several brain regions, which have previously been implicated in behavioral regulation, including the hypothalamus, thalamus, and habenula. These analyses reveal an expansion of the hypothalamus across all three cavefish populations relative to surface fish, as well as subnuclei-specific differences within the thalamus and habenulae. Taken together, these analyses support the notion that changes in environmental conditions are accompanied by neuroanatomical changes in brain structures associated with behavior. This atlas provides a resource for comparative neuroanatomy of additional brain regions and the opportunity to associate brain anatomy with evolved changes in behavior.

How Amira-Avizo Software is used

“After locating individual neuroanatomical regions, we defined each brain nucleus by demarcating the boundaries of the region throughout serial sections using AMIRA. We then quantified a volume of each region. (…)

.TIF image sequence was uploaded into the AMIRA software. To create proper demarcations, neuroanatomical regions of interest (ROIs) from Nissl stains were set under the “segmentation” tab using the lasso tool. To view 3-dimensional reconstructions of neuroanatomical ROI’s, a ‘volren’ object was created under the “project” tab. Volren object was connected to the original .tif image sequence as well as the label fields used to create demarcated neuroanatomical ROI’s. (…)

To quantify total volume of individual demarcated regions (i.e., each ROI), we used the ‘volume per VOI’ result of the ‘material statistics’ function in AMIRA. (…)”.