DOI: 10.5061/dryad.w9ghx3frw
title: Data from: A brain-wide analysis maps structural evolution to distinct anatomical modules

description: Brain anatomy is highly variable and it is widely accepted that anatomical
 variation impacts brain function and ultimately behavior. The structural
 complexity of the brain, including differences in volume and shape,
 presents an enormous barrier to define how variability underlies
 differences in function. In this study, we sought to investigate the
 evolution of brain anatomy in relation to brain region volume and shape
 across the brain of a single species with variable genetic and anatomical
 morphs. We generated a high-resolution brain atlas for the blind Mexican
 cavefish and coupled the atlas with automated computational tools to
 directly assess variability in brain region shape and volume across all
 populations. We measured the volume and shape of every neuroanatomical
 region of the brain and assessed correlations between anatomical regions
 in surface fish, cavefish, and surface to cave F2 hybrids, whose
 phenotypes span the range of surface to cave. We find that dorsal regions
 of the brain are contracted in cavefish, while ventral regions have
 expanded. This trend is true for both volume and shape, suggesting that
 these two parameters share developmental mechanisms necessary for
 remodeling the entire brain. Given the high conservation of brain anatomy
 and function among vertebrate species, we expect these data to reveal
 generalized principles of brain evolution and show that Astyanax provides
 a system for functionally determining basic principles of brain evolution
 by utilizing the independent genetic diversity of different morphs, to
 test how genes influence early patterning events to drive brain-wide
 anatomical evolution.  
description: Brains were stained with p44/42 MAP Kinase (L34F12) Mouse mAb,
 which detects endogenous levels of total p44/42 MAP kinase (Erk1/Erk2)
 protein. This antibody provides a brain-wide immunolabeling stain that was
 then used to register all surface fish, Pachon cavefish and surface to
 Pachon hybrid (F1 and F2) to a common Astyanax Mexicanus atlas. This atlas
 was then inverse registered to each indivdual brain (see paper for
 technical details), providing automated segmentation of upto 180 unique
 brain regions. These segmented brains were then run through the
 morphometric analysis program CobraZ (Gupta et al. 2018), providing brain
 region volume in percentage of total brain volume. Populations were then
 compared statistically using a hom's corrected t-test in CobraZ for
 wildtype surface and Pachon populations, and a holm's corrected ANOVA
 in graphpad Prism for wildtype and hybrid populations. After extracting 3D
 models of the preoptic region of the hypothalamus and pineal body of the
 diencephalon, we characterized shape variation using 3D geometric
 morphometrics (LandmarkEditor (v3.0) (47). To assess differences we
 performed a procrustes superimposition on our shape data to remove the
 effects of translation, rotation, and scaling from all individuals using
 the gpagen function from the geomorph (v4.0) package in R. We then
 assessed differences in shape among populations and performed a
 multivariate regression of shape on centroid size and population (i.e.,
 surface, cave, hybrid) using the procD.lm r function from
 geomorph.
description: The .tiff and .nii.gz files can be opened using any imaging
 software (e.g. Fiji), text files can be opened using any text editor (e.g.
 Microsoft Word, VIM) and xmls and xlsx files can be opened using
 excel.