(a) Map showing the 29 independently evolved cave populations (black dots) of the El Abra region in Mexico. The Pachón cavefish population used for this project is marked as a red dot. Scale bars = …
Surface × Pachón F2 hybrid brain atlas in nifty format.
Whole-brain segmented z-stack that outlines 180 defined brain regions. Z-projections of atlas stack were used to generate images.
(a) Larval fish were imaged at 5 dpf to measure external anatomical features (e.g. standard length). (b) Larvae were fixed at 6 dpf, immunostained with total-ERK (tERK) and imaged on a two-photon …
(a) Optical sections (coronal) through the and optic tectum (white matter light blue and gray matter red) and pallium (dark blue). Hand segmentations are in color, while automated versions are shown …
Segmentation of (a) otx2 positive neurons in the optic tectum, (b) gbx1 neurons in the subpallium, (c) nos1 neurons in the thalamus, (d) oxt positive neurons in the medial preoptic regions, (e) …
(a) Volumetric comparison of the diencephalon in surface fish, Pachón and Molino cavefish. Percent total brain volume represents pixels of segment divided by total pixels in the brain. Sagittal …
Volumetric values for the diencephalon of wildtype larvae.
Three columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish. Populations were analyzed via one-way ANOVA.
Volumetric values for the dorsal diencephalon of wilid-type larvae.
Three columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish. Populations were analyzed via one-way ANOVA.
Volumetric values for the habenula of wildtype larvae.
Three columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish. Populations were analyzed via one-way ANOVA.
Volumetric values for the ventral thalamus of wildtype larvae.
Three columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish. Populations were analyzed via one-way ANOVA.
Volumetric values for the dorsal thalamus of wildtype larvae.
Three columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish. Populations were analyzed via one-way ANOVA.
Volumetric values for the hypothalamus of wildtype larvae.
Three columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish. Populations were analyzed via one-way ANOVA.
Volumetric values for the preoptic region of wildtype larvae.
Three columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish. Populations were analyzed via one-way ANOVA.
Volumetric values for the intermediate zone of wildtype individual larvae.
Three columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish. Populations were analyzed via one-way ANOVA.
Volumetric values for the caudal hypothalamus of wildtype individual larvae.
Three columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish. Populations were analyzed via one-way ANOVA.
(a) Major brain divisions of the vertebrate brain and box plots comparing the volume of each region between surface and cave. Volumes are reported as percentage of total brain volume, calculated by …
(a) Volumetric comparison of the mesencephalon in surface fish, Pachón cavefish, Molino cavefish, surface × Pachón F2 hybrid (SPF2), and surface × Molino F2 hybrid (SMF2) larvae. Sagittal sections …
Volumetric values for the mesencephalon of wildtype and F2 hybrid larvae.
Five columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish, and F2 surface × cave populations. Populations were analyzed via one-way ANOVA.
Volumetric values for the tegmentum of wildtype and F2 hybrid larvae.
Five columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish, and F2 surface × cave populations. Populations were analyzed via one-way ANOVA.
Volumetric values for the optic tectum of wildtype and F2 hybrid larvae.
Five columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish, and F2 surface × cave populations. Populations were analyzed via one-way ANOVA.
Volumetric values for the optic tectum gray matter of wildtype and F2 hybrid larvae.
Five columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish, and F2 surface × cave populations. Populations were analyzed via one-way ANOVA.
Volumetric values for the optic tectum white matter of wildtype and F2 hybrid larvae.
Five columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish, and F2 surface × cave populations. Populations were analyzed via one-way ANOVA.
Volumetric values for the rostral optic tectum of wildtype and F2 hybrid larvae.
Five columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish, and F2 surface × cave populations. Populations were analyzed via one-way ANOVA.
Volumetric values for the dorsal optic tectum of wildtype and F2 hybrid larvae.
Five columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish, and F2 surface × cave populations. Populations were analyzed via one-way ANOVA.
Volumetric values for the ventral optic tectum of wildtype and F2 hybrid larvae.
Five columns of normalized volumetric values for wildtype surface, Pachón and Molino cavefish, and F2 surface × cave populations. Populations were analyzed via one-way ANOVA.
Representative regions for hybrid larvae that show (a) an intermediate brain size between wildtype surface and cave values, (b) genetic dominance with Pachón cavefish (dorsal diencephalon) or …
(a) Volumetric comparison of the telencephalon in surface fish, Pachón cavefish, Molino cavefish, and surface × cave F2 hybrids. Percent total brain volume represents pixels of segment divided by …
(a) Cross-correlation analysis of surface to Pachón F2 hybrids for the 180 segmented Astyanax brain atlas. (b) Cluster analysis array showing six clusters exhibiting positive volumetric …
Correlation coefficient matrix for 180-brain region atlas volumetric comparisons of surface × Pachón F2 hybrid larvae.
Pairwise correlation coefficients for pairwise comparisons between each brain region within the F2 population. Each individual coefficient represents the relationship between two individual brain regions within the F2 population.
Correlation coefficient matrix for 180-brain region atlas volumetric covariation of surface × Molino F2 hybrid larvae.
Pairwise correlation coefficients for pairwise comparisons between each brain region within the F2 population. Each individual coefficient represents the relationship between two individual brain regions within the F2 population.
(a) Pairwise correlation and (b) clustering matrices comparing covariation for surface to Pachón F2 hybrids between 13 brain segments. (c) Illustrations depicting clustered segments: cluster 1 …
Representatives of shape for the cerebellum and hypothalamus of pure populations (a) principal component 1 (PC1) and (b) principal component 2 (PC2). (c) Correlation matrix comparing the covariation …
Correlation coefficient matrix for 13 brain region atlas shape covariation of surface × Pachón F2 hybrid larvae.
Each individual coefficient represents the relationship between two individual brain regions within the F2 population.
(a) Principal component analysis (PCA) capturing 54% of the variation across surface, cave, and surface × cave F2 hybrids. PC1 describes preoptic width, while PC2 describes length. (b) Illustrations …
(a) Principal component analysis (PCA) capturing 50% of the variation across surface, cave, and surface × cave F2 hybrids. PC1 describes pineal length, while PC2 describes pineal width across …
(a) Principal component analysis (PCA) capturing 52% of the variation across surface × cave F2 hybrid optic tectums. PC1 describes optic tectum curvature and length (b), while PC2 describes optic …
(a) Principal component analysis (PCA) capturing 39% of the variation across surface × cave F2 hybrid cerebellums. PC1 describes cerebellar curvature and length (b), while PC2 describes cerebellar …
(a) Principal component analysis (PCA) capturing 39% of the variation across surface × cave F2 hybrid hypothalamus. PC1 describes hypothalamic length and center depth (b), while PC2 describes …
Gene | A. mexicanuspopulation | Ensembl ID | Molecular Instruments Lot # |
---|---|---|---|
gbx1 | Surface | ENSAMXT00000037099.1 | PRO705 |
gbx1 | Pachón | ENSAMXT00005023309.1 | PRO706 |
otx2b | Surface | ENSAMXT00000055482.1 | PRQ451 |
otx2b | Pachón | ENSAMXT00005060650.1 | PRQ452 |
oxt | Surface | ENSAMXT00000041101.1 | PRQ449 |
oxt | Pachón | ENSAMXT00005006990.1 | PRQ450 |
README.md file that includes text describing the material in Source code 2, a repository of scripts used in this study.
Kozol et al. Code.zip file containing bash (.sh), fiji (.ijm), and matlab (.m) files used for this study.