Analysis / Spatial

Ancient Genes in Vertebrate Brain Space

Spatial validation of gene-age conservation across four species

To test whether the ancient program that dominates the cross-species analysis layer has a spatial correlate, we paired gene-level (SBP) age scoring with spatial transcriptomic maps in four divergent vertebrates: red-eared slider (telencephalon), bearded dragon (telencephalon), lungfish and bichir (whole brain). Across all four, the fraction of branch0 (euteleostome-stem-or-older) genes per spot is high and weakly spatially clustered, supporting the idea that the ancient gene-age dominance observed in single-nucleus data is preserved in intact tissue.

4
Spatial Species
turtle, lizard, lungfish, bichir
0.85–0.88
Median branch0 Fraction
per-spot, all four species
≤0.01
Spatial Clustering (null A)
absolute clustering of branch0 scores
0.011–0.037
branch0 Moran's I
positive in all four species
Spatial Summary

Branch0 Gene Fraction Across Spots

For each species, single spots or bins have an SBP gene-age score; the branch0 fraction is the per-spot proportion of mapped genes whose SBP branch is 0 (euteleostome stem or older). Moran's I (kNN k=6) quantifies spatial autocorrelation of this score, tested against two nulls: bin shuffling (absolute spatial signal) and gene-age label permutation (age-specific signal beyond the location of any high-expression genes).

Species Section Bins Mapped Genes Median branch0 Fraction branch0 Moran's I Clustering p (null A) Age-specific p (null B)
Red-eared slider Telencephalon 10,535 12,773 0.852 0.034 0.003 0.345
Bearded dragon Telencephalon 10,540 13,120 0.855 0.037 0.003 0.181
Lungfish Whole brain 13,938 12,259 0.883 0.011 0.010 0.559
Bichir Whole brain 20,503 12,123 0.881 0.025 0.003 0.221

Across all four species the branch0 fraction per spot is uniformly high (median 0.85–0.88), reflecting that the detectably mapped genes themselves are biased old relative to the genomic background. The spatial autocorrelation of the branch0 score is positive and significant against the location (bin-shuffle) null, indicating that old-gene abundance is not spread uniformly across the tissue.

Interpretation

High Abundance, Weak Age-Specific Compartmentalization

The per-spot branch0 fraction being high and weakly clustered is a spatial echo of the single-nucleus finding that identity genes are as old as the brain background itself: the ancient program pervades the tissue rather than being confined to a few specialist niches. The one consistently strong age-specific signal is the old score in bichir (z = 5.2, p ≈ 0), with marginal signals in bearded dragon (p = 0.047) and red-eared slider (p = 0.050); the branch0 measure itself did not reach age-specific significance in any species.

≈85–88%
median branch0 fraction per spot across the four species, far above the genomic background of ≈59%
≤0.01
p for absolute spatial clustering in every species (bin-shuffle null)
z = 5.2
strongest age-specific signal: the old-gene score in bichir (p ≈ 0)

Method note: the analysis layer is restricted to human-anchored orthologs retained across species, so these spatial observations hold within the cross-species-retained gene universe; both a bin-shuffle and a gene-age-label permutation null were used (299 permutations each, seed=0), with SBP branch labels harmonized to the 15-stratum scheme (branch0 = euteleostome stem or older).