Sulcal landmarks reveal lineage-specific trajectories and multi-scale specialization of the mammalian cortex

An important topic of evolutionary neuroscience is to understand how brain function and structure across evolutionary time. In the absence of functional data for ancestral species, studies often rely on structural features such as cortical volume or surface area. However, atlas-based metrics derived from human or a few model organisms lack biological interpretability across species with divergent cortical architectures. Here, we investigate sulcal pits—the locally deepest points of cortical folds—as conserved, atlas-independent landmarks that provide a robust basis for cross-species comparison. Using cortical surface reconstructions from 90 mammalian species, we show that sulcal pit distribution patterns partly recapitulate phylogenetic relationships, independent of overall brain size (volume and surface area), and vary systematically with ecology and lifestyle. By tracing pit-based evolutionary trajectories from 80 million years ago to the present, we found pronounced differences across ecological and behavioral categories, indicating that cortical folding has diversified in close association with species’ habitats, lifestyles, and social structures. Using sulcal pits, we identified Homo sapiens -specific regions and species-shared regions. The Homo -specific areas were functionally associated with higher cognitive and emotional processes, distinguished by unique histological features, enriched for gene sets related to neural regulation, and exhibited markedly different cell-type abundance profiles compared to shared regions. Together, these results establish sulcal pits as a robust, evolutionarily informative feature for cross-species cortical alignment, offering new insights into the structural innovations underlying brain evolution study.