Tracing the Deep Ancestry of the Vertebrate Brain: Academia Sinica Researchers Construct the First 3D Amphioxus Brain Atlas｜ Institute of Cellular and Organismic Biology, Academia Sinica

Tracing the Deep Ancestry of the Vertebrate Brain: Academia Sinica Researchers Construct the First 3D Amphioxus Brain Atlas

How did the highly complex vertebrate brain evolve from a simple ancestral blueprint? This enduring question in evolutionary biology has taken a major leap forward. In a recent study published in Science Advances, a research team led by Research Fellow Jr-Kai Yu and Postdoctoral Fellow Che-Yi Lin from the Institute of Cellular and Organismic Biology at Academia Sinica has constructed a spatially resolved cell-type atlas of the adult amphioxus brain, unveiling the deep ancestry of our own central nervous system. Amphioxus, an early-branching invertebrate chordate, occupies a key phylogenetic position for decoding the origins of the vertebrate brain. By combining single-nucleus RNA sequencing with spatial transcriptomics, the team confirmed that the amphioxus brain shares a deeply conserved tripartite organization with vertebrates. This structural blueprint features molecular boundaries similar to key vertebrate brain organizers—the zona limitans intrathalamica (ZLI) and the midbrain-hindbrain boundary (MHB)—challenging long-held assumptions that these critical developmental landmarks were missing in amphioxus. Crucially, this high-resolution atlas revealed the absence of key telencephalic marker expression in the amphioxus forebrain, suggesting that the telencephalon—the region driving complex cognitive processing—is a unique vertebrate innovation rather than an inherited ancestral trait. Beyond a technical milestone, the research team establishes a critical phylogenetic baseline for chordate neuroanatomy. By successfully separating ancient, conserved features from evolutionary novelties, this research provides a foundational framework for understanding the evolutionary trajectory of vertebrate brain complexity.

This study was supported by the Academia Sinica Grand Challenge Program and research grants from the National Science and Technology Council (NSTC) of Taiwan. Crucial technical assistance was provided by the High-Throughput Genomics Core Facility at the Biodiversity Research Center, Academia Sinica. The co-authors included Wen-Hsin Hsu, Mei-Yeh Jade Lu, Yi-Hua Chen, Kun-Lung Li, Yi-Chih Chen, Yi-Hsien Su, and Shen-Ju Chou.

Publication: https://www.science.org/doi/10.1126/sciadv.aee5076

A three-dimensional point cloud model of the amphioxus brain with color-coded anatomical regions.