The thorniest problem in comparative neurobiology is the identification of the particular brain region of birds and reptiles that corresponds to the mammalian neocortex [Butler AB, Reiner A, Karten HJ (2011) Ann N Y Acad Sci 1225:14-27; Wang Y, BrzozowskaPrechtl A, Karten HJ (2010) Proc Natl Acad Sci USA 107(28):12676-12681]. We explored which genes are actively transcribed in the regions of controversial ancestry in a representative bird (chicken) and mammal (mouse) at adult stages. We conducted four analyses comparing the expression patterns of their 5,130 most highly expressed one-to-one orthologous genes that considered global patterns of expression specificity, strong gene markers, and coexpression networks. Our study demonstrates transcriptomic divergence, plausible convergence, and, in two exceptional cases, conservation between specialized avian and mammalian telencephalic regions. This large-scale study potentially resolves the complex relationship between developmental homology and functional characteristics on the molecular level and settles long-standing evolutionary debates.cerebral cortex | Wulst | equivalent circuit hypothesis | brain evolution | dorsal ventricular ridge D espite recent advances in our knowledge of comparative aspects of cortical neurogenesis, migration, clonal relationships, and gene expression patterns, there is no consensus on how these processes evolved together to determine the adult brain structures across diverse amniotes (1-5). Anatomical, hodological, embryological, and gene expression data (based on few select genes) provide conflicting answers on brain homology across vertebrates. Studies of embryonic neurogenesis and cell migration have informed homology of developmental territories (6-8), but the striking similarities in lamination, connectivity, and physiological properties observed between adult forms derived from noncorresponding pallial regions remain unexplained (3-5, 9). Comparative transcriptomics is a powerful approach to interrogating regional correspondence without resorting to limited lists of selected genetic markers. Recent methodological advances in profiling mammalian cerebral cortical layer transcriptomes (10-12) could objectively test the validity of proposed, yet controversial, relationships between regions of adult mammalian and avian brains. These comparisons are motivated by our understanding of the evolution of mammals from a reptilian subclass, represented by the synapsid condition (with a cranial opening in the cheek region of the skull), and of birds from another reptilian subclass, represented by the diapsid condition (two postorbital skull openings).
ResultsWe extended our previous transcriptomic analysis of cortical layers in the adult mouse (13) to additional structures, 16 in total, and compared these with seven regions of the adult chicken brain (Fig. 1A and SI Appendix, Figs. S1 and S2). All dissected regions in both species (except the striatum, which is subpallial) develop primarily from one of four morphogenetically delineated sector...