The six-layered neocortex is a uniquely mammalian structure with evolutionary origins that remain in dispute. One long-standing hypothesis, based on similarities in neuronal connectivity, proposes that homologs of the layer 4 input and layer 5 output neurons of neocortex are present in the avian forebrain, where they contribute to specific nuclei rather than to layers. We devised a molecular test of this hypothesis based on layer-specific gene expression that is shared across rodent and carnivore neocortex. Our findings establish that the layer 4 input and the layer 5 output cell types are conserved across the amniotes, but are organized into very different architectures, forming nuclei in birds, cortical areas in reptiles, and cortical layers in mammals.T he evolutionary origins of the mammalian neocortex have been the subject of debate for over a century (1-3). Although the six-layered neocortex is remarkably well conserved in all extant mammals, it is not present in our closest living relatives, the reptiles and birds. Birds in particular are an extremely successful radiation with large brains, but the bird dorsal telencephalon does not include a morphologically identifiable cortex; it is, instead, a collection of nuclei (4).Studies of the neurochemistry, anatomy, and physiology of the central region of the bird telencephalon, which is called the dorsal ventricular ridge (DVR), have shown conclusively that the DVR is a pallial structure (2). In mammals the pallium (dorsal telencephalon) includes the neocortex and the nuclei of the piriform lobe, specifically the claustrum and parts of the amygdala. A classical hypothesis that has attracted renewed interest from modern neuroembryologists and neuromorphologists proposes a field homology between the nuclei of the bird DVR and the mammalian piriform lobe nuclei, including the amygdala (5, 6). A second, more controversial hypothesis proposes that, despite the gross differences in morphology between bird DVR and mammalian neocortex, these structures share a homology (7-9).The best evidence for neocortex-DVR homology lies in their circuitries. Both the mammalian neocortex and avian DVR receive ascending sensory input from the thalamus, and both send outputs to brainstem premotor areas. These input and output territories form specific, well-defined populations of neurons in both mammals and birds. In mammals, layer 4 neocortical neurons receive thalamic input, and layer 5 neocortical neurons project to the brainstem. In birds there are separate DVR nuclei that receive projections from the thalamus or send axons to the brainstem. The most developed version of the neocortex-DVR hypothesis proposes homology between these input and output neurons at the cell-type level (7); specifically, that the layer 4 input (L4/I) and layer 5 output (L5/O) neurons of the neocortex share a common ancestry with neurons that populate the input and output nuclei of the DVR.These two prevailing hypotheses about DVR homology are in direct conflict; one is a field homology argument comparing...

The avian dorsal telencephalon has two vast territories, the nidopallium and the mesopallium, both of which have been shown to contribute substantially to higher cognitive functions. From their connections, these territories have been proposed as equivalent to mammalian neocortical layers 2 and 3, various neocortical association areas, or the amygdala, but whether these are analogies or homologies by descent is unknown. We investigated the molecular profiles of the mesopallium and the nidopallium with RNA-seq. Gene expression experiments established that the mesopallium, but not the nidopallium, shares a transcription factor network with the intratelencephalic class of neocortical neurons, which are found in neocortical layers 2, 3, 5, and 6. Experiments in alligators demonstrated that these neurons are also abundant in the crocodilian cortex and form a large mesopallium-like structure in the dorsal ventricular ridge. Together with previous work, these molecular findings indicate a homology by descent for neuronal cell types of the avian dorsal telencephalon with the major excitatory cell types of mammalian neocortical circuits: the layer 4 input neurons, the deep layer output neurons, and the multi-layer intratelencephalic association neurons. These data raise the interesting possibility that avian and primate lineages evolved higher cognitive abilities independently through parallel expansions of homologous cell populations.

Molecular markers that distinguish specific layers of rodent neocortex are increasingly employed to study cortical development and the physiology of cortical circuits. The extent to which these markers represent general features of neocortical cell type identity across mammals is, however, unknown. To assess the conservation of layer markers more broadly, we isolated orthologs for fifteen layer-enriched genes in the ferret, a carnivore with a large, gyrencephalic brain, and analyzed their patterns of neocortical gene expression. Our major findings are: (1) Many but not all layer markers tested show similar patterns of layer-specific gene expression between mouse and ferret cortex, supporting the view that layer-specific cell type identity is conserved at a molecular level across mammalian superorders; (2) Our panel of deep layer markers (ER81/ETV1, SULF2, PCP4, FEZF2/ZNF312, CACNA1H, KCNN2/SK2, SYT6, FOXP2, CTGF) provides molecular evidence that the specific stratifications of layer 5 and 6 into 5a, 5b, 6a and 6b are also conserved between rodents and carnivores. (3) Variations in layer-specific gene expression are more pronounced across areas of ferret cortex than between homologous areas of mouse and ferret cortex; (4) This variation of area gene expression was clearest with the superficial layer markers studied (SERPINE2, MDGA1, CUX1, UNC5D, RORB/NR1F2, EAG2/KCNH5). Most dramatically, the layer 4 markers RORB and EAG2 disclosed a molecular sublamination to ferret visual cortex and demonstrated a molecular dissociation among the so-called agranular areas of the neocortex. Our findings establish molecular markers as a powerful complement to cytoarchitecture for neocortical layer and cell-type comparisons across mammals.

SummaryBirth dating neurons with bromodeoxyuridine (BrdU) labeling is an established method widely employed by neurobiologists to study cell proliferation in embryonic, postnatal, and adult brain. Birth dating studies in the chick dorsal telencephalon and the mammalian striatum have suggested that these structures develop in a strikingly similar manner, in which neurons with the same birth date aggregate to form "isochronic clusters." Here we show that isochronic cluster formation in the chick dorsal telencephalon is an artifact. In embryos given standardly employed doses of BrdU, we observed isochronic clusters but found that clusters were absent with BrdU doses close to the limits of detection. In addition, in situ hybridization experiments established that neurons in the clusters display errors in cell type specification: BrdU cell clusters in nidopallium adopted a mesopallial neuronal fate, mesopallial clusters were misspecified as nidopallial cells, and in some instances, the BrdU clusters failed to express neuronal differentiation markers characteristic of the dorsal telencephalon. These results demonstrate that the chick dorsal telencephalon does not develop by isochronic cluster formation and highlight the need to test the integrity of BrdU-treated tissue with gene expression markers of regional and cell type identity. (J Histochem Cytochem 60:801-810, 2012)

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