The chick pallium displays divergent expression patterns of chick orthologues of mammalian neocortical deep layer-specific genes

The avian pallium is organised into clusters of neurons and does not have layered structures such as those seen in the mammalian neocortex. The evolutionary relationship between sub-regions of avian pallium and layers of mammalian neocortex remains unclear. One hypothesis, based on the similarities in neural connections of the motor output neurons that project to sub-pallial targets, proposed the cell-type homology between brainstem projection neurons in neocortex layers 5 or 6 (L5/6) and those in the avian arcopallium. Recent studies have suggested that gene expression patterns are associated with neural connection patterns, which supports the cell-type homology hypothesis. However, a limited number of genes were used in these studies. Here, we showed that chick orthologues of mammalian L5/6-specific genes, nuclear receptor subfamily 4 group A member 2 and connective tissue growth factor, were strongly expressed in the arcopallium. However, other chick orthologues of L5/6-specific genes were primarily expressed in regions other than the arcopallium. Our results do not fully support the cell-type homology hypothesis. This suggests that the cell types of brainstem projection neurons are not conserved between the avian arcopallium and the mammalian neocortex L5/6. Our findings may help understand the evolution of pallium between birds and mammals.

of motor output projections to sub-pallial targets between the DVR and neocortex.Whilst their results therefore support the cell-type homology hypothesis, a limited number of genes was used.A recent largescale transcriptomic analysis revealed a mostly divergent pattern in pallial compartments between chicken and mouse 14,15 , suggesting the possibility that the expression of chick orthologues of L5/6 genes do not fully support the cell-type homology hypothesis.
In this study, we examined the expression of more chick orthologues of L5/6 genes and tested whether their expression patterns supported the cell-type homology hypothesis.If cell types are conserved between the brainstem projection neurons in the mammalian L5/6 and the avian arcopallium, most of the chick orthologues of L5/6-specific genes should be selectively expressed in the arcopallium.We used chick orthologues of mammalian neocortical L5/6 markers and performed in situ hybridisation in the chick telencephalon.We found nuclear receptor subfamily 4 group A member 2 (NR4A2) and connective tissue growth factor (CTGF) expression in the arcopallium which reflected the neural connection patterns between avian DVR and mammalian neocortex.However, the gene expression patterns of the other four did not.Their major expression regions were outside of the arcopallium, which shows that the expression patterns of the four genes did not reflect the neural connections in terms of motor output.Our results on the expression patterns of chick orthologues of L5/6 genes do not fully support the cell-type homology hypothesis, which suggests that the cell types of brainstem projection neurons are not conserved between the avian arcopallium and the neocortex L5/6.
We also found different expression patterns of NR4A2 and CTGF in the arcopallium (Fig. 3,A7.6 and A7.0).NR4A2 was expressed almost ubiquitously in the lateral, ventral, and intermediate arcopallium, while CTGF was highly expressed in the medial and ventral arcopallium, but not in the lateral arcopallium.Neither NR4A2 nor CTGF was expressed in the dorsal arcopallium.(Fig. 4a-f,A12.6-A7.4).The regions in which we detected strong signals appeared to correspond to a part of the intercalated nidopallium, which Jarvis et al. proposed to be a distinctive and continuous formation of the entopallium, basorostralis, and Field L 26 .Strong NEFH expression was restricted to the basorostralis and entopallium, but was not found in the Field L.

Discussion
One feature shared by the avian arcopallium and mammalian neocortex L5/6 consists of the neural connections of motor output neurons projecting to sub-pallial targets [5][6][7][8][9][10][11][12] .In this study, we found that chick orthologous genes of mammalian neocortical L5/6 markers, NR4A2 and CTGF, were strongly expressed in a neuronal population of the arcopallium (Fig. 7).Thus, the expression of NR4A2 and CTGF orthologues in the arcopallium could reflect the neural connections in terms of motor output projection between birds and mammals.In contrast, we also found that chick orthologous genes of mammalian neocortical L5/6 markers, TOX and NEFH, were strongly expressed in regions other than the arcopallium (Fig. 7), which suggests that the expression pattern of these two genes does not reflect the neural connections in terms of motor output.In addition, CTIP2 was strongly expressed in regions other than the arcopallium and FOXP2 was expressed in the entire pallium (Fig. 7).The expression of chick orthologues of L5/6 genes did not always support the cell-type homology hypothesis, which suggests that the cell types of brainstem projection neurons between the avian arcopallium and the neocortex L5/6 were not conserved.The genes we used are also expressed in other part of pallium in mammals.However, those genes are basically not expressed together outside of neocortical layers.Neocortical deep layers are the only pallial regions in which all six genes we studied are expressed together (Table S1).Therefore, if the cell-type of brainstem projection neurons in arcopallium and those in deep layer L5/6 are homologous, all six chick orthologues for deep layer markers should be expressed in the arcopallium.Contrary to this assumption, our results showed that two of them were majorly expressed in the arcopallium, while the other genes were not.Thus, not all expression patterns of chick orthologues of L5/6 genes support the cell-type homology hypothesis.
In birds, the arcopallium has motor output neurons that project to sub-pallial targets and is considered to be involved in motor control [27][28][29] .For example, arcopallium-ablated chicks exhibit less approach behaviours to the imprinting object during filial imprinting 30 , which suggests that the arcopallium is involved in enhancing the subject's motivation for approach behaviour and/or locomotor activity.We previously found that NR4A2 was upregulated, accompanying filial imprinting, using cDNA microarray and quantitative RT-PCR 31 .NR4A2 is a transcription factor activated by several signalling cascades 32 .It is possible that NR4A2 modulates arcopallium activity and increases the subject's motivation for approach behaviour and/or locomotor activity during filial imprinting.
CTGF is a secreted protein which belongs to the Cyr61/CTGF/NOV (CCN) protein family.It binds to and modulates the activity of other growth factors, including insulin-like growth factor, transforming growth factor ß, and bone morphogenetic proteins [33][34][35] .One study found that CCNs in the nervous system are involved in neuroprecursor proliferation, neuronal survival, and differentiation in mice 35 .Recently, Khodosevich et al. found that changes in CTGF expression levels in the olfactory bulb led to modifications in local neuronal circuitry and olfactory behaviours 36 .It is possible that CTGF modulates the activity of efferent neurons in the arcopallium and increases the subject's motivation for approach behaviours or locomotor activity during filial imprinting.NEFH encodes one of the neurofilament triplet components.The level of neurofilament protein has been associated with the extent of neuronal cell myelination 37 , whereby NEFH-positive cells are a more heavily myelinated neuronal population.We found that the major expression regions for NEFH were the basorostralis and entopallium in the DVR and globus pallidus.The major expression regions for NEFH appeared to correspond to a part of the intercalated nidopallium, which supports previous work from Jarvis et al. 26 .Those authors found that the intercalated nidopallium receives sensory projections from the thalamus out of the pallium 26 , which suggests that NEFH is involved in roles in the cells that have input projection from the thalamus.It is likely that in chicks, NEFH-positive cells are a highly myelinated neuronal population within which projection neurons with long dendrites can be found.
TOX is a multifunctional transcription factor involved in corticogenesis via the promotion of neurite outgrowth and regulating the fate of newborn neurons in mouse embryos 20,38 .TOX is expressed in the thymus, liver, and brain, and has been studied on the role in lymphocyte development of mice 39 .We found that TOX was primarily expressed in the mesopallium in chicks (Fig. 7), which is not known to have the characteristic projections to sub-pallial targets [40][41][42] .We think that TOX is likely to be involved in roles such as neurite outgrowth in neurons within the telencephalon.
The arcopallium is a heterogeneous organisation that consists of a somato-motor region and a limbic region [27][28][29] .We are beginning to understand which subregions of the arcopallium are related to motor or limbic functions.Recently, one study that used an anterograde tracer found that the lateral arcopallium had characteristic projections to the hippocampus and septum, as well as wide areas of limbic nuclei in the hypothalamus and medial areas of the striatum 11 .These results suggest that the lateral arcopallium is involved in emotion-related behaviours.In addition, diverse projections to midbrain areas were found to derive from the medial arcopallium region 40 .The NR4A2 and CTGF expression patterns found in the present study indicate that the cell populations in the lateral arcopallium were NR4A2 + /CTGF − and that those in the medial arcopallium were NR4A2 + /CTGF + (Fig. 3).Therefore, a combination of NR4A2 and CTGF expression could be used to precisely characterise cell populations in the subregions of the arcopallium in the chick brain.
Much like the mammalian L5/6, the hyperpallium also has motor output neurons projecting to the spinal cord or thalamus 5,6,12 .All six orthologues for L5/6-specific genes used in this study were expressed in neural populations of the hyperpallium of chicks (Fig. 7), which shows that the expression patterns reflected the neural connections patterns in terms of motor output projections to sub-pallial targets.Given that the avian dorsal pallium derivative region (hyperpallium) is considered to be homologous to the mammalian neocortex 43,44 , this is reasonable.
The mesopallium is not known to have the characteristic projections to sub-pallial targets.The major projections from the mesopallium are distributed within the telencephalon, and the mesopallium has strong reciprocal fibre connections with regions in the nidopallium [40][41][42] .We found that all six orthologous genes used in this study were expressed in the mesopallium (Fig. 7).This suggests that, in the mesopallium, these six genes were expressed in neurons projecting within the telencephalon rather than in neurons projecting to the spinal cord out of the telencephalon.In the case of NR4A2, mouse Nr4a2 has been reported to be expressed not only in the neocortex, but also in other parts of the pallium (the claustrum) 25 .Furthermore, one study reported that an early NR4A2-positive population within the chick mesopallium represents the lateropallial claustrum homologue in mouse embryos 25 .It is important to consider the gene expression patterns in other parts of the pallium, such as the claustrum, together with a hodological analysis of connections to compare the gene expression patterns in the mammalian cortex and in birds' DVR.
Analysing homologies through developmental origins is useful to understand the evolution of brain complexities between mammals and birds.As mammalian neocortex derives from the dorsal pallium, while the DVR of birds derives from the lateroventral pallium 43,44 , the neocortex and DVR are not homologous in terms of developmental-based homology.In contrast, the mammalian brain regions derived from the lateroventral pallium such as the amygdala, claustrum and dorsal endopiriform nucleus might be homologous to the parts of the birds' DVR in terms of developmental-based homology.For example, the whereabouts of the avian pallial amygdala remain uncertain, but there are several studies suggesting that a part of the caudal DVR, including at least the caudal nidopallium and the whole arcopallium of birds, may be avian pallial amygdala [43][44][45] .As for the claustrum, a recent study suggested that a part of the avian lateral mesopallium (superficial mesopallial cortical structure) is the strict homologous region of the mammalian claustrum 25,44,46 .A part of lateral nidopallium is the homologous region of mammalian dorsal endopiriform nucleus 25,46,47 .
We found that chick NR4A2 was majorly expressed in the arcopallium (Fig. 7) which was suggested to be avian pallial amygdala, whereas mouse Nr4a2 was not expressed in the pallial amygdala during embryonic development nor in adults 24,25 .This evidence showed that chick NR4A2 expression in the arcopallium did not reflect developmental-based homologies.Similarly, we also found that chick CTGF was majorly expressed in the arcopallium (Fig. 7) whereas mouse Ctgf was not expressed in the pallial amygdala (P8 and adult) 24 .This evidence showed that chick CTGF expression in the arcopallium did not reflect developmental-based homologies.One feature shared by the avian arcopallium and mammalian neocortex L5/6 consists of the neural connections of motor output neurons projecting to sub-pallial targets.We assume that the similarity in the expression pattern might better reflect function than homology and be the result of convergent evolution.Chick TOX were majorly expressed in the medial mesopallium (Fig. 7), which was not the avian homologous region of mouse Tox expressing domains (the hippocampus and claustrum, Table S1).Chick NEFH were expressed in the basorostralis (Fig. 4a,b) and entopallium (Fig. 4c,d).All of these NEFH-expressing domains were not the avian homologous region of mouse Nefh-expressing domains (hippocampus, piriform cortex and olfactory bulb, Table S1).
In this study, we only tested a small number of genes.However, our results suggested that avian hyperpallium, which share developmental-based homology and functional-based analogy between birds and mammals, displayed conserved expression patterns of neocortical deep layer genes (Fig. 7).In contrast, our results suggest that most pallial regions have undergone major reorganisation in terms of gene expression patterns between birds and mammals.This is consistent with the findings of recent comprehensive transcriptome analyses 14,15 , which have demonstrated that gene expression patterns in the adult mouse cortex are not compatible with those of the adult chick pallium.Over hundreds of millions of years, pallium of birds and mammals has become astonishingly diversified.

conclusion
The avian arcopallium and mammalian neocortex L5/6 share the feature of neural connections of motor output neurons projecting to sub-pallial targets.We used chick orthologues of mammalian neocortical L5/6 markers and performed in situ hybridisation in the chick telencephalon.We found that NR4A2 and CTGF expression reflected the neural connection patterns between avian DVR and mammalian neocortex, but TOX, NEFH, CTIP2 and FOXP2 expression patterns did not.Thus, not all the expression patterns of chick orthologues of L5/6 genes support the cell-type homology hypothesis.This suggests that the cell types of brainstem projection neurons are not conserved between the avian arcopallium and the mammalian neocortex L5/6.

Methods
Animals and tissues.Fertilized eggs of domestic chicks (Gallus domesticus, the Cobb strain) were purchased from a local dealer (3-M, Aichi, Japan) and incubated at Teikyo University (Kaga, Itabashi-ku, Tokyo).Animal experiments were carried out as described previously 48,49 .Briefly, newly hatched chicks (P0) were captured and placed in dark plastic enclosures in a breeder at 30 °C for one day (P1).P1 chicks were deeply anesthetized with a 1:1 mixture solution of ketamine (10 mg/ml, ketalar-10, Sankyo Co., Tokyo, Japan) and xylazine (2 mg/ml, Sigma, St. Louis, Missouri, USA) by intraperitoneal injection (0.40 ml/individual) and perfused through the heart with 4% paraformaldehyde in 0.1 M phosphate buffered saline (pH 7.5) (PFA-PBS).In this study, we used 2 chicks for the NR4A2 condition, 3 for the CTGF condition, 4 for the NEFH condition, 3 for the TOX condition, and 4 for the CTIP2 and FOXP2 conditions (a total of 7 chicks).Dissected brains were immersed in PFA-PBS overnight at 4 °C and placed in an 18% sucrose/PFA-PBS solution for cryoprotection for two days at 4 °C.Next, brains were embedded in Tissue-Tek OCT compound (Sakura Finetechnical, Tokyo, Japan), frozen immediately on dry ice, and stored at −80 °C until use.All procedures were reviewed and approved by the committee on animal experiments of Teikyo University and conducted under the guidelines of the national regulations for animal welfare in Japan.
imaging.Digital images of sections were obtained with NanoZoomer 2.0HT or NanoZoomer XR systems (Hamamatsu Photonics, Shizuoka, Japan) and microscopic fields of interest were cropped using NDP.view2 software (Hamamatsu Photonics, Shizuoka, Japan).The images were then converted to 8-bit and the brightness and contrast of images was adjusted using ImageJ (https://imagej.nih.gov/ij/).

Figure 1 .
Figure 1.In situ hybridisation of NR4A2 in P1 chick brains.DIG-labelled RNA antisense (a-f) NR4A2 probe was used for in situ hybridisation in P1 chick brain coronal sections.For NR4A2, sections of two chicks were analysed, and representative images of chick brain sections are shown.(g-l) Diagrams of coronal sections are shown on the right panels.The levels of the sections (A12.6 to A7.8) correspond to those of the chick atlas by Kuenzel and Masson 50 .A, arcopallium; H, hyperpallium; M, mesopallium; N, nidopallium.Scale bar = 2.5 mm.

Figure 2 .
Figure 2. In situ hybridisation of CTGF in P1 chick brains.DIG-labelled RNA antisense (a-f) CTGF probe was used for in situ hybridisation in P1 chick brain coronal sections.For CTGF, sections of three chicks were analysed and representative images of two chick brain sections are shown.(g-l) Diagrams of coronal sections are shown on the right panels.The levels of the sections (A13.8 to A7.4) correspond to those of the chick atlas by Kuenzel and Masson 50 .A, arcopallium; Aph, area parahippocampalis; E, entopallium; H, hyperpallium; M, mesopallium; N, nidopallium.Scale bar = 2.5 mm.

Figure 3 .
Figure 3.In situ hybridisation of NR4A2 and CTGF in P1 chick brains using neighboring sections.In situ hybridisation using DIG-labeled RNA antisense NR4A2 (a,e) and CTGF (b,f) probes with P1 chick brain coronal sections were shown, respectively.Panels (c), (d), (g), and (h) indicated the diagrams of the panels of the (a), (b), (e), and (f), respectively.The shaded regions, (c,g) for NR4A2 and (d,h) for CTGF, indicated the regions of signal detected in the arcopallium (dot pattern regions), respectively.Arrows indicated the area of the lateral arcopallium (a-h).The levels of the sections (A7.6 to A7.0) correspond to those of the chick atlas by Kuenzel and Masson 50 .A, arcopallium; Aph, area parahippocampalis; H, hyperpallium; M, mesopallium; N, nidopallium.Scale bar = 2.5 mm.

Figure 4 .
Figure 4.In situ hybridisation of NEFH in P1 chick brains.DIG-labelled RNA antisense (a-f) NEFH probe was used for in situ hybridisation in P1 chick brain coronal sections.For NEFH, sections of four chicks were analysed and representative images of three chick brain sections are shown.(g-l) Diagrams of coronal sections are shown on the right panels.The levels of the sections (A12.6 to A7.4) correspond to those of the chick atlas by Kuenzel and Masson 50 .A, arcopallium; Aph, area parahippocampalis; B, basorostralis; E, entopallium; G, globus pallidus; H, hyperpallium; M, mesopallium; N, nidopallium.Scale bar = 2.5 mm.

Figure 5 .
Figure 5.In situ hybridisation of TOX in P1 chick brains.DIG-labelled RNA antisense.(a-f) TOX probe was used for in situ hybridisation in P1 chick brain coronal sections.For TOX, sections of three chicks were analysed and representative images of two chick brain sections are shown.(g-l) Diagrams of coronal sections are shown on the right panels.The levels of the sections (A13.8 to A7.6) correspond to those of the chick atlas by Kuenzel and Masson 50 .A, arcopallium; H, hyperpallium; M, mesopallium; N, nidopallium.Scale bar = 2.5 mm.

Figure 6 .
Figure 6.In situ hybridisation of CTIP2 and FOXP2 in P1 chick brains.DIG-labelled RNA antisense (a-c) CTIP2 and (d-f) FOXP2 probes for in situ hybridisation in P1 chick brain coronal sections.For CTIP2 and FOXP2, sections of four chicks were analysed, and representative images of three chick brain sections are shown.(g-i) Diagrams of coronal sections are shown on the right panels.The levels of the sections (A9.0 to A7.0) correspond to those of the chick atlas by Kuenzel and Masson 50 .A, arcopallium; Aph, area parahippocampalis; G, globus pallidus; H, hyperpallium; Ins, intrapeduncular nucleus; Lst, lateral striatum; M, mesopallium; N, nidopallium.Scale bar = 2.5 mm.

Table 1 .
Overview of markers of cortical layers 5 and 6 in this study.